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OLD _NRSP008: National Animal Genome Research Program

Annual/Termination Reports (SAES-422): [03/03/2004] [03/18/2005] [03/16/2006] [08/13/2007] [05/27/2008]

Date of Annual Report: 03/03/2004

Report Information:
  • Annual Meeting Dates: 01/10/04 to 01/12/04
  • Period the Report Covers: 01/2003 to 12/2003

    • Participants:
    Brief Summary of Minutes of Annual Meeting:
    I Approval of minutes: Minutes of the January 2003 meeting were distributed. Deb Hammernik moved the approval of minutes. Motion was seconded by Max Rothschild and unanimously approved.

    II. Old Business
    Cattle: Jim Womack presented the annual report of the species activities. The highlights included active support by the coordinator, NRSP8 participants and the cattle community developed a white paper and generated financial support for sequencing the cattle genome. The sequencing program was officially initiated in December 2003, and the first set of sequence data is expected to be made available by February/March 2004. The coordinator continues to maintain the RH-analysis website but has transferred other bovine genome database responsibilities to Database coordinator Jim Reecy at Iowa State University. DNA from the 5,000 and 12,000 rad panels is being distributed by the coordinator to all researchers interested in developing fine physical maps. Additionally, bovine BAC libraries, DNA from somatic cell hybrid panel, and DNA from the International Bovine Reference family panel (IBRP) are also being made available to scientists needing these mapping resources.
    Cattle administrative advisor Colin Kaltenbach lauded the efforts and industry representative Elizabeth Dressler promised continuous support and interest of the industry in enhancing research strengths of the group.

    Sheep: Noelle Cockett reported the progress currently being made through the coordinator?s funds to develop, analyze and distribute the ovine radiation hybrid panel. Efforts are underway to develop a framework map for the sheep genome with ~2,500 loci. A memorandum of understanding has been signed with Peter de Jong (BACPAC resources) to acquire the sheep BAC library, make copies and develop high density filters for distribution to the sheep gene mapping community. Progress on the BAC end sequencing and fingerprinting was reported. Currently end sequencing of 150,000 to 200,000 BACs is being carried out at INRA (France) and Roslin Institute (UK) in conjunction with NRSP8 sheep coordinator. A seed grant from Utah State University is currently being used to end sequence some (unspecified number) ovine BACs. Sheep administrative advisor Colin Kaltenbach commended the work of the sheep group and described them as strong and highly regarded internationally.

    Equine: Ernie Bailey provided an overview of the equine workshop. The invited presentations focused on bioinformatics and MHC. He elaborated the coordinated progress of the equine group in the areas of RH and linkage mapping and defined the goals agreed upon by the community for the next year. Publication of the first generation RH map in horse was a highlight. Progress made at the Havermeyer International Equine Genomics meeting in South Africa was also briefly mentioned. Coordinator funds were used for development and distribution of resources (reference family material, genome scan panel, etc.), and for travel support to technical committee members and a graduate student for PAGXII. Horse administrative advisor Bill Trumble pointed out that despite a late start, the horse group has done an amazing job.

    Poultry: Jerry Dodgson reported that the PAG XII chicken workshop was the best the group ever had. The first generation physical map was ready in December; the 2nd generation map will probably be obsolete with the sequence information being made available soon. The current focus of the chicken community is primarily on the sequencing project ? mainly getting the finished sequence data. The linkage map generated up till now was reported to be well used. He emphasized the importance of NRSP8 in getting the sequencing efforts on track, making the East Lansing International reference family DNA, primer pair kits, BAC libraries filters and PCR-screenable pooled DNA (superpools) and other resources to several laboratories around the world. He also mentioned the availability of chicken microarray from FHCRC (Jeff Delrow and Paul Neiman). The Poultry Genome News letter supported through NRSP8 is constantly providing updates and details on research activities to researchers around the world. On behalf of the poultry administrative advisor, Margaret Dentine greatly appreciated the efforts of the poultry gene mapping group.

    Pig: Max Rothschild reported that the swine genome workshop had the biggest crowd compared to earlier meetings (~120 people). Several developments were reported including: active use of markers by the swine industry, constant rapid expansion of the maps, availability of 2 RH panels (one from MN/INRA and the other from Reno, Nevada), etc. Intense efforts being made by Larry Schook and the entire pig community to get funding for sequencing the pig genome was a major activity of the group. Submission of the white paper was mentioned. Efforts made by the entire pig community to generate funds to the tune of $20 million were stated. This includes requests made to the Pork Board. Further, the importance of NRSP8 in facilitating database activities, distribution of various resources/materials including the Pig Genome Update, and providing travel and meeting support were acknowledged. Swine administrative advisor Margaret Dentine was very supportive of the intense efforts made by the swine genomics group in development of a high resolution map and sequencing.

    With permission from the Chair, Larry Schook requested to discuss about the critical situation pig researchers are facing for generating matching funds required for getting the pig genome sequencing on track. On behalf of the Swine sequencing committee, Schook requested for ?support and endorsement from the NRSP8 group to empower USDA/NRI to provide financial support because it is in the best interest of the entire animal genome community?. The motion was moved for approval.

    Jim Womack (TAMU) supported the motion stating that the window of opportunity is narrow and all efforts must be made to capitalize on what is available. He requested the group to embrace the pig genome sequencing efforts.

    Noelle Cockett (U of Utah) wanted to know the current status regarding the availability of funds for sequencing (primarily the amount that has been committed) and how much would be needed.

    Larry Schook replied that $20M needs to be generated by October 1. He mentioned about some international commitments and various steps (not specified) that are being taken to achieve the target.

    Max Rothschild clarified that the pig community has at least $10M and is reasonably comfortable to raise another $5M for whole genome sequencing. It is the remaining $5M that needs to be obtained from some source.

    Chris Biddwell wanted to know whether support of the motion automatically implies availability of lesser federal (USDA/NRI) funds for competitive proposals.

    It was finally suggested that the Chair of the meeting (F. Abel Ponce de León) will draft a letter of support and circulate it to chairs of different species committees, get a consensus and then send it to USDA/NRI-CREES.

    Finally, Max Rothschild (ISU) suggested adoption of two motions:
    Motion 1: NRSP8 group is supportive of efforts for sequencing the swine genome
    Motion 2: The group is also supportive of the efforts by the USDA to find additional financial resources to support the swine sequencing effort.

    Questions were raised whether this will authorize USDA to provide financial support to the pig group (Noelle Cockett, U of Utah). There were propositions that other agencies like DOE must be approached. Schook said that the possibility to get funds from DOE is bleak.

    At the end of the discussion, the motion: ?The NRSP8 group is supportive of the efforts for sequencing the swine genome, and the group recommends USDA to make efforts to find financial resources supporting the sequencing project?. Deb Hamernik clarified that this does not bind USDA in anyway to commit financial resources to the pig genome sequencing project.

    The motion was carried unanimously with Max Rothschild moving it and Jim Womack seconding it.

    Database: James Reecy summarized about the presentations he made to different species workshops. He reiterated his eagerness to hear from species coordinators and participants regarding the database needs of individual groups.

    Aquaculture: John Liu reported that the rather newly formed aquaculture group is very diverse with 6 different species. This year?s workshop organized by Tom Kocher was very strong in science. International participation was strong, especially by Tilapia researchers. Prospects of sequencing salmon in the near future were discussed.

    Administrators reports:

    Lead Administrative advisor Margaret Dentine reported about the new five year cycle for NRSP8 program. She welcomed the aquaculture group within the fold of the program. The participants were informed about the setting up of a database that is expected to provide detailed information about the project. All participants (~72, with 6 new from Beltsville) were asked to fulfill their reporting commitments on time because documentation of progress is important for the project. The new members were requested to provide complete addresses and e-mails, and current members were requested to update their e-mail addresses (if changed). Margaret said that the NRSP8 project is indeed in good shape and the progress made is excellent.

    Program Leader Muquarrab Qureshi introduced himself to the NRSP8 community and provided an overview of CSREES activities. A summary of National Public Funding and the latest NRI funding was given. Stating that these are exciting times for genomics, he said that he will take the message regarding various developments to Washington DC, in particular the developments relating to sequencing efforts currently underway in chicken and cattle. He provided a brief overview of the ?Discover? conference, thanked species coordinators for providing impact statements for the new CSREES website, and mentioned about the current stand of USDA regarding consumption of cloned and genetically engineered food. Muquarrab expressed great enthusiasm to be a part of the NRSP8 community. He looked forward to regularly receiving constructive comments and suggestions for improvement in the program.

    III New business
    1. Meeting day and time for 2005: It was agreed that in January 2005, the executive committee of NRSP8 will meet at noon (instead of early morning; as has been the case in the past). Further, it was also unanimously agreed that in January 2005, the NRSP8 annual meeting will be held on Sunday, one day before the start of the PAG meeting, from 4:30 to 6:00 PM (instead of late evening or night). These changes will be reviewed after 2005 PAG meeting.

    2. Election of officers for 2004: Tom Kocher (New Hampshire) was nominated and unanimously elected Secretary of the NRSP8 Animal Genome Technical Committee for 2004-2005. Current Chair Abel Ponce de León thanked everyone present for participation and fruitful discussions and handed over the responsibilities for the next year to current secretary Bhanu Chowdhary.

    3. Selection of next meeting location and date: The next NRSP8 meeting will be held in conjunction with PAGXIV.

    IV Adjournment: The meeting was adjourned at 8:45 P.M. with a vote of thanks to F. Abel Ponce de León for a very successful organization of the meeting.

    Accomplishments:
    Progress Toward Objective 1:

    Aquaculture:
    Catfish ? AL has constructed a genetic linkage map for catfish containing 418 AFLP markers. This work has been published (see below under publications). EST project has now 4,103 gene-associated microsatellites and 145 gene-associated SNP markers.
    Rainbow trout - NCCCWA have developed more microsatellite and single nucleotide polymorphism markers for mapping in salmonid and Morone species. A high-density genetic map for rainbow trout is expected to be continued through 2004.
    Tilapia - NHAES has completed a genetic linkage map for tilapia containing more than 550 microsatellite and gene-based markers. A physical map based on the restriction fingerprints of 35,000 BAC clones (5x genome coverage) has also been completed (http//:www at hcgs.unh.edu)
    Oysters (Crassostrea virginica and C. gigas) - NJ has generated AFLP-based linkage maps for the eastern and Pacific oysters. VIMS and DE have analyzed inheritance of a set of microsatellite markers in the eastern oyster observing a high incidence of null alleles and distorted segregation ratios.
    Clams ? VA have initiated work on genetic improvement of the hard clam Mercenaria mercenaria. To date, four microsatellite libraries have been developed. Efforts have begun at VIMS to develop a set of Type I SNP markers for the hard clam. Of the 8 loci screened to date in a panel of clams from diverse commercial stocks, six have shown polymorphisms, with several containing more than two alleles.


    Cattle:
    Collaboration between TX and IL has produced a second-generation 5000 rad radiation hybrid (RH) EST map of the cattle genome covering gaps in the existing cattle-human comparative map as well as sparsely populated map intervals. A cattle-human comparative map containing 1463 comparative anchor points has been created using human genome sequence coordinates for paired orthologs to define boundaries of conserved chromosome segments. Approximately 312,000 BAC end sequences are in the public domain as a result of this collaborative effort, and a minimal tiling path of BACs for the bovine genome-sequencing project has been generated by an international consortium (including TX, IL, USDA-ARS). The class IIB and class III regions of the bovine MHC have been sequenced (TX). Future plans include development of a 1MB resolution comparative map (TX, IL), a bovine HapMap (TX) and finished sequence for the class IIB and class III regions of the bovine MHC (TX). The bovine genome is currently being sequenced making sequence annotation and integration with map data a high priority.

    Horse:
    The latest reiteration (MN, CA, Japan Laboratory of Racing Chemistry) and England Animal Health Trust, Newmarket) of the horse linkage map includes 801 markers and covers all autosomes with an average spacing of 6.8 cM. A radiation hybrid map (TX) now includes over 2000 markers. BAC libraries are being characterized and new markers being developed at TX, MN, France and Germany. A BAC contig has been developed (TX, NY) as well. Efforts are underway to utilize conserved, heterologous or horse-specific primers to generate 1-5 Mb marker density on selected equine chromosomes.

    Poultry:
    Numerous labs have cooperated in mapping DNA-based polymorphic markers by genotyping samples on three international reference crosses, the Compton population, the East Lansing population and the Wageningen population. The consensus map includes 1965 markers, placed into 50 linkage groups, covering around 4000 cM. Several laboratories have cooperated to generate a second generation BAC contig map comprised of about 280 contigs, two-thirds of which have been anchored to the genetic linkage/chromosome map. The Washington U. Genome Sequencing Center (WUGSC) has completed ~6X sequencing of the chicken genome (primarily whole genome shotgun) and this is now being assembled.

    Sheep:
    An ovine whole-genome radiation hybrid (RH) panel of 5,000 rad has been constructed (TX, UT). The resulting ovine framework/comparative map will contain about 500 microsatellite markers previously assigned to ovine and bovine linkage maps and about 500 ovine ESTs with known human map locations. A 10-fold redundant BAC library has been purchased from BACPAC Resources (AgResearch (New Zealand), the National Meat and Livestock Board (Australia), the USDA/ARS Meat Animal Research Center (Nebraska), and the NRSP-8 Sheep Coordinator, UT).

    Swine:
    Physical and genetic maps of the pig genome continue to be enhanced (BARC, IA, MI, NC, WA, MN, NE, and NV) through mapping of candidate genes, EST, SNP, and microsatellite markers using RH mapping panels, FISH, and reference population resources. Significant milestones toward the completion of Objective 1 include detailed comparative maps focusing on swine chromosomes 3 and 4, description of a second generation map of the IMpRH7000Rad RH mapping panel with an estimated 98% coverage of the human genome, and identification of polymorphisms within several new genes that may be important QTL.

    Progress Toward Objective 2:

    Aquaculture:
    Catfish ? AL has continued to produce expressed sequence tags in channel catfish and blue catfish. Over 37,000 ESTs representing 25,334 unique sequences have been generated. These ESTs have been all deposited to GenBank. Using the EST resource, researchers have characterized expression of chemokine CXCL10 and CXCL8 in catfish with different resistance, both before and after infection.
    Rainbow trout - NCCCWA has continued to identify expressed sequence tags in rainbow trout for identification of functional candidate genes affecting aquaculture production traits and the development of microarrays for functional genomics.
    Tilapia - Sex linked markers have been identified on two linkage groups in Nile tilapia and blue tilapia. The locus on LG1 is an XY (male heterogametic) system. The locus on LG3 is a WZ (female heterogametic) system. Both loci segregated in a single family of blue tilapia. Work is underway to positionally clone these sex-determining genes.
    Oyster ?SC led a successful effort to develop BAC libraries for both the eastern and Pacific oyster, receiving funding from NIH (National Human Genome Research Institute). NJ obtained 500+ sequences from suppression subtractive hybridization (SSH) libraries built to identify up-regulated genes in eastern oysters infected by Dermo and MSX (two parasitic pathogens). Analysis of these sequences has led to the identification of about 170 unique genes.

    Cattle:
    A first generation bovine adipose tissue microarray (OSU) comprised of 1100 unique cDNAs has been generated. A second bovine microarray has been constructed (IA) that includes 10,604 unique bovine cDNAs from the BOV1-4 cDNA libraries.
    QTL mapping for various traits is underway (TX, WI, IL, CA). A new ovulation rate QTL was found (WI) on chromosome 14. Two regions show evidence of QTL segregation for ovulation rate or twinning rate in multiple families, and strong support for a previously reported BTA5 QTL \was found in a combined analysis of four related families. An F2 resource population (Bos taurus x Bos indicus) to investigate maternal reproductive traits is being developed (TX). Males will be used for feed efficiency experiments. A number of candidate genes for growth, disease resistance and reproduction have been evaluated in association studies (TX, NM). Mapping and identification of QTL provide the precursors for a better understanding of biological traits.

    Horse:
    About 11,000 high-quality, well characterized ESTs from stimulated and non-stimulated leukocytes were developed (GA) http://fungen.org/. ESTs (ca 14,000) from articular cartilage are being developed (KY) for the purpose of generating a microarray to study transcriptional changes in equine chondrocytes in osteoarthritis and other arthropathies. Additional ESTs are being developed at (MA, TX, NY). The use of genome mapping, comparative biochemistry and pathology and candidate gene evaluation resulted in the identification (MN) of a genetic change associated with glycogen storage disease IV (GBE1), a fatal disease in Quarter Horses.

    Sheep:
    The high growth (hg) mouse mutation is a 460 Kb deletion of mouse chromosome 10 which causes a 30-50% increase in growth in the homozygous animal. The research group (CA) has observed that the effect of hg can be modified dependent on the genetic background. They propose that the hg phenotype is influenced by genetic interactions between members of the Gh signaling pathway as a result of the absence of the SOCS-2 protein. A core cluster of imprinted genes (DLK1, GTL2, PEG11, and MEG8) located at the distal end of ovine chromosome 18A have been identified (UT, IN, USDA/ARS, and University of Liége). The callipyge (CLPG) mutation enhances the expression of genes in this core cluster when it is inherited in cis.
    Interval mapping (LA) in an F2 population [Gulf Coast Native (resistant) and Suffolk (susceptible)] generated to identify chromosomal regions in the ovine genome that play a role in resistance to gastrointestinal parasites revealed a putative QTL localized on the central region of chromosome 1.

    Swine:
    IA, IL, MI reported progress toward the identification of QTL influencing the genetic regulation of meat quality traits. Also, BARC, IA, IN, MI, NC are using differential gene expression to identify genes controlling physiological traits of economic importance. Based on a microarray experiment NE identified approximately 100 genes putatively differentially expressed between reproductive selection lines. A number of QTL influencing meat quality traits have been identified, and fine mapping of causative genes is currently underway. Results from initial gene expression studies have identified gene expression patterns associated with muscle growth and development, immune responses, and tissue specificity. Additionally, the porcine long oligo microarray is being validated and will rapidly be put to use investigating a variety of experimental models.

    Progress Toward Objective 3:

    Aquaculture:
    Catfish - A web-based EST database for catfish is under construction. Data mining of EST databases has generated large numbers of type I molecular markers.
    Tilapia ? NHAES has developed WWW-based software for comparing the tilapia map with the linkage maps of medaka and zebrafish, and with the sequence scaffolds of pufferfish. The tilapia genetic and physical linkage maps are available in these browsers at hcgs.unh.edu

    Cattle:
    Two groups have begun to implement QTL databases on the web for bovine QTL data (CA,TX). One strategy has been to use the Generic Genome Browser (http://www.gmod.org) as the front end for a MySQL database. The other strategy has been to use the RatMap QTL browser (http://ratmap.org/qtler/) as the basis for an improved interface. Both databases will contain public domain QTL data and one of them will feature password protected log on for investigators to edit or submit QTL data prior to publication.

    Horse:
    The website at the University of Kentucky (http://www.uky.edu/Ag/Horsemap/) continues to be maintained and provides information describing workshop efforts, significant developments for the horse gene map. This site also provides links to other databases and communal resources. A graphic map viewer (HorseMap Viewer) is in final stages of development (CA) and will be also available to investigators.

    Swine:
    MN, NV, WA provided updates on their ongoing efforts to establish integrated database systems for multiple types of data relating to pig genes.

    Impact Statements:
    1. Aquaculture: The set of genomic tools and reagents being developed is accelerating our understanding of the genomes of the species under investigation. The use of these genomic tools to investigate resistance and susceptibility to disease has identified differentially expressed genes that are relevant in disease control.
    2. Cattle and Sheep: The new, more detailed cattle-human comparative map will provide a resource for the analysis of mammalian chromosome evolution and will facilitate the identification of candidate genes for economically important traits.
    3. The BAC clone-based comparative map provides a foundation for the evolutionary analysis of mammalian karyotypes and for sequencing of the cattle genome.
    4. Transcriptional profiling using the newly developed bovine microarrays will allow identification of pathways and candidate genes responsible for economically important traits.
    5. The use of a common microarray by multiple researchers will facilitate a global understanding of gene function across multiple biological models.
    6. Horse: Advancements in developing the genetic and physical map of the horse has allowed to the identification of a genetic change associated with glycogen storage disease IV (GBE1), a fatal disease in Quarter Horses. This latter finding will help develop genetic test to facilitate breeding decisions.
    7. Swine: The genetic regulation of multiple traits of economic importance is being defined through QTL studies. These results will impact the swine industry by providing additional information to be incorporated into selection programs, ultimately providing more economical and desirable products to consumers of pork.
    8. Current efforts focusing on database development will impact the rate at which experimental results can be applied in industries because they will facilitate the integration of information from multiple sources, allowing genes with a significant impact on swine production to be identified.
    Last Modified: unknown

    Date of Annual Report: 03/18/2005

    Report Information:
  • Annual Meeting Dates: 01/16/05 to 01/16/05
  • Period the Report Covers: 01/2004 to 12/2004

    • Participants:

    URL: Copy of participant list
    Brief Summary of Minutes of Annual Meeting:
    I. Call to order at 4:30 pm by Dr. Bhanu Chowdhary, NRSP8 Technical Committee Chair

    a. Dr. Max Rothschild made a motion to approve the last meetings minutes, second by Dr. Joe Cassidy and approved by a voice vote

    II. Old Business

    a. Summary of the Executive Committee Meeting

    i. In 2006 the committee meeting must return to an early Sunday morning breakfast meeting at 7:00am

    ii. All species workshops must finish by 4:00 pm Sunday so participants may attend the General Membership Business Meeting from 4:30 to 6:00 pm

    b. Species Reports

    i. Equine-Dr. Ernest Bailey 1. NRSP8 Objective 1. Most efforts have focused on adding to linkage and radiation hybrid maps 2. NRSP8 Objective 2. Limited activity in this area, four institutions are working on a plan 3. NRSP8 Objective 3. Genome Viewer at UC Davis integrates linkage information 4. Workshop participants will meet in Dublin in July 2006 to discuss mapping, functional genomics, and their applications.

    ii. Poultry-Dr. Jerry Dodgson 1. This year the chicken genome sequence was published in Nature 2. This was the first post sequence workshop, topics included: a. Draft sequence has some miss-assemblies and places that require further annotation b. Use of sequence to improve genetic analyses c. Application of chicken sequence to other poultry

    iii. Cattle -Dr. James Womack 1. Draft sequence of 3.3X coverage was completed this fall 2. Now focus is on adding animals other than the original Hereford 3. Will keep fibroblast cell lines for these animals and others 4. The ArkDB server is no longer maintained at TAMU, moved to ISU 5. Online radiation hybrid mapping at TAMU using first generation RH map, will soon update to a more recent version 6. Somatic Cell hybrid panel still available 7. IBRP usage has dropped off significantly

    iv. Sheep-Dr. Noelle Cockett 1. An NRI Tools and Reagents Grant was awarded to Dr. Cockett and Dr. Womack to construct an ovine radiation hybrid panel, now using coordinators funds to distribute 2. this will strengthen comparative maps between species, Dr. Harris Lewin will map markers 3. CHORI 243 BAC library constructed by Pieter DeJong available since last year, also gridded filters, Dr. Cockett purchased some with Coordinators funds for distribution 4. BAC end sequencing project is a collaborative effort, USDA has also funded through NRI Tools and Reagents. Dr. Cockett can do .5X of the library, she leveraged funding for the rest through other international sources which will result in full library, work to be done at TIGR 5. collaboration with national animal germplasm group has been set up to collect/conserve germplasm in US. Attended meeting in Cheyenne, great info for genetic diversity study, will supply this group with primers to study their collections and use this germplasm for SNP validation

    v. Swine-Dr. Max Rothschild 1. design oligos for a 13K oligo array, sent to 35 labs, primarily in US, also Europe and Asia 2. Discussed a second generation oligo microarray 3. PigQTLdb on angenmap website 4. Expeditor primer design tools, other database tools 5. Swine Genome Sequencing Consortium, worked with industry to raise funds, big news is that USDA/CSREES will issue an RFA in the ball park of $10 million, possibly $1 million more from ARS, matching funds from Sanger, puts them much closer to goal of $30 million, hope to start sequencing in summer 2005 6. Industry was well represented at the workshop by Sygen and Monsanto, who are actively using molecular genetic tools from this effort

    vi. Aquaculture-Dr. John Liu 1. The Aquaculture group is very complex, with 6 primary species and additional sub species, includes an executive committee. 2. This year 3 species coordinators Program Chair and Chair Elect changed 3. Four proposals for sequencing project were submitted to the JGI Community Sequencing Program (trout, catfish, oyster, tilapia) oyster and tilapia scored well. 4. Aquaculture species need to set priorities 5. Two white papers were developed, one to addressed to save the NRI Tools and Reagents Program, a second distributed to other funding agencies concerning the genomic enablement of these species 6. The Aquaculture Genome website was developed and moved to ISU this year. 7. Dr. Caird Rexroad summarized the workshop report including plenary speakers, student presentations, and evening poster session

    vii. Database-Dr. James Reecy 1. work on objective to centralize resources for all species with bioinformatic expertise to ISU 2. team involves Dr. Chris Tuggle, Dr. Max Rothschild, Dr. Sue Lamont, and Dr. Zhiliang Hu 3. The species coordinators serve as a consulting board 4. The ISU database is a place to put programs used by all, also resources like maps, etc& 5. PigQTLdb-a database for pig QTL information, can do other species 6. Expeditor-primer design software for SNP discovery 7. in-house blast server 8. The website and Angenmap both continue to increase in number of hits and usage 9. This year the group will assist in pig oligo microarray construction, would like to make pipeline for other species

    c. Administrators Reports

    i. Margaret Dentine, Lead Administrative Advisor 1. NRSP8 is a model of how support program should work a. Democratic process, funding spread around, successful workshops 2. New review for NRSPs in experiment station system, NRSP8 received a good review and did get the budget requested. This is significant as funding comes from directors budgets 3. We all bear responsibilities to work with coordinators 4. Project will be up for review again, it is important to do a good job

    ii. Dr. Dr. Muquarrab Qureshi, USDA/CSREES National Program Leader 1. Thank species coordinators and executive committee for good job, help to accomplish mission, of advancing knowledge 2. Strategic goals-enhance efficiency of agricultural production systems, including genetics, under programs 303 and 304, genetics and genomics 3. Help meet performance based budget progress 4. High priority area for USDA 5. $15 million per year 6. pleased with updates in meeting including sequencing efforts 7. NRSP8 received excellent reviews, complemented for adding aquaculture 8. funded Shrimp Genome Consortium 9. hosted Animal Bioinformatics Workshop 10. NRI RFP 2006 planning is underway 11. 2005 budget is flat compared to previous year

    III. New Business

    a. NRSP8 Business Meeting schedule-see above

    b. USDA/CSREES workshop on Animal Genomics held in September 2004, summary by Dr. Ronnie Green

    i. Summary report given in swine meeting, copies available ii. Workshop came about by charge by Dr. Joseph Jen, USDA Undersecretary for Research, Education and Extension. iii. Once we are passed sequencing genomes of major species, what next? iv. Dr. Green and Dr. Qureshi were asked to put workshop together to ask scientist and administrators what to do v. Asked subset to stay and brief the Interagency Working Group on the workshop, the working group was pleased to see scientists priorities of long term needs for animal genomics. vi. A summary of the workshop will be made public and published in Animal Genetics in March vii. Also charged to take out strategic planning exercise in this effort in 2005, involving all agencies in animal genomics, will do in 2nd and 3rd quarters of this year viii. Interagency report on NSTC website , have 2003 report now, 2004 soon

    c. Animal Genome Tools and Reagents Program-future prospects

    i. Discussion initiated by Dr. Anna Palmisano, USDA/CSREES Deputy Administrator 1. NRI is the largest competetive program in USDA 2. Now starting 2006 planning 3. Need help setting priorities-How can we make the greatest impact? 4. Need to develop linkages with other agencies, but limit overlaps 5. In FY06 planning we need to think long term approaches 6. Think big, think about more comprehensive approaches to animal genomics portfolio at CSREES 7. Question-Dr. Bob Chapman-We have an opportunity to think big, how about incorportative ecogenomics, as all of our species have environmental impacts. Answer-CSREES is working on a program for FY06 concerned with ecogenomics, mostly at the microbial level. Also, the Natural Resources group is thinking about ecogenomics. 8. Comment-Dr. Jerry Dodgson-on the importance of Tools and Reagents. Response-CSREES needs to know the priorities for Tools and Reagents for this group. 9. Comment-Dr. Max Rothschild-for swine SNPs are a high priority not funded in pigs, have for chicken and cattle. So we must prioritize not between species, but within. Response-to increase success rate may require a better, more focused RFP. 10. Comment-Dr. John Liu-Tools and Reagents has generated tools and science, still need tools for Aquaculture species, need to apply different criteria to different species. Response-group needs to articulate needs. 11. Comment-Dr. Bhanu Chowdhary-Species coordinators need to conduct prioritization. Response-Asked to provide input to Dr. Qureshi and Dr. Brayton. 12. Summary-to impact the planning process submit comment in next 2-3 months, remember to think long term.

    d. Motion by Dr. Noelle Cockett to include goats on the Cattle/Sheep committee.

    i. Not a request to re-allocate funds, goats would be a subcommittee of sheep ii. Second by Dr. Max Rothschild iii. Discussion-Virginia State, Valley State, and Prairie A&M, 1890s schools, want to move towards genomics to study traits iv. Passed voice vote

    e. Election of officers for 2005

    i. Cattle/Sheep committees turn to nominate-nominate Dr. Clair Gill ii. Second by Dr. Max Rothschild iii. Passed voice vote

    f. Other

    i. suggestions for future plenary speakers for PAG on animal genome side, send to Dr. Hans Cheng or Dr. Max Rothschild

    IV. Adjournment 5:53 pm

    Respectfully submitted,

    Caird E. Rexroad III for Thomas Kocher, Co-Chair

    Overall attendance to the NRSP-8 species workshops: 65 (Aquaculture), 56(Cattle & sheep), 51 (Horse), (Poultry), 97 (Swine).

    Accomplishments:
    For a complete report, please see: http://www.wisc.edu/ncra/NRSP8-2004-SAES422Link.doc

    Progress toward Objective 1: Enhance and integrate genetic and physical maps of agriculturally important animals for cross species comparisons and sequence annotation.

    Aquaculture. Good progress has been made toward reaching objective 1 among aquaculture species in 2004. The current state of aquaculture genomics include availability of relatively high-density genetic linkage maps from Atlantic salmon and rainbow trout (with over 1000 markers), moderate density linkage maps for tilapia and catfish (with several hundreds of markers), and framework linkage maps of for oysters and shrimps. BAC-based contigs have been established for Atlantic salmon and tilapia, but are lacking for catfish, rainbow trout, striped bass, shrimps, and oysters. In spite of the lack of one or the other maps, efforts were devoted to enhance and integrate these maps as detailed below:

    Cattle. Jim Womack from Texas A&M University gave a detailed presentation titled "Highlights of the bovine sequencing project. He reviewed that discussion to sequence a bovine genome occurred as early as 1993 by NRSP-8. Much of the initial sequencing effort is occurring at the Human Genome Sequencing Center at Baylor College of Medicine in Houston, TX. Richard Gibbs and George Weinstock are directing these efforts and a ~3X working draft was published in October of 2004 and is available at Genbank. The animal resources from this project were derived from the historic linebreeding Hereford project at the Fort Keogh United States Department of Agriculture  Agriculture Research Service (USDA-ARS) station in Miles City, Montana. A Bacterial Artificial Chromosome (BAC) DNA library was originally created from tissues of the bull L1 Domino 99375 and the whole genome shotgun sequences were derived from DNA extracted from the white blood cells of his daughter, L1 Dominette 01449. Dominette was selected since her sire was used to create the BAC library and because of the concept that sequence assembly could be made easier working with sequences from animals with similarities in their genetic background. Other contributions to this project now include sequencing within other breeds such as Holstein, Angus, Brahman, Jersey, Limousine and Norway Red. Some of these other efforts include SNP mapping as well as ~10,000 full-length mRNA sequences to be provided by Genome Canada. A 7 to 8X coverage map is expected by late summer of 2005. Other mapping efforts were presented by H. Lewin of the University of Illinois. In brief, a second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using cattle ESTs that were targeted to gaps in the existing cattle-human comparative map as well as to sparsely populated map intervals. Discussion also occurred regarding an international consortium formed to create a sequence-ready comparatively anchored bacterial artificial chromosome (BAC) map of the cattle genome.

    Horse. The resources now used most frequently for equine genome mapping include a 5000 rad horse x hamster whole genome radiation hybrid panel, a collection of stallion-based half-sib families comprising 500 offspring, and a pedigree in which a single stallion sired over 60 conceptuses from two sets of identical twin mares. Two new genetic linkage maps are in the publication process. The first contains 766 markers on the half-sib families (combined with previous maps from other families) with a single linkage group on all autosomes, and the second contains 745 markers on the 3 generation full-sibling family and reports a single linkage group on all autosomes plus the X. Microsatellite markers continue to be developed and mapped on both resource populations. Gene markers from individual human chromosomes, as well as markers from across the genome, are being mapped on the RH panel, frequently accompanied by FISH localization. Many microsatellites are also being mapped on the RH panel. More than 2,500 markers have been typed on this panel and the goal is to soon have a greater than 3,000 marker RH and comparative map. Dense (greater than 1 marker/Mb) maps are now in process for many of the autosomes as well as the X and the Y. The two genetic linkage maps, as well as the RH map are becoming increasingly integrated through the mapping of common markers on all three resources. In addition to the mapping efforts, over 2,000 BAC end sequences comprising 1.8 Mb of sequence have been collected and being used for prediction of gene content and comparative sequence alignment with human and other species, as well as for selected inclusion on the RH map. Poultry. High resolution poultry genome maps.

    The Reference Linkage Map(s). Numerous labs have cooperated in mapping DNA-based polymorphic markers by genotyping samples from the same two international reference crosses, the Compton population (Bumstead and Palyga, Genomics 13, 690-697, 1992), and the East Lansing population (Crittenden et al., Poultry Science 72, 334-348, 1993). This map has been enhanced by genotyping of a third cross, the Wageningen population, by Martien Groenen and colleagues (Groenen et al., Genomics 49, 265-274, 1998). A consensus map based on all three map populations has been published (Groenen et al., Genome Res. 10:137-147, 2000). Updates bring the number of markers on the consensus map to 2204, placed into 51 linkage groups, covering nearly 4000 cM (International Chicken Genome Sequencing Consortium, Nature 432:695-716, 2004). The East Lansing map has expanded to 1276 markers on 42 linkage groups (other evidence places E46 on GGA2 and E66 on GGA5, but there is not enough statistical support in our map alone to establish these linkages). This map includes 326 mapped genes. In connection with the genome sequence, the Beijing Genomics Institute randomly sequenced 0.25X, each, of a broiler, layer and Silkie genome, generating 2.8 million potential SNPs for future high resolution linkage mapping experiments (International Chicken Polymorphism Map Consortium, Nature 432:717-722, 2004).

    Sheep. (Develop high resolution comparative genome maps):

    NRSP-8 Sheep Coordinator funds have contributed to the development of an ovine radiation hybrid (RH) panel in a collaborative project between Utah State University and Texas A&M University. Ninety clones with retention frequencies between 15-40% have been selected for inclusion in the 5,000 rad RH panel. Large DNA preparations have been made for the 90 clones and the panel has been distributed to Dr. Tom Goldhammer, Research Institute for Biology of Farm Animals, Dummerstorf, Germany, and Dr. John Williams, Roslin Institute, Edinburgh, UK. An on-line, real-time comparative database being developed at Texas A&M University will be used for web-based transmission of mapping data on the distributed ovine RH panels. Database displays will include ovine RH maps of each chromosome that are cross-referenced to homologous human and bovine chromosome segments, with lines between orthologous markers indicating internal rearrangements. The goal is to type the ovine panel with 500 microsatellite markers that have been mapped on the ovine and bovine linkage maps, as well as 500 ESTs developed from ovine and bovine cDNA sequences with known locations on the human genome map. These data will be used to develop a framework/comprehensive RH map for sheep.

    Swine BARC and Baylor Univ researchers, with the ISAG SLA committee, established an internationally recognized nomenclature to identify and classify SLA class I gene polymorphisms. This will serve as a basis for determining critical genetic effects on infectious disease and vaccine responses. They have made data fully accessible at an international website, the IPD-MHC Sequence Database website: www.ebi.ac.uk/ipd/mhc/sla/nomenclature.html. A large number of genes continue to be identified and mapped by ISU researchers. An emphasis has been made (and will continue to be made) on genes that improve the comparative map as well as in connecting the genetic and physical pig genome maps. Several new genes that may be important QTL are being mapped by ISU researchers. These include genes associated with cured meat quality and sow longevity. QTL for several meat quality traits have been discovered. Additional fine mapping is underway and positional candidate genes are being considered. Mapping of over 400 comparative loci to pig chromosomes SSC1, 4, 7, 8 and X adds additional information to comparative maps.

    Progress towards Objective 2: Facilitate integration of genomic, transcriptional, proteomic and metabolomic approaches toward better understanding of biological mechanisms underlying economically important traits.

    Aquaculture. In 2004, great progress has been made in the area of transcriptome analysis using ESTs. A summary of current available ESTs in various aquaculture species is listed below. These ESTs has allowed the development of microarrays in various species as detailed below.

    Species Current ESTs Approximate unique sequences Rainbow trout 160,816 50,773 Atlantic salmon 120,000 40,000 Catfish 45,000 30,000 Oyster Crassostrea gigas 3,300 Crassostrea virginica 9,200 5,900 Shrimps 9,400 3,300 Tilapia 1,700 Striped bass <500

    The largest progress in this area was made with salmonids. A 16,000 gene array has been developed by GRASP using salmon and trout EST data sets. This array has been tested for use in various salmonid fishes. The array has been used to study developmentally regulated genes and genes induced under various environmental conditions.

    Cattle. Several universities reported progress in this area. In brief, these reports included advancements in understanding of genes regulating milk production traits, muscle development (i.e, callipyge), marbling, growth hormone, disposition, gastrointestinal nematode infection, and tolerance to endophyte toxicity in cattle grazing fescue grass. Invited speakers for the cattle and sheep symposium presented that a new SNP marker in CAPN-1 associated with tenderness in cattle of indicine, taurine, and admixed decent. There is tremendous interest in the trait of tenderness in the basic scientific community and in the commercial genotyping industry. A challenge in the application of some of the initially discovered polymorphisms related to tenderness was that the markers inferred variability in prediction of tenderness traits and had diversity among genotypes in Bos taurus cattle, but not in Bos indicus cattle. These studies revealed that chromosome 29 contained an important gene defined as µ-calpain (CAPN-1) which has a large role in postmortem tenderization. There are a series of SNPs within or closely linked to this gene. Two of these SNPs appear to be informative in Bos indicus and Bos taurus cattle (316 and 4753), but a SNP at 530 only appears to be informative in Bos taurus cattle. Moreover, it appears that these markers maybe more useful in predictions using analytical procedures involving haplotypes. Stephen Moore from the University Alberta-Edmonton delivered a talk on Candidate genes of feed efficiency. The trait of residual feed intake was introduced and efforts to find genetic tools to select for this trait were discussed. Data of other measure of animal efficiency were also presented which involved evaluating oxygen consumption and methane production using a respiratory calorimetry hood. The rationale for these measures were from the concept that measures of gas consumption or production could be used to estimate metabolic rate/efficiency in cattle. Efforts to use these measures to identify candidate genes were also presented, particularly their associations with hormones such as leptin. Jeremy Taylor (University of Missouri) reported results in fine quantitative trait loci (QTL) mapping in dairy cattle (in collaboration with scientists at USDA-ARS and University of Arizona) as well as results in positional cloning in beef cattle. To fine-map QTL affecting milk production traits in dairy cattle on BTA6, 3317 bulls comprising 45 half-sib families were genotyped for 38 markers. The data were analyzed using least squares regression (QTL Express), linkage disequilibrium (LDVCM) and full pedigree MCMC (LOKI) methods. A total of 19 sires were segregating for at least one QTL under a half-sib model at chromosome-wide P < 0.05. LD results across families indicated the presence of up to 7 QTL (3 within a 6 cM region) whereas LOKI revealed only 3 QTL. Positional/functional candidate genes have been identified for five of the QTL. Osteopontin (OPN or SPP1) is a strong candidate for the QTL near marker BM143. The entire OPN gene and 5kb upstream was sequenced from four segregating sires and four non-segregating sires (12.3kb per animal). A total of 15 SNPs were identified but only one SNP resulted in sire genotypes that were concordant with the segregation status of all eight sires. For position cloning in beef cattle, the strategy outlined in Taylor and Schnabel was applied and built upon the previous projects involving Bos taurus x Bos indicus crosses and study of Bos taurus autosomal (BTA) chromosome 2 and 14. A DNA Repository from semen on 1,660 registered bulls representing 14 generations of the American Angus Association was assembled. Expected progeny differences (EPD)s and reliabilities for 20 traits are available for this population. In addition, 5,300 DNA samples were collected on commercial Angus steers (36 halfsib families have at least 30 progeny) with growth and slaughter phenotypes. A total of 113,637 genotypes for 56 microsatellite loci and SNPs for thyroglobulin in exon 5 (TG5) and diacyl glycerol acyltranferase in exon 1 (DGAT1) on BTA2 and BTA14 in 1,361 Angus sires and 559 steers were scored. Results suggested TG5 had no effect on sire Marbling EPDs or steer marbling phenotypes. Three previously published marbling QTL, 1 birth weight QTL and 1 carcass weight QTL are segregating within Angus and map to identical locations to the published reports.

    Horse. ESTs have been collected from unstimulated and stimulated equine leukocytes, from articular cartilage, from brain, and from skeletal muscle. 1,000 element microarray has been printed from the leukocyte EST collection and is being used to study genes involved in pathogenesis of experimentally-induced laminitis. A 9,410 element microarray is under development from the cartilage ESTs. Discussions of combining sequences from all sources and developing a larger oligo-based microarray have been initiated. It is anticipated that this resource would assist the group in defining the processes associated with many disease and economically important traits, such as laminitis, joint disease, colic, etc. A contig of 23 overlapping BAC clones comprising the equine MHC (ELA) has been assembled and subclones scheduled for an estimated 7X sequencing of the region. Description of the gene loci in this region will help to define genetic influences on disease susceptibility and resistance. In addition, studies to characterize the T-cell receptor B gene family in horses are ongoing. Recently the molecular genetic basis of glycogen storage disease type IV (GBED) in Quarter Horses and junctional epitheliosis bullosa (JEB) in Belgian horses have been described through the use of genome mapping tools. Studies to define the molecular basis polysaccharide storage myopathy (PSSM) and hyperelastosis cutis (HERDA) in Quarter Horses, and exertional rhabdomyolysis (RER) in Thoroughbreds are ongoing as are studies to identify the gene responsible for Degenerative Suspensory Ligment Disease and the grey, sabino overo, and appaloosa coat color patterns.

    Poultry. Physical maps and map integration. A library of over 115,000 BACs (~15X; Lee et al., Animal Genetics 34:151-152, 2003) was generated and 65,000 of these were fingerprinted at Texas A&M, leading to a first generation physical map (Ren et al., Genome Research 13:2754-2758, 2003). P. de Jong (Childrens Hospital of Oakland Research Institute, CHORI) generated a ~10X BAC library (CHORI-261) with extra large inserts using DNA we provided from the same bird used for the Texas A&M BACs and for sequence analysis. CHORI also prepared a large insert turkey BAC library (CHORI-260). The Washington U. Genome Sequencing Center (WUGSC) was provided copies of the Texas A&M and CHORI-261 chicken BAC libraries and fingerprinted over 150,000, generating over 130,000 useable BAC fingerprints. These were employed to generate a second generation BAC contig map comprised of 260 contigs, 226 of which have been anchored to the genetic linkage/chromosome map (Wallis et al., Nature 432:761-764, 2004). Several labs participated in integrating the BAC contigs and sequence with the linkage map, primarily using overgo hybridization (Romanov et al., Cytogenetics and Genome Res., 102:277-281, 2003). This research generated over 7800 BAC assignments to over 900 distinct markers or genes. Recently, similar efforts applied to the turkey CHORI-260 library have generated over 2400 BAC assignments for 176 markers/genes.

    Boardman et al. (Current Biology 12:1965-19-69, 2002) announced the sequencing of over 300,000 chicken ESTs from a wide variety of tissues and developmental stages. A joint project between the U. of Manchester and the Sanger Institute (Jane Rogers) sequenced full length chicken cDNA clones using both UMIST and other libraries. A world-wide consortium of investigators report 19,626 finished cDNAs and 485,337 ESTs (Hubbard et al., Genome Research advance Epub, Dec. 8, 2004). NCBIs dbEST (http://www.ncbi.nlm.nih.gov/dbEST/) presently lists 531,351 chicken ESTs. Array development will be reported below.

    Masabanda et al. (Genetics 166:1367-1373, 2004) generated a molecular cytogenetic analysis of the chicken, including identification of all microchromosomes, either by chromosome paints or BAC FISH probes. Radiation hybrid (RH) panels have been constructed by Vignal and colleagues at INRA (Morisson et al., Genet. Sel. Evol. 34:521-533, 2002), and a framework RH map is being constructed (e.g., Morisson et al., Mamm. Genome 15:732-739, 2004).

    The Washington U. Genome Sequencing Center (WUGSC) has completed 6.6X sequencing of the chicken genome (primarily whole genome shotgun) and the first assembly of the draft chicken sequence was released on March 1, 2004. The initial analysis and annotation of the sequence was recently published (International Chicken Genome Sequencing Consortium, Nature 432:695-716, 2004). In addition to the companion physical map and SNP papers mentioned above, the January, 2005 issue of Genome Research will be devoted to companion chicken sequence analysis papers (Genome Research advance Epub, Dec. 8, 2004).

    Sheep. (Increase marker density of existing linkage and physical maps): The ovine linkage map is continuously updated, primarily through the efforts of Dr. Jill Maddox, University of Melbourne, Australia. The linkage map now includes over 1,250 loci [http://rubens.its.unimelb.edu.au/~jillm/jill.htm ]. A collaborative project including the US, Australia, New Zealand, and the UK will soon commence with the objective of developing a whole genome physical map (see below).

    Swine. BARC researchers have provided means to study expression and function of additional immune genes in normal breeding populations to identify early responders which might be more disease resistant/susceptible. New work in porcine reproductive and respiratory syndrome virus (PRRSV) resistance with UNE researchers may help identify pigs which are more disease resistant and the protective mechanisms they employ to induce resistance. ISU researchers have used two molecular techniques to identify some of the genes which increase or decrease expression levels in the early response to Salmonella choleraesuis or S. typhimurium infection. These are subtractive suppression hybridization (SSH) and microarray. Genes include signal transduction and steroid biosynthesis which are involved in the embryo elongation process. ISU and NADC researchers have begun to analyze the lungs of pigs infected with S. choleraesuis by using the NRSP8 funded long oligonucleotide microarray, and find 57 genes with some statistical evidence (P <0.001) for differential expression; of the 40 genes from this group with human functional annotation, 40% are related to the immune system. The transcriptional profiling results were verified by quantitative techniques with BARC researchers. Transcriptional profiling of skeletal muscle tissue at Michigan State Univ. reveals important genes in the pathways regulating skeletal muscle growth and development. Their development of a unique pig resource population provides a novel resource for identifying QTL associated with growth and carcass merit in pigs. NCSU researchers are characterizing changes in allelic frequencies for two RFLPs associated with the follistatin gene in a line of pigs selected for increased litter size (LS). In a separate project they are working to identify genes associated with adipose metabolism. For this they are analyzing gene expression during t10c12-CLA-induced body fat reduction in a polygenic obese line of mice. In an effort to identify genes responsible for anti-microbial responses in the gut, UMN researchers isolated expressed sequence tags (EST) from an activated porcine Peyers patch cDNA library. 3687 ESTs, representing 2414 unique nucleotide sequences were analyzed and spotted onto a microarray for gene expression profiling. Approximately 30% of these ESTs BLAST to genes of unknown function and 20% appear to be novel, i.e., have no known homology in the public databases. To determine chromosomal location, PCR-based mapping was performed across a swine radiation hybrid panel; 125 ESTs were mapped with a lod score > 6.0. These ESTs therefore should provide insight into early immune mechanisms and processes activated in Peyers patches. Islet gene expression profiles were assessed at UMN using the NRSP8 funded porcine 70-mer oligonucleotide microarray and real-time PCR. Microarray data were analyzed by direct pairwise comparison between culture conditions and by loop design using GeneSpring and R/maanova, respectively. Cytokine treatment resulted in increased expression of genes involved in stress, immune response, apoptosis, and cellular defense. Islets cultured under conditions of elevated glucose showed increased expression of genes involved in intracellular protein transport, glucose and lipid metabolism, and stress response. Transcriptional profiling of the response of porcine islet beta cells to inflammatory and hyperglycemic conditions will help identify molecular targets that are likely to protect porcine islets during islet isolation and engraftment.

    Progress Toward Objective 3: Facilitate and implement bioinformatic tools to extract, analyze, store and disseminate information.

    Aquaculture: Overall, bioinformatic tool development is a very weak area in aquaculture genomics.

    Thomas Kochers group continues to build informatic tools to integrate the genetic and physical maps of the tilapia genome with with the genome sequences now available for Fugu, Tetraodon, medaka and zebrafish. The comparative genome databases and browsers are available at http://hcgs.unh.edu/. Greg Warrs group continue to maintain the website www.marinegenomics.org for the archiving of EST and microarray data, and as a resource for on-line tools that can be used in the analysis of genomic and transcriptomic data. They have developed tools for the design of microarrays from species with limited genomic information (see Chen et al., 2004). In collaboration with Dr. Lei Liu at the Keck Bioinformatics Center, an ESTIMA system has been developed that provides searchable databases for the catfish ESTs at Auburn University. As soon as it is tested, the website will be available to the research community.

    Cattle: Jim Reecy of Iowa State University presented information regarding database activities of NRSP-8. During the symposium, Trey Ideker of the University of California, San Diego, gave a presentation titled Modeling cells with molecular interaction networks. Molecular interaction networks are experimentally derived connections of metabolites and proteins within pathways. While these molecules may not directly interact, they likely are related through the enzymes that process them. Dr. Ideker presented evidence that overlays, the alignment of pathways according to protein sequence or other data where similarity scores are available, may be of great use. Specifically, overlays of known networks from well studied species may elucidate the function or role of unknown metabolites and proteins in less well understood organisms. The implications of this research involve an increase in the speed of which function can be ascribed to unknown compounds in bovine using information gathered in human, mouse, and rat. Christine Elsik of Texas A&M University (TAMU) spoke on the current state of the bovine long oligo array developed among a consortium of researchers at TAMU, University of Missouri, Iowa State University, and The University of Minnesota. Sequences mined from GenBank are currently undergoing a screening process to remove duplicated sequences, vector sequences, and other artifacts of the cloning process. It is expected that a first draft of the sequences to be spotted on the array will be available by Summer of 2005.

    Horse: This objective is not currently a major focus of the equine group. Bioinformatic tools available include a Web interface for RH panel typing data submission and mapping, a publicly available and searchable database that houses the leukocyte ESTs at the University of Georgia, and DNA marker databases maintained at INRA and Roslin.

    Poultry: Database and other map resources. Sequence and Map: The sequence, along with a variety of options and tools, can be accessed at three different browsers: the UCSC Chicken Genome BrowserGateway, (http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chicken&db=0&hgsid=30948908); the NCBI Chicken Genome Resources, (http://www.ncbi.nlm.nih.gov/genome/guide/chicken/); and the EBI's Ensembl Chicken Genome Browser, (http://www.ensembl.org/Gallus_gallus/). See also the WUGSC chicken site at http://genome.wustl.edu/projects/chicken/. SNP data can be accessed at http://chicken.genomics.org.cn/index.jsp or the UCSC or Ensembl browsers. The ChickFPC browser at http://www.bioinformatics.nl/gbrowse/cgi-bin/gbrowse/ChickFPC allows for various searches of the BAC contig map. Similarly, BAC locations denoted by BAC end sequences can be found on other sequence browsers noted above. The BAC map can also be obtained by ftp at http://genome.wustl.edu/projects/chicken/. The SNP data generated by the Beijing Genomics Institute (described above) can be accessed on the UCSC or Ensembl browsers, but more extensive descriptions (including QTL information) are available at the BGI site at http://chicken.genomics.org.cn/index.jsp.

    ChickGBASE: The latest version of ChickGBASE is constructed in the comparative mapping Arkdb format. Arkdb was primarily developed at the Roslin Institute. ChickGBASE is available in the Arkdb format at http://www.thearkdb.org/browser?species=chicken . A mirror site for the poultry database has been mounted at the Iowa State database site, http://www.genome.iastate.edu/. James Reecy at Iowa State has taken over direction of all bioinformatics efforts for the NAGRP, including chicken. WWW Homepage: We maintain a WWW homepage (http://poultry.mph.msu.edu) for the Poultry Genome that provides a variety of genome mapping resources, including the latest EL maps and mapping data, an updated list of published microsatellites, descriptions of available resources, the latest cytogenetic map, and access to a host of other information relating to both genetic and physical maps.

    Sheep: (Expand species genome databases and provide other genome mapping resources): An informational database for the ovine genome map continues to be enhanced. SheepBase contains an up-to-date compilation of published data from sheep genome mapping projects, along with physical and linkage maps of the sheep genome, and information on individual loci and associated references. The information is presented using the WWW interface and can be accessed through a number of nodes including Roslin Institute (UK) and the University of Melbourne (Australia). Currently, there are 2832 map assignments in SheepBase, with 1988 derived through linkage analysis and 844 via physical mapping. Dr. Jill Maddox, University of Melbourne, Australia, has been updating the database using NRSP-8 coordinator funds to serve as the curator of SheepBase.

    A memorandum of understanding was established among AgResearch (New Zealand), Meat and Livestock Australia, the USDA/ARS Meat Animal Research Center (Nebraska), and the NRSP-8 Sheep Coordinator in order to fund the construction of a 10-fold redundant BAC library by BACPAC Resources. A copy of the library has been received by Utah State University. In addition, arrayed filters have been purchased and are distributed upon request.

    Swine: Database development is continuing at ISU. An EST database has been developed and is quite useful. ISU researchers developed a relational pig quantitative trait loci (QTL) database (PigQTLDB) to integrate all available pig QTL data in the public domain and thus facilitate the use of QTL data in further studies. PigQTLdb has been well used since its release last December (http://www.animalgenome.org/QTLdb/). They developed a trait ontology to standardize names of traits and to simplify organization of the data making it possible to compare primary data from diverse sources and methods. The database contains all pig QTL data published during the past 10+ years. The database and its peripheral tools were made to compare, confirm, and locate on pig chromosomes the most feasible location for a candidate gene responsible for quantitative trait(s) important to pig production. To date, 791 QTL from 73 publications have been curated into the database. Those QTLs cover more than 300 different traits. Contact Zhiliang Hu (zhu@iastate.edu) with any suggested improvements or additional data to add to the database. These data have been submitted to the Gene and Map Viewer resources at NCBI, where the information about markers has been matched to marker records in NCBI's UniSTS database. This allows automatic matching of markers to public sequence data by e-PCRand data retrieval from NCBI resources. Efforts at ISU and UMN have been aimed at developing better annotation of the NRSP8 funded porcine 70-mer oligonucleotides for microarray data analyses. WSU researchers have take 3 steps to collect and generate full-length cDNA sequences of orthologous genes in livestock species, i.e., puzzle sorting, puzzle retrieving and puzzle making for a final puzzle solving. They have developed a bioinformatics tool, ELF-Walking (electronic flanking walking) to facilitate large-scale in silico cloning of full-length cDNA sequences by mining the sequence databases. All sequence data and annotation information can be downloaded from our Bioinformatics website at http://www.ansci.wsu.edu/programs/bioinformatics/.

    Impact Statements:
    1. NRSP8 Objective 3. Genome Viewer at UC Davis integrates linkage information
    2. This year the chicken genome sequence was published in Nature
    3. Draft sequence of 3.3X coverage was completed this fall
    4. An NRI Tools and Reagents Grant was awarded to Dr. Cockett and Dr. Womack to construct an ovine radiation hybrid panel, now using coordinators funds to distribute
    5. Design oligos for a 13K oligo array, sent to 35 labs, primarily in US, also Europe and Asia
    6. The Aquaculture Genome website was developed and moved to ISU this year.
    7. PigQTLdb-a database for pig QTL information, can do other species
    Last Modified: unknown

    Date of Annual Report: 03/16/2006

    Report Information:
  • Annual Meeting Dates: 01/14/06 to 01/15/06
  • Period the Report Covers: 01/2005 to 01/2006

    • Participants:
    Brief Summary of Minutes of Annual Meeting:
    I. Call to order at 4:30 pm by Caird Rexroad, Chair.

    Minutes taken by David Adelson (standing for Clare Gill).

    Sue Lamont moved to approve minutes from January 16, 2005 meeting. Motion was unanimously affirmed.

    II. Old Business 1. Species Reports: a. Cattle/Sheep/Goat i. Noelle Cockett, Sheep Genome Coordinator

    Progress on sheep RH panel: distributed to 4 labs (see coordinators report). Significant typing efforts in Cockett lab include: 257 markers screened so far, about 50% of which are scoreable, with about 2/3 of those results duplicated. Efforts now are aimed at scaling up to type large numbers of markers. There will soon be a need for a data repository and infrastructure for the analysis of typing data.

    A Tools and reagents proposal was funded for BAC end sequencing and construction of a physical map from the CHORI sheep library. Kellye Eversole negotiated a very favorable price with TIGR to end sequence the full 200,000 clones from the library. Related statistics are in the coordinators report, but a key feature is that ~6% of the ovine genome is represented. A whole genome physical map is being constructed by Brian Dalrymple (CSIRO Australia) using end sequences.

    International Scientists linkage program. A large scale SNP discovery project (30,000 total sheep SNPS to create a 20,000 SNP chip) was initiated with Frank Nicholas (Sydney University).

    Dr. Cockett invited scientists to attend the meeting of International Sheep Genome Consortium to be held at PAG Jan. 16.

    ii. James Womack, Cattle Genome Coordinator

    The Cattle genome sequencing project has consumed most of the resources and attention of the coordinator. At present there are efforts to develop a cell culture repository to immortalize DNA from the animals used in the sequencing project and first phase of SNP detection. Live cell lines will be provided to investigators upon request.

    The 5000RH panel is still available and results can be mapped automatically via web site supported by Womack lab. Web site is being updated to the 3rd generation IL/TX RH map, skipping the 2nd generation map.

    Water buffalo RH panel made in collaboration with Brazilian investigator.

    iii. Colin Kaltenbach, Administrative Advisor

    Very positive comments about progress in the Bovine Genome Sequencing Project. NRSP8 was praised for its role.

    iv. No Industry Representative comments.

    v. No discussion.

    b. Equine i. Ernest Bailey, Equine Genome Coordinator: not present

    ii. William Trumble, Administrative Advisor

    Administrative Advisor (William Trumble) spoke in lieu of Ernie Bailey. Next year Jamie MacLeod will be the equine chair, Terje Raudsepp secretary. He praised the equine research community within NRSP8.

    iii. Industry Representatives not present.

    iv. No discussion.

    c. Poultry i. Jerry Dodgson / Hans Cheng, Poultry Genome Co-Coordinators

    Jerry Dodgson: A draft genome sequence is out, described in a Nature paper. Many investigators are now finding the sequence very useful. To rectify some flaws in the sequence, NHGRI has approved funds to finish the chicken genome to the quality of the mouse genome. The second build is due out imminently.

    Efforts are expanding to improve the linkage map and enhance the physical map between turkey and chicken.

    Biggest event: a huge expansion in SNP mapping with tremendous engagement of the poultry industry. Coordinator funds were used to add birds to the group for SNP typing. This is a work in progress which will provide insights into evolution. Animals used represent birds from 75% of commercial populations world wide (Hans Cheng).

    ii. Administrative Advisor not present.

    iii. Industry Representatives not present.

    iv. No discussion.

    d. Swine i. Max Rothschild, Swine Genome Coordinator

    $10M (USDA) granted over the next two years for sequencing the pig genome. Industry money has gone to Sanger with sequencing under way. Larry Schook was thanked for efforts.

    Affymetrix chips have been made available to investigators, still have some to distribute.

    Oligonucleotide microarray efforts continue. Final clustering work is to be done by Christine Elsik, array to be ready for printing/distribution perhaps in May.

    ii. Administrative Advisor Bert Stromberg

    Positive endorsements of sequencing efforts.

    iii. Industry Representatives not present.

    iv. No discussion.

    e. Aquaculture i. Caird Rexroad (organizer) and John Liu (interim coordinator)

    Caird Rexroad: Reported on aquaculture workshop. This year the workshop broke into finfish and shell fish groups in the afternoon. Named next years chair (Dennis Hedgecock) and chair elect (Geoff Waldbieser).

    John Liu: Aquaculture is not a species, covers ~20 species of 200 cultured world wide, ~60 species in USA. Current report lacks shrimp and striped bass, which will be added later.

    Joint Genome Institute sequencing support: 1) Catfish - 300,000 bidirectional ESTs. 2) Tilapia - 0.1x coverage of 5 species of cichlid fishes. 3) Oysters - 300,000 ESTs and 50 BACs

    Tilapia, salmonids and catfish are making good progress, shell fish are lagging behind a bit most likely due to a late start. The Tilapia map has been increased by new markers and a BAC physical map. QTLs for color and sex determination are being mapped and investigators are close to identifying genes responsible. Catfish physical mapping has 6x coverage using BAC fingerprinting. An additional 57,000 BAC end sequences have been done and a microarray is now available.

    ii. No comments from advisor.

    iii. No discussion.

    f. Database i. James Reecy, Database Lead Coordinator

    Significant progress this year. Pig QTL db to be moved into other species. Support of EST clustering in various species to support microarray efforts. NRI now has RFA targeting bioinformatics. This is welcomed.

    Database use logged 2.5 million hits last year. Efforts continue to improve resources from a QTL centric view.

    Next year focus on supporting and facilitating dialog between investigators to develop and use bioinformatics tools.

    2. Administrators Reports a. Colin Kaltenbach, Lead Administrative Advisor

    Flat funding at 99% expected this year. Stressed the importance of getting final report in on time, 60 days from PAG. There is more and more demand for impact statements; these should be included in reports submitted to coordinators/chairs. NRSP8 is held up as the model for such multi-state projects.

    b. Muquarrab Qureshi, Program Leader Very positive about animal genome research and the contribution of NRSP8, in particular for feedback at the federal level. Joe Jens leadership is acknowledged by and appreciated for bringing NRSP8 and CSREES to this point in terms of funding and genome sequencing in chicken, cow and pig.

    Thanks to Ronnie Green for his sterling efforts with the interagency working group.

    To NRSP8, keep up the good work and send in those impact statements.

    c. Peter Burfening, NRI Animal Genomics

    Update for NRI efforts and team. Last year Peter Burfening took over Animal Genome in CSREES. The PART program (program assessment and rating tool) was used to evaluate NRI. Review of the program has stressed accountability as the key. The logic model was used to evaluate and provide new (current) priorities and goals for the program.

    Funding is flat, making it difficult to fund at high levels. ~22% of proposals get funded. A recommendation from National Academy of Sciences to increase award sizes has led to a decrease in funding success rates for investigators. Now awards (when made) are not significantly cut, but fewer awards are made. Over the last 6 years 139 awards were made for $53M. This is more per project than for NRI as a whole. Peter Burfening discussed the breakdown of success rate in funding by species/group as delineated in the report.

    Peter Burfening is very concerned about the low success rate.

    Comments about panel composition: it is very difficult to find ~15 individuals that meet all the diversity requirements for panel composition.

    Peter Burfening discussed the process and mechanics of proposal ranking. 8% ranked outstanding in the last few years. Only 95% of these outstanding proposals were funded indicating how tight the funding situation is. To fund all outstanding and high priority proposals an additional $6.6M would be needed. To fund at a 40% level would entail a doubling of the budget (additional ~$12.6M).

    Taking input from NRSP8 to help prioritize funding, one example is the tools and reagents program which is now split to separate out bioinformatics. As a result of internal deliberations and not in response to species lobbying, this year only proposals from species with 5x genome sequence coverage or better will be considered. This is done to focus the program and narrow down the number of proposals. The due date is June 15; the panel manager has not yet been officially named.

    d. Discussion followed. Question from Noelle Cockett who questioned the effective limitation of species that can apply for funding by using sequencing data as the metric for funding. NC urged a re-visitation of the effective moratorium this imposes. Members of the audience endorsed this.

    Peter Burfening replied to reaffirm that the door is not shut to other species, but that the significant expense on genome sequences is a priority maker.

    Dissent for this view from the audience who questioned the wisdom of this approach.

    Peter Burfening acknowledged this objection and said that one item that is being considered is prioritizing high risk research.

    Max Rothschild commented that the current rule to consider applications only from 5x genome sequence organisms makes haves and have nots. He said that this is a very dangerous road that marginalizes other species.

    Anna Palmisano commented on success rates. She is concerned that many young scientists are not submitting to NRI. But the flat budget is a limiting factor that leads to hard choices. She solicited advice and guidance from the community.

    Jerry Dodgson commented that while disappointing, this (22%) funding is not worse than NIH RO1 success rate. He also endorsed the view that there should not in the future be a restriction on species restrictions as imposed by 5x rule.

    Anna Palmisano said that current success rate this last year is 14% compared to NSF and NIH at ~30%.

    James Reecy commented that the problem is not the success rate but rather the lack of sufficient funding. There were suggestions to lobby congress to change the situation.

    John Liu commented about the ethics of urging students and young researchers to enter a field that has no funding. He thanked CSREES for their responsiveness to the community in the past and endorsed that restrictions for grant applications based on species of >5x genome coverage should not be continued.

    Colin Kaltenbach suggested writing to ones congress person.

    3. Suggestions for future plenary speakers for PAG

    Max Rothschild asked for suggested speakers. Discussion by audience about how speakers are selected and the timing for this activity.

    Frustration was expressed over crowding in the cattle session. Chairs need to make sure that expected attendance is relayed to organizers to make sure adequate sized rooms are provided.

    Scheduling issue: Species groups overlap, making it difficult to cross the species barrier.

    III. New Business 1. Election of Officers for 2006

    Clare Gill to serve as chair next year (Dave Adelson filled in as secretary for meeting due to bereavement in Clare Gills family).

    Nomination for Mary Delany as secretary seconded and approved by acclamation.

    2. Selection of next meeting location and date to be discussed with Mary Delany.

    IV. Adjournment. 5:45 pm

    Accomplishments:
    Progress toward Objective 1: Enhance and integrate genetic and physical maps of agriculturally important animals for cross species comparisons and sequence annotation. Aquaculture Catfish: Progress in mapping the catfish genome has focused on the addition of Type I loci to genetic maps and BAC fingerprinting and end sequencing. A total of 54 genes and 26 BACs have been added to the channel catfish intraspecific genetic map at the USDA/ARS Catfish Genetics Research Unit and 350 Type I loci to the channel catfish x blue catfish interspecific map at Auburn University.

    An NRI Genome Tools and Resource Program was awarded to Auburn University which has resulted in 20,366 BAC end sequences (BES). BLAST analyses has identified homology to 1130 genes revealing 23 regions of conserved synteny among the catfish, zebrafish, and tetraodon genomes. Microsatellites were identified in 17% of these sequences, which will facilitate the integration of the BAC physical map with the genetic maps.

    At the USDA/ARS Catfish Genetics Research Unit 6X genome coverage of the CCBL1 BAC library constructed from a gynogenetic female has been fingerprinted resulting in a preliminary assembly generating 2000 contigs. Progress has also been made in the sequencing of BAC ends with 3X coverage completed to date.

    Oysters: Researchers at the University of Delaware and the University of Southern California are cooperating on the development of a linkage-mapping family for the Pacific oyster (Crassostrea gigas), which will be made available to the oyster community as a resource. The current focus is on mapping Type I loci using SNPs. More than 90% of the primer sets developed for C. gigas amplify in the related oyster species C. ariakensis which is an important cultured species in Asia and is currently being considered for introduction into U.S. waters owing to its resistance to the two major diseases affecting the native eastern oyster. Researchers at Rutgers University have developed 16 SNP and 53 microsatellite markers from eastern oyster (C. virginica) ESTs for use in genetic mapping. They have also constructed a preliminary genetic map for the bay scallop (Argopecten irradians) using primarily AFLP markers.

    Salmonids: This year a collaboration led by Washington State University at Vancouver has integrated the cytogenetic with the Nichols et. al 2003 genetic maps. The USDA/ARS National Center for Cool and Cold Water Aquaculture and the University of Guelph have developed microsatellite markers for ESTs. A BAC physical mapping project was initiated by NCCCWA, West Virgniai University, and UC Davis. Members of NRSP8 participated in two workshops discussing sequencing a salmonid genome. The first Workshop was held in Oslo, Norway during October 24-26, 2005 to discuss sequencing the Atlantic salmon genome, while the second Workshop, a Tri-lateral Workshop (US/Canada/Norway) hosted by the Royal Norwegian Embassy in Washington DC November 2 - 3, 2006 was entitled "Marine Fish Aquaculture: Genomics.

    Striped Bass: Collaboration between researchers at North Carolina State University, Kent SeaTech Corporation, and the USDA National Center for Cool and Coldwater Aquaculture in Kearneysville, WV has resulted in the development of 498 microsatellites markers for use in genome mapping and selective breeding of striped bass (Morone saxatilis). The majority (90%) of these markers were successfully t amplified in the white bass (Morone chrysops), which is important to the industry in the production of the hybrid.

    Tilapia: A second generation genetic linkage map was produced in at University of New Hampshire containing 550 markers (Lee et al., 2005). A physical map has been constructed by BAC fingerprinting resulting in a tilapia physical map with 3,000 contigs (Katagiri et al., 2005).

    Cattle Texas A&M University continues to lead an international effort to build bovine radiation hybrid maps. RH panels are freely distributed to investigators world wide, data can be analyzed with the first generation RH map of the cattle genome (Band et al. 2000) at . A third generation comparative map 3000 containing BAC end sequences has been published (Everts-van der Wind et al, PNAS 102:18526-18531, 2005). The BESs selected for mapping are ~1 Mbp apart on the human chromosomes as determined by BLASTn analysis. The map has 3,484 ordered markers, of which 3,204 are anchored in the human genome. Two hundred-and-one homologous synteny blocks (HSBs) were identified, of which 27 are newly discovered, 79 are extended in length, 26 were formed by newly found breakpoints in 18 previously defined HSBs, and 23 are the result of fusions. The comparative coverage relative to the human genome is ~91 percent, or 97 percent of the theoretical maximum.

    Efforts at TAMU have been directed towards identification, validation and analysis of variation in the 3 Mb of genomic sequence that constitutes the bovine major histocompatibility complex (BoLA). The primary goal of this research was to determine the haplotype structure of BoLA to provide a more efficient platform for analysis of inherent disease resistance in cattle. More than 400 simple sequence repeats in BoLA have been identified from the genomic sequence, 22 of which useful variation in the BoLA IIb region (~400kb). An area of high recombination in the region near the proteosome locus, PSMB9 has been identified.

    Equine During 2005 significant numbers of new markers were added to the half sibling linkage map (766 markers spanning 3740 cM, Penedo et al, 2005), the full sibling linkage map (742 markers spanning 2772 cM, Swinburne et al., 2006, Genomics 87: 1-29) and the RH map for the horse. In addition, significant efforts were made to integrate the existing horse genome maps. Those efforts are summarized in the Horse Map Viewer (http://www.vgl.ucdavis.edu/equine/caballus/).

    Poultry The University of Michigan has been generating avian BAC contig maps and integrating them with the respective linkage maps. Efforts have also recently begun to develop a BAC contig map for the turkey, along with a comparative turkey-chicken map.

    The University of Minnesota has continued to expand turkey genetic mapping by expanding the genetic map to include 438 linked markers representing a 39% increase in marker number and increases marker density to an estimated at 5 cM.

    The USDA-ARS Avian Disease and Oncology Laboratory coordinated the screening of 3072 SNPs on 2580 experimental and commercial birds resulting in new genetic markers and providing a high confirmation rate of the ~3 million in silico chicken SNPs. This generated a much higher density genetic map that has enhanced the second genome sequence assembly, and demonstrated that a high density SNP map can identify tightly linked markers for simple and complex traits.

    North Carolina State University further characterized the MHC B locus at the sequence level in numerous layer lines to provide a reproducible means to determine B haplotypes. The microsatellite marker LEI0258 known to be physically located within the MHC, was sequenced resulting in the identification of 28 distinct haplotypes. This information will be a useful tool to identify new MHC haplotypes in outbred populations of chickens.

    Sheep A joint collaboration has been established between Utah State University, The Institute for Genomic Research (TIGR), Australian Wool Innovation, Meat and Livestock Australia, AgResearch (New Zealand), and Genesis-Faraday (UK), with support of the Alliance for Animal Genome Research, to obtain and characterize end-sequences from the CHORI-243 BAC library. In addition, these sequences will be ordered against the soon-to-be-completed bovine genomic sequence, providing a whole genome physical map for sheep. The sequences will also be incorporated into the emerging ovine RH map. The sequencing portion of the project is complete, with 376,493 BAC-end sequences (BES) from 193,073 BAC clones hazving average insert size of 184 kb. A total of 258,650,691 bp sequence (approximately 6% of the genome) was produced from this project.

    A collaborative project between Utah State University and Texas A&M University has produced an ovine whole-genome radiation hybrid (RH) 5,000-rad panel consisting of 90 clones, with retention frequencies between 15-40%. To date, Utah State University has 257 markers selected from the autosomes have been screened against the panel; 131 (51%) of these markers produce resolvable patterns and will be typed in duplicate across the panel.

    Swine New gene markers continue to be identified and mapped; some integration of the maps continues as QTL maps are expanded. However, no new large-scale maps have been published recently. In total there are over 1,588 genes and 2,493 markers in the database. The physical map is also growing quickly and there are now nearly 6,000 genes and anonymous markers; thanks to a very useful somatic cell hybrid panel from INRA and two radiation hybrid panels (IMpRH7000 from INRA and the U. of Minnesota; IMNpRH12000 from INRA, U. Nevada-Reno and the U. of Minnesota).

    The Swine Genome Sequencing Consortium (SGSC) continued its efforts this past year and considerable advances have been made. Meetings have occurred at PAG and in the UK. The meetings included individuals from a number of countries including the US, France, Britain, Denmark, China, Korea, and Japan. Representatives from the USDA, the Alliance for Animal Genome Research and several of the authors of the Pig Genome Sequencing White paper participated. Funds have been committed by the National Pork Board, Iowa Pork producers Association, University of Illinois and Iowa State University, with other groups likely to follow. USDA committed a total of 10-12 million and the Sanger Institute has also participated and will commit considerable funding. Progress towards Objective 2: Facilitate integration of genomic, transcriptional, proteomic and metabolomic approaches toward better understanding of biological mechanisms underlying economically important traits. Aquaculture Catfish: Researchers at the University of Mississippi Medical Center have completed the sequencing of 6 BACs covering part of the catfish immunoglobulin heavy chain locus. This group has continued characterization and functional studies of catfish immune molecules, such as, T Cell Receptors and their accessory molecules CD4 and CD8, Novel Immune Type Receptors, Leukocyte Immune Type Receptors (LITR), Immunoglobulin D, FcRs and the B cell accessory molecules CD79a and 79b. Monoclonal and polyclonal antibodies specific for various LITRs, IgD, CD79b and IpFcR have been produced and are being characterized.

    At Auburn University much effort was made to characterize innate immune genes and analyze their expression in the resistant blue catfish as compared to the susceptible channel catfish after infection with the bacterial pathogen causing enteric septicemia of catfish (ESC). A total of 26 CC chemokine genes, 6 CXC genes, 4 antimicrobial peptide genes, interleukin-1 beta gene, 23 selenoprotein genes, 6 toll-like receptors, and a few dozens of other genes were completely sequenced, mapped to BACs, and expression analyzed.

    Work at the USDA/ARS Catfish Genetics Research Unit was focused on the development of a 19,000 gene (oligonucleotide) microarray developed (via Nimblegen). The microarray was tested on Lipopolysaccharide-exposed fish and initial results demonstrated good correlation between levels of hybridization to the microarray and real-time PCR expression levels for several candidate genes. Currently tests are being conducted to observe differential expression of these potentially important immune receptors in various catfish families and strains after exposure to pathogens. Also, work characterizing catfish growth hormone and the various steroidogenic factors involved in catfish growth and reproduction continues. A patent was awarded for a real-time PCR assay detecting Edwardsiella ictaluri in channel catfish.

    Oysters: Researchers at the University of Southern California have mapped candidate genes for growth heterosis; more samples for expression profiling and QTL-mapping from F2 populations were obtained in summer 2005. Researchers at Rutgers University have mapped twelve disease/mortality-resistance QTL in two families of the eastern oyster; at least seven of the twelve QTL are independent of each other. These results indicate that resistance to Dermo-infection or summer mortality is affected by at least seven quantitative trait loci.

    Salmonids: The number of ESTs for rainbow trout and Atlantic salmon increased to 239,512 and 186,364, respectively. These sequences represent transcripts from tissues and lifecycle time points not previously included in the database. Microarrays are increasingly being used to study responses to stress and chemical contaminants as well as basic biological processes.

    Shrimp: As a part of the USDA funded project "Shrimp gene discovery: Enlarging the EST collection for the Pacific white shrimp, Litopenaeus vannamei" (NRI Grant #2005-35205-15459), six high quality tissue specific cDNA libraries have been constructed and analyzed for depth and redundancy, with 1000 EST being collected from each library to date. Redundancy depletion and full sequencing of a minimum of 120,000 ESTs (20,000 from each library) is expected to be complete in the coming year. A first generation microarray containing in excess of 3000 unigenes has been printed and initial validation has been completed. These microarrays and are currently in use in the first round of experimental research. It has been discovered that long dsRNA of virus-specific sequence evokes a potent and specific anti-viral immune response. Continuing research in the area of antimicrobial peptides and their importance in shrimp immunity has yielded data on the structure of the Penaeidin gene family, its control elements, and specificity for microbial targets.

    Striped Bass: Several collaborations were established with industry members Keo Fish Farms and Kent SeaTech Corporation to extend ongoing selective breeding efforts conducted at the North Carolina State University Pamlico Aquaculture Field Laboratory. These selective breeding studies have led to the identification of broodstock showing superior growth characteristics in both extensive pond-based and intensive production systems.

    Tilapia: Researchers at the University of New Hampshire have mapped the tilapia gene for red skin color leading to positional cloning of tilapia mutation to a single BAC containing 2 genes. Great progress was also made in mapping and characterization of the sex determining mechanism in several species of tilapia.

    Cattle Dwarfism has been a problem with American Angus cattle for decades. Dwarves are inefficient in beef production systems and are undesirable for Angus breeders. Researchers at Iowa State university have fine mapped the dwarfism locus to bovine chromosome 6 (BTA 6). On further analysis of candidate genes in the region, they have discovered a mutation in bovine PRKG2 gene that introduces a premature stop codon to the open reading frame. The mutation is in 100% concordance with dwarf, carrier and wild-type status. The detection of causal mutation or closely linked markers for dwarfism is of great use to Angus producers as this gives them the ability to detect carriers in breeding populations and the potential to eliminate dwarfism from their herds.

    Researchers at New Mexico State University have identified polymorphisms within the growth hormone gene that seem to be a significant source of variation in average daily gain and carcass traits in Bos Taurus or Bos TaurusX Bos indicus composit cattle. They have identified that polymorphisms in the genes of the GH axis or its transcriptional regulators differ among Angus, Brangus or Brahman cattle.

    A QTL on chromosome 6 affecting milk fat and protein concentration was previously localized to a 4-cM confidence interval, centered on the microsatellite BM143. In collaboration with ARO, the University of Illinois has characterized the genes and sequence variation in this region and identified common haplotypes spanning five polymorphic sites in the genes IBSP, SPP1, PKD2, and ABCG2 for two sires heterozygous for this QTL (Cohen-Zinder et al., 2005). Expression of SPP1 and ABCG2 in the bovine mammary gland increased from parturition through lactation. SPP1 and all the coding exons of ABCG2 and PKD2 were sequenced for these two sires.

    Equine ESTs were identified by laboratories at Cornell University, University of Kentucky and Texas A&M University and the data pooled with the objective of creating a microarray tools for investigating gene expression in horse tissues. Over 45,000 ESTs were evaluated and approximately 10,000 unique genes were identified for incorporation into a microarray chip.

    Poultry The USDA-ARS Avian Disease and Oncology Laboratory continues to work on genetic resistance to Mareks disease (MD). Reassessment of the ADOL 6 x 7 F2 MD resource population confirmed at least 5 of the 15 previously identified QTL, has revealed 2 new QTL, and identified 2-way epistatic interactions that shared a QTL on chr1. Efforts are underway to identify optimal MD virus challenge conditions to characterize the lines. Polymorphisms in avian leucosis virus (ALV) receptor genes tva and tvb that confer genetic resistance were confirmed, and Pyrosequencing assays developed.

    Iowa State University and Hy-Line International have cooperated to conduct candidate gene and genome scan analyses in an advanced (F6) intercross between two partially inbred commercial Leghorn lines that differed in resistance to Marek's disease to detect QTL for survival following challenge with highly virulent Marek's disease virus. A total of 11 putative QTL were identified including a polymorphism in the Rh-associated glycoprotein gene which was found to be associated with survival.

    The University of Delaware has further mapped the chromosome 1 QTL that affected oocyst shedding during coccidiosis infection of broiler chickens. An interesting candidate gene is lymphocyte activation gene 3 (LAG-3; CD223) which was simultaneously identified in DNA microarray studies to be reduced in expression after Eimeria infection of chickens. The lympocyte-specific expression of LAG-3 has been confirmed by RT-PCR and demonstrated a rapid down-regulation of LAG-3 with coccidial infection.

    The University of Arkansas has characterized the vasotocin II receptor (VT2R) that was recently cloned and sequenced in the chicken using immunocytochemistry (ICC) and was found predominantly in the cephalic region of the anterior pituitary, associated with cell membranes of specific pituitary cells. Research at the University of Arkansas has also been aimed at identifying the underlying genetic and physiological causes of sperm degeneration to better understand the origins of the defect and develop genetic tests that can be used to increase male fertility.

    Work to define the identity and function of genes within the major histocompatibility complex (MHC) in the chicken continues at the City of Hope Medical Center with progress made on three fronts. First, CD1 genes (one active and one likely a pseudogene), encoding MHCI molecules that present lipid-type antigens to T cells, were mapped to the MHC region. Second, Y MHCI molecules were shown to be alloimmunogenic and well-expressed on blood cells providing data supporting the likelihood for a role of Y MHCI in immunity. Lastly, BG1 has been identified as a candidate gene influencing the incidence of Mareks disease in chickens.

    In mammals, natural killer (NK) cell C-type lectin receptors are encoded in a gene cluster called nature killer receptor gene complex (NKC). At Texas A & M University two chicken C-type lectin-like receptors were identified in a region on Chromosome 1 that is syntenic to the mammalian NKC region. The region containing NK C-type lectin like receptors in GGA 1 has been previously identified to be associated with disease resistance in chickens.

    The University of Maryland has performed transcriptional profiling screens using their cDNA microarrays to identify genes that respond directly to glucocorticoids in cultures of anterior pituitary cells. Six candidate genes for mediating the effects of glucocorticoids on expression in the anterior pituitary were identified. Gene expression profiles in the anterior pituitary and hypothalamus were also compared between lines of chickens genetically selected to have high or low abdominal fat identifying the same six candidate genes. The 5'-flanking region of these candidate genes are currently being sequenced in a Fat X Lean reference population in an attempt to identify genetic markers associated with differences in body fat.

    Virginia Tech has been studying the transport of nutrients (amino acids, peptides and sugars) across the intestinal epithelia, which is mediated by membrane bound transporter proteins. The abundance of mRNA for these transporters was determined by real time PCR and was found to vary depending upon the intestinal segment and the time of development (embryonic day 20 to 7 days post hatch). This work has shown that nutrient transporters are differentially expressed in a temporal and spatial manner.

    The efficient production of germ line chimeras using PGC transfer into early embryos has been hampered by the limited availability of PGCs obtained from blood and the early germinal ridge. North Carolina State University has produced germ line chimeras by using sorted gonadal germ cells when injected into stage X, germinal crescent and stage 17. This observation taken together with the scientific literature indicates that germline chimeras can be made using any source of PGCs up to stage 27-28 as the donor cells and any stage of embryo development up to stage 17 can be used as a recipient.

    Iowa State University maintains many unique chicken lines (highly inbred; MHC- congenic; closed populations; advanced intercross lines) for research. These lines serve as valuable resources for identifying genes of economic importance. Semen from all of the highly inbred and partially inbred lines was collected at ISU, and the staff of the National Animal Germplasm program cryopreserved the samples on site and then transported them to Ft. Collins for long-term storage.

    The feasibility of detection and mapping QTL in breeding populations with a high-density marker map using population-wide linkage disequilibrium was investigated by simulation at Iowa State University. Designs that allow adequate power and mapping precision were developed. Designs and statistical models for global gene expression analysis using micro-arrays based on pools of mRNA samples from multiple individuals were also investigated. For a given total number of individuals and arrays, simulated pooling resulted in loss of power compared to arraying all samples individually but under some conditions, loss of power was small and it was possible to find a low-cost pooling design with power close to that of an individual design.

    North Carolina State University has continued to develop new microsatellite markers mining the genome sequence data for use in fine-mapping QTL regions. This data indicates that there is at least one usable microsatellite marker every 40,000 bp and at least one polymorphic microsatellite marker every 115,000 bp in commercial chicken populations.

    Sheep A collaboration including Utah State University, Purdue University, USDA/ARS, and the University of Liége has identified a core cluster of imprinted genes (DLK1, GTL2, PEG11, and MEG8) located at the distal end of ovine chromosome 18. Using quantitative PCR, they have shown that the inheritance of the callipyge (CLPG) SNP in cis alters the expression of genes with a paternal allele-specific expression (DLK1 and PEG11) and maternal allele-specific expression (GTL2 and MEG8) in muscles that undergo hypertrophy in a genotype and age specific manner. Also, the effects of age and genotype are also significant for expression of the CLPG1 RNA that is transcribed from the intergenic region between DLK1 and GTL2 and spans the CLPG SNP.

    Gastrointestinal parasites have a profound effect on sheep production. In a collaborative study between Utah State University and Louisiana State University, a genome-wide QTL scan was implemented to identify chromosomal regions in the ovine genome that play a role in resistance to gastrointestinal parasites. Suggestive QTLs have been identified on ovine chromosomes 1, 6, 9 and 19.

    A large-scale EST sequencing project for goats has been implemented at Virginia State University. To date, sequences have been obtained from about 10,000 clones from a cDNA library constructed from goat uterine/embryonic tissues collected between days 5 and 8 pregnancy.

    Swine QTL have continued to be reported on all chromosomes for many traits, often identifying imprinted QTL. Candidate gene analyses have proved successful with several gene tests being used in the industry for many traits including, fat, feed intake, growth, meat quality, litter size and coat color.

    Progress towards Objective 3: Facilitate and implement bioinformatic tools to extract, analyze, store and disseminate information. Researchers at universities and other research institutions are conducting multifaceted research to develop bioinformatics programs and database resources for livestock species and this research is supported in part by the NAGRP. Continued efforts to inform scientists and lay persons about genome databases have been made and many new entries are now available at www.animalgenome.org. The NAGRP genome databases were accessed over 2.2 million times by over 140,000 users world-wide.

    A bioinformatics program (Expeditor) was developed to design primers for livestock species. This program takes advantage of the information from the human genome and applies it to livestock cDNA. This program can be used at http://www.animalgenome.org/~hu/expeditor.

    With the rapid progress in genetics and genomes, there are an increasing number of genetic analysis software programs. Each program has its own pre-defined scope, assumptions, and applicability. With the large number of available programs, it can be a challenge to identify suitable options. Thus, we have created a database and related tools to effectively archive, annotate, and manage the wealth of the software information so that researchers can easily identify, locate, and retrieve appropriate software. We have also introduced ontology concepts and tools to manage the proper classification and feature annotation of this resource. To date, there are 331 software programs listed in the category of genetic analysis. We plan to add other genomics and computational biology software in the near future.

    As in past years the Pig Genome Database has received considerable updating. There are over 1,254 citations in the database describing 4081 loci, over 602 clone entries and 96 library entries. This last year the US Pig Genome database had over 149,600 users making more than 3 million hits. New QTL continue to be curated into the Pig QTL Database. Up to date there are 1,263 QTLs in the database representing 236 pig traits. In addition, new functions have been added to the PigQTLdb tools to align pig RH map-human comparative maps, and pig BAC physical maps, against pig QTL. It can be seen at http://www.animalgenome.org/QTLdb/. Database activities were transferred to the Bioinformatics Coordinator.

    The NAGRP database has a newly developed Porcine QTL database that graphically displays QTL from over 70 experiments and can be used at http://www.animalgenome.org/QTLdb/. All information has been cross-listed at NCBI and can be viewed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&term=pig+QTL. Over the past year, links have been added to the viewer allowing researchers to visualize QTL on the human genome.

    Texas A&M has worked to cluster and annotate porcine and bovine EST clusters. This work supports the development of a new long-oligo arrays in collaboration with the Swine Genome Coordinator and the Bovine Oligo Microarray Consortium.

    The marine genomics group at the Holling Marine Laboratory and MUSC maintains www.marinegenomics.org for the archiving of shrimp EST and microarray data, and as a resource for on-line tools that can be used in the analysis of genomic and transcriptomic data, which are being used to archive and analyze shrimp metagenomic and microarray data. In addition, in collaboration with IFREMER at the Universite de Montpellier, a standardized nomenclature database for Penaeidin anitmicrobial peptide has been developed.

    Tools for comparative mapping are available from the University of New Hampshire (www.hcgs.unh.edu/comp). They include - comparative maps among cichlids, comparative maps among fishes, mapping of cichlid ESTs onto genome sequences of Tetraodon and Fugu.

    Personnel at the University of California-Davis are developing a cattle genome database and browser compiling QTL and sequence information as a tool for comparative mapping and gene discovery. Currently the database contains 580 QTL entries from 109 traits and 295 molecular markers (69% mapped to human. The database is in MySQL with a Common Gateway Interfaces (CGI) front end.

    Sequences from the ovine BAC end sequencing project are now publicly available at http://www.ncbi.nlm.nih.gov/genome/guide/sheep/index.html. Matches of the ovine BAC-end sequences to the bovine and human sequences and identity of clones can be obtained through a database established by CSIRO (Australia) at http://www.livestockgenomics.csiro.au/SheepGenomics/.

    The Bovine QTL viewer (http://bovineqtl.tamu.edu/) developed by researchers at Texas A&M University has been updated and linked to the 6.2x build of the bovine genome to show existing SNPs and gene models.

    Impact Statements:
    1. The USDA-ARS Avian Disease and Oncology Laboratory coordinated the screening of 3072 SNPs on 2580 experimental and commercial birds resulting in new genetic markers. This generated a much higher density genetic map that has enhanced the second genome sequence assembly, and demonstrated that a high density SNP map can identify tightly linked markers for simple and complex traits.
    2. It has been discovered that long dsRNA of virus-specific sequence evokes a potent and specific anti-viral immune response. Continuing research in the area of antimicrobial peptides and their importance in shrimp immunity has yielded data on the structure of the Penaeidin gene family, its control elements, and specificity for microbial targets.
    3. Collaborations with industry members Keo Fish Farms and Kent SeaTech Corporation to extend ongoing selective breeding efforts conducted at the North Carolina State University Pamlico Aquaculture Field Laboratory have led to the identification of broodstock showing superior growth characteristics in both extensive pond-based and intensive production systems.
    4. Dwarves are inefficient in beef production systems and are undesirable for Angus breeders. Researchers at Iowa State university have fine mapped the dwarfism locus to bovine chromosome 6 (BTA 6) revealing a mutation in the PRKG2 gene. The detection of causal mutation or closely linked markers for dwarfism is of great use to Angus producers as this gives them the ability to detect carriers in breeding populations and the potential to eliminate dwarfism from their herds.
    5. Iowa State University and Aviagen studied 12 immune-related genes for associations with general mortality and other performance traits in three elite commercial broiler chicken lines raised in high and low hygiene environments. Ten of the 12 immune-related genes had associations with at least one trait; most detected effects were on mortality and growth. These results indicate that variation in candidate genes associated with important broiler traits can be identified in multiple environments.
    6. Iowa State University maintains many unique chicken lines (highly inbred; MHC- congenic; closed populations; advanced intercross lines) for research. These lines serve as valuable resources for identifying genes of economic importance. Semen from all of the highly inbred and partially inbred lines was collected at ISU and cryopreserved by the staff of the National Animal Germplasm program in Ft. Collins, CO.
    7. Gastrointestinal parasites have a profound effect on sheep production. In a collaborative study between Utah State University and Louisiana State University, a genome scan was implemented to identify chromosomal regions in the ovine genome that play a role in resistance to gastrointestinal parasites. Suggestive QTLs have been identified on ovine chromosomes 1, 6, 9 and 19.
    8. A bioinformatics program, Expeditor, was developed to design primers for livestock species. This program takes advantage of the information from the human genome and applies it to livestock cDNA. This program can be used at http://www.animalgenome.org/~hu/expeditor
    9. Virginia Tech has been studying the transport of nutrients (amino acids, peptides and sugars) across the intestinal epithelia, which is mediated by membrane bound transporter proteins. The levels of mRNA for these transporters was determined by real time PCR and was found to vary depending upon the intestinal segment and the time of development (embryonic day 20 to 7 days post hatch). This work has shown that nutrient transporters are differentially expressed in a temporal and spatial manner.
    10. Researchers at Rutgers University mapped twelve disease/mortality-resistance QTL in two families of the eastern oyster; at least seven of the twelve QTL are independent of each other. These results indicate that resistance to Dermo-infection or summer mortality is affected by at least seven quantitative trait loci.
    11. UC Davis is utilizing mouse congenic strains to understand the biological mechanisms underlying growth traits in animals. A unique mouse model has been characterized that produces a 30-50% increase in post-weaning growth rate and mature body size, as well as a substantial increase in feed conversion efficiency during growth. Understanding the processes controlling growth in this model organism will aid in identifying genes for investigation in livestock species.
    12. UC Davis has developed ArrayGene, a software package that allows researchers to create custom databases on genes from sequenced organisms. This tool can be implemented for any sequenced organism, and it can be very valuable in choosing microarray platforms for fine mapping and genomic dissection of chromosomes.
    13. Researchers at New Mexico State University have identified polymorphisms within the growth hormone gene that seem to be a significant source of variation in average daily gain and carcass traits in Bos Taurus or Bos TaurusX Bos indicus composit cattle. They have identified that polymorphisms in the genes of the GH axis or its transcriptional regulators differ among Angus, Brangus or Brahman cattle.
    Last Modified: unknown

    Date of Annual Report: 08/13/2007

    Report Information:
  • Annual Meeting Dates: 01/13/07 to 01/14/07
  • Period the Report Covers: 10/2005 to 10/2006

    • Participants:
    Brief Summary of Minutes of Annual Meeting:
    Brief Summary of the Minutes of Annual Meeting:

    Chair: Clare Gill (TAMU) Secretary: Mary Delany (UCD) Notes for renewal objectives: Cathy Ernst (MSU)

    Clare Gill revised the business meeting agenda by suspending the species reports due to the need for membership discussion on the renewal proposal. The new proposal must be written during 2007. Consensus on an overall theme and objectives became the goal for the business meeting.

    Colin Kaltenbach (NRSP-8 Lead Adm. Advisor, Univ. AZ) described the target deadline for the proposal as early December 2007 reiterating the need for the theme, draft of objectives, and identification of the writing team to be established at the present meeting. Timelines and organizational scheme will be decided by the writing team. Colin reported that NRSP-8 is considered a model project with strong support. Colin informed the attendees that a renewal discussion was held earlier in the day during a morning meeting involving all the species coordinators. Additional comments: the 2006 final report is due within 60 days. Eric Young (Southern Association of Agricultural Experiment Station Directors) was introduced as the new Southern administrator and advisor for the poultry group.

    Chair Gill called for a motion to approve last years meeting minutes. Max Rothschild made the motion which was seconded by Jim Reecy and approved by members. Martina Newell-McGloughlins 6 pm PAG-opening session presentation was announced. Discussion returned to the project renewal.

    RENEWAL DISCUSSION: The three objectives of the current project were read and projected on a screen for membership review. Commentary was offered that some species had sequences in hand which was not predicted at the last re-write and that others are moving toward the sequenced-genome goal  thus species are at different stages although having many in-common needs and goals still (e.g., even the sequenced genomes need more sequencing). Chair Gill called for ideas for an overall theme, emphasizing that this is a research support project and that the species coordinator discussion at the morning meeting focused on the view that we are in a position for the development of tools and analysis in a post genome era.

    Ernie Bailey remarked on the old Objective 1, noting it never included any hint of genome sequencing. He suggested that all agriculturally important species should have a sequence draft and that Objective 1 remains an important goal for species that do not have a sequence.

    Jerry Dodgson suggested that we shouldnt necessarily worry about who has and who doesnt have a sequence because those species that now possess sequence information will continue to need/require refinement of that sequence and further that one sequence isnt enough as researchers need a diversity of sequences from different populations.

    Joan Lunney remarked that the swine sequence is at 4x coverage but the Swine group discussed a clear need for 8x and as well as need for annotation. So the Swine group needs both more of the same along with new and different tools.

    Max Rothschild articulated three renewal objectives related to more sequence information and tool development for discovery, collection of new phenotypes for future discovery, and bioinformatics. Max provided these in written form to Cathy Ernst for screen-projection for the membership to review and discuss. The objectives formulated by Max were as follows (Delany removed the numbers as these were rearranged in the ensuing discussion):

    New: Develop and share reagents, sequence information and genetic discovery tools to facilitate discovery of underlying genetic mechanisms affecting traits of interest. New: Facilitate better understanding of biological mechanisms underlying important economic traits by measuring more complex phenotypes, and collecting and developing populations of new and interesting phenotypes. New: Continue to facilitate and implement bioinformatics tools to extract, analyze, store and disseminate information.

    Max elaborated on the need to have SNP chips, arrays, and essentially any variety of tools to assist in discovery; also, in the past coordinators used the money available in partnership with matches and other options to create and distribute tools to the community  Max noted one cant even predict what these tools should or will be for the next half decade so that need must be written with a broad view. Within the discussion flexibility became a clear concept to emphasize.

    Chair Gill asked for additional comments.

    Bill Trumball suggested that more of an emphasis on comparative genomics be included.

    Jim Reecy commented that perhaps comparative genomics should actually be the theme.

    Chair Gill commented that in the cattle/sheep group, participants expressed at their meeting that there is a need for ways to characterize and define phenotypes as well as physically collect phenotypes.

    Noelle Cockett remarked that the emphasis in the objectives should be on animals rather than families as in developing animals or developing populations. From the discussion collections reflecting diverse phenotypes and genetic diversity are key concepts to emphasize.

    Chair Gill remarked that we cant do without bioinformatics and there was great validity in keeping support in the project for such program development.

    Colin Kaltenbach suggested that the word smithing for the third objective needed to reflect the progress made to date and be worded to indicate such that and what advanced are still needed.

    Jerry Dodgson suggested that leading off with new Obj 2 (making it Obj. 1) might be better, i.e., that the writing team needs to consider the order of the objectives.

    Ernie Bailey suggested that the new Obj 1 is about application and that applying our information should have emphasis.

    Joan Lunney remarked on the new Obj 1, suggesting some other emphasis and words.

    Max Rothschild asked that we come to agreement on the objectives as to what the communities need and get these affirmed/established and that the writing team can then further develop.

    Ernie Bailey felt it important that specific phrases and thoughts really needed inclusion: sequence variation/genetic variation emphasis is needed, that the concept of variation is important to include in the renewal.

    John Liu emphasized the importance to continue to acquire sequence information.

    Kent Reed emphasized the importance for integrated bioinformatics to be applied across species to address needs.

    Chair Gill suggested that in the renewal preamble there would be a section dealing with needs held in common across species. She asked for objective alternatives, further discussion and whether species coordinators foresaw any issues or problems for their groups. No comment was offered.

    Ernie Bailey made that we motion that we move to adopt the new Objectives in principle. This was seconded by Sue Lamont, and the motion was passed by the ayes.

    The writing committee was established to work on the theme/three objectives and document writing. A timeline will be established shortly. The committee: Chair - Mary Delany (UC Davis), plus each species coordinator will be involved (Jim Reecy agreed at the outset!) and including Jerry Dodgson (poultry, MSU), Max Rothschild (swine, ISU), Jim Reecy (bioinformatics, ISU), John Liu (aquaculture, Auburn Univ), Ernie Bailey (equine, UKY), Noelle Cockett (sheep/goats, Utah State). One additional person per species-group may be designated to assist. Muquarrab Qureshi suggested Doug Antczak (equine, Cornell University) be involved. A timeline will be established by the NRSP-8 chair and administrative advisors; e-mail will be the primary mode of communication with occasional conference calls.

    ADDITIONAL BUSINESS: Muquarrab Qureshi suggested the group consider novel options and format for how future NRSP-8 meetings might be organized to be inclusive of all groups at the same time. Max Rothschild emphasized logistical issues were critical in terms of dealing with PAG and that the current design allowed for attendees to bounce around yet kept an important species focus and opinioned we should keep the format the same. Max proposed the group focus on an alternate idea  that we need better and more suggestions for the animal plenary session speakers. There is always a struggle to get novel and great speakers. Chair Gill mentioned that the suggestions are needed directly after the meeting for next year. Max further explained how quickly the decisions are made; by March 1 a short list is in hand. No other comments were indicated and so NRSP-8 will stay the course with its current species workshops.

    Officers were elected for the next year; Joan Lunney (USDA-ARS, swine) was nominated and approved by vote for the secretary position. Mary Delany moves from the secretary to the chair slot. The meeting will be held January in conjunction with PAG XVI (San Diego, CA).

    Max Rothschild remarked that the 2008 species work shop schedules need to conclude on Sunday by 4:15 pm to allow for the NRSP-8 business meeting to begin by 4:30. PAG organizers and species workshop chairs will need reminder of this.

    Muquarrab Qureshi suggested that Peter Burfening provide an update on the USDA efforts toward development of an animal genomics road map. Peter described the charge from USDA administrators in spring of 2006 for the development of a roadmap to outline the future of USDA agricultural animal genomics efforts. A task force was developed for this blueprint purpose with the following composition: Chair Ronnie Green (ARS) and co-chair Muquarrab Qureshi (CSREES), Peter Burfening (NRICGP), Deb Hamernik (CSREES), Mark Mirando (NRICGP), Jim Womack (Texas A&M), Noelle Cockett (Utah State Univ.), Hans Cheng (ARS), Daniel Pomp (UNC-Chapel Hill), Curt Van Tassel (ARS), Gary Rohrer (ARS), ex officio Steve Kappes (ARS) and Anna Palmisano (NRICGP). One objective is to focus and bring USDA operations closer together. The 35 page draft document remains in discussion internally (USDA). The plan is to seek public comment from the research community via NRSP 8 on the revised draft document during the winter months, revise accordingly and proceed to gain USDA administrative approval of the document as a plan for implementation. Max Rothschild suggested that the draft document be established on a website, with an announcement note to the ANGENMAP listserv to gain input as well as to NRSP-8 members.

    A call for further business was made.

    No new business was suggested by attendees and the meeting was adjourned at 5:10 pm with a reminder by Chair Gill to attend the PAG XV opening plenary session at 6 pm.

    Accomplishments:
    Progress toward Objective 1:

    Aquaculture Catfish: Framework genetic linkage maps for channel catfish intraspecific resource families (Waldbieser et al., 2001), and channel catfish x blue catfish interspecific families (Liu et al., 2003) were reported. Several hundred more microsatellites were added in the past year to the linkage maps, especially gene-associated type I markers. A gene-based linkage map has been constructed. Physical maps of the catfish genome have been constructed by fingerprinting the CHORI 212 (5.6X genome coverage) and CCBL1 (7X genome coverage) BAC libraries. A large number of BAC end sequences have been generated and over 20,000 have been deposited in GenBank from Auburn University. BAC-associated microsatellites have been identified for the integration of linkage and physical maps.

    Salmonids: Linkage mapping efforts are ongoing for several salmonids species. The cGRASP Project in Canada has mapped hundreds more microsatellites, especially those from BAC ends, to the linkage map of Atlantic salmon. Over 228,000 BAC clones have been fingerprinted from the Atlantic salmon BAC library, and 4338 contigs have been assembled. Efforts to obtain genome sequences for rainbow trout and Atlantic salmon continued.

    Tilapia: A BAC-based physical map and 2nd generation genetic map were published Kochers group. Genoscope will sequence 35,000 BAC clones in early 2007. The proposal to sequence the tilapia genome was approved by the NIH, with sequencing to begin in late 2007. A draft assembly of the tilapia genome, together with 2x sequencing from each of three closely related haplochromine cichlid fish will be produced.

    Oysters: Gaffneys lab at the University of Delaware is completing a project on SNP marker development and mapping in the Pacific oyster. A total of 53 loci have been amplified and sequenced in multiple individuals representing the geographic range of the species, as well as two parents from a mapping family provided by the Hedgecock lab. A BAC-based physical map of the C. gigas genome will be constructed by BAC fingerprinting. For the eastern oyster, Guos lab at Rutgers developed 53 SSR and 44 SNP markers from putative host-defense gene and ESTs. These are now being scored in two mapping families for placement on the AFLP scaffold linkage map.

    Shrimps: A genetic linkage map of the Pacific white shrimp was constructed, and more markers were added to the existing genetic linkage map of the tiger shrimp.

    Striped Bass: In a collaboration between North Carolina State University and the USDA National Center for Cool and Coldwater Aquaculture polymorphic microsatellite markers are being developed for use in large-scale breeding experiments and for future development of the first linkage map in this species. Over 500 microsatellite markers in striped bass have now been deposited in GenBank.

    Cattle At the University of Illinois, the Evolution Highway tool (http://evolutionhighway.ncsa.uiuc.edu) was modified to perform automated identification of regions of synteny in vertebrate genomes, including mammals and birds. This analysis demonstrated the presence of reuse breakpoint regions in amniote genomes. The significant number of large syntenic blocks shared among amniotes and the non-random assortment of genes within vertebrate chromosomes support a model of non-random breakage of vertebrate chromosomes in the course of 300-430 million years of evolution. As part of collaborative work on the bovine genome sequencing project, the third generation ILTX cattle RH map developed in the Lewin laboratory (Everts van der Wind et al., PNAS 102:18526, 2005), was contributed to USDA-MARC for integration with other mapping information. The process of integrating map information is ongoing. They have integrated the ILTX RH map with the BAC fingerprint map produced in Vancouver and found ~94% agreement between them. At Texas A&M University, the Womack laboratory is targeting specific genes and gene families as candidates for conveying differential resistance/susceptibility to infectious diseases. In addition to mapping the bovine toll-like receptor, cathelicidin, and defensin genes in the radiation hybrid panel, they have initiated searches for SNPs and Indels using a panel of common cattle breeds of both taurus and indicus origin. They are collaborating with Dr. Elisabete Amaral and Brazilian agencies in the development of a RH panel for river buffalo. Cattle markers are being used to populate the map. The Skow laboratory at Texas A&M University is focused on the identification, validation and analysis of variation in the 3 Mb of genomic sequence that constitutes the bovine major histocompatibility complex (BoLA). They have used the bovine RH12,000 panel to conduct high density mapping of STS in the BoLA region. Single nucleotide polymorphisms (SNPs) from the bovine HapMap project have been integrated into STR haplotypes to provide robust marker sets for haplotype determinations. The Gill laboratory is working to map genes associated with production efficiency and nutrient utilization. They are continuing to develop an F2 Nellore-Angus resource population the McGregor Experiment Station. Due to the long term nature of collection of female productivity traits, they are currently focusing their attention on analysis of phenotypes collected on the steer progeny. The Medrano laboratory (University of California, Davis) in collaboration with the Thomas laboratory (New Mexico State University) are investigating QTL related to carcass traits, growth, reproduction, and milk composition that have been identified on BTA5. It is likely that genes within the GH-IGF endocrine axis have important regulatory roles affecting these traits. From the GH pathway pathway, they selected the genes IGF1, IGFBP6, PMCH and STAT2 that map to BTA5 as primary candidates for SNP discovery.

    Equine The status of the equine genome assembly resulting from the sequencing initiative was reported as: 6.8x coverage, ~2.7 Gb genome size, N50 contig size of 116kb, N50 supercontig size of 29Mb with 80% of the sequence anchored to chromosomes. The assembly was made independently of existing linkage and RH maps. Subsequent comparison between the assembly and the maps showed good agreement. The final assembly will be available within 3 months that has a few more BAC end reads and more genome anchoring. Genome anchoring will be based on FISH mapping of contigs by Teri Lear or based on previously unreported FISH mapping assignments of genes by Bhanu Chowdhary and Terje Raudsepp. A set of 1.5 million SNPs were identified and soon will be released publicly; scientific programs are underway to assess optimum gene mapping methods for the horse using this tool. Investigation of gene expression (involving oligo arrays) and association studies (involving SNP arrays) are being considered. With respect to the oligo array, EST information would be very useful and the Broad Institute could investigate ESTs from 8-16 tissues. With respect to the SNP array, preliminary studies on linkage disequilibrium among horse breeds suggested that association studies would require an array with 150,000 SNP elements.

    Poultry The genetic linkage map of the chicken has provided a framework for numerous QTL and other mapping experiments and a platform on which genome sequences have been assembled and linked to chromosomes. In connection with the genome sequence, the Beijing Genomics Institute randomly sequenced 0.25X, each, of a broiler, layer and Silkie genome, generating 2.8 million potential SNPs for high resolution linkage mapping experiments (International Chicken Polymorphism Map Consortium, Nature 432:717-722, 2004). In work supported by a consortium of industry, NRI Tools & Reagent grant, ARS and NRSP-8 funding, Illumina Corp was contracted to obtain ~3000 SNP genotypes, each, from ~5300 birds (about half the birds and data will be in the public domain). About 88% (2733) of the SNP assays worked and almost all of the submitted DNAs were successfully typed. Since members of the East Lansing and Wageningen reference linkage families were included among the panel, these data greatly enhanced the chicken linkage map, more than doubling the number of markers, and were critical in the second build of the genome sequence. A parallel effort by EU scientists genotyped approximately 13,000 SNPs in a variety of birds, including a Red Junglefowl (RJF) x White Leghorn F2 cross, similar to the East Lansing reference backcross. During the past year, coordination funds contributed to another Illumina Corp. SNP typing consortium initiated by NRSP-8 members. This project could only have occurred with the re-use of the SNP genotyping reagents developed by the first Illumina consortium. Together, the rapid expansion of SNP data will provide a high density linkage map and should aid numerous on-going attempts to identify the causative genetic changes involved in many chicken QTL (see http://www.animalgenome.org/QTLdb/chicken.html.)

    Sheep A collaborative project between Utah State University and Texas A&M University has produced an ovine whole-genome radiation hybrid 5,000-rad panel (USUoRH5000) consisting of 88 clones. Over 1500 loci have been typed across the panel, including microsatellites from the ovine and bovine linkage maps, genes and ESTs mapped in cattle and humans, and BAC end-sequences from the sheep virtual genome. High-density RH maps have also been developed for OAR1, OAR2, OAR3, OAR8, OAR9, OAR20, and OAR23. While the first generation whole genome RH map for sheep now exists, a whole genome high density RH map will be completed in 2007. Two ovine BAC libraries are now available. The Texas A&M library was used to identify about 100 genes mapped by FISH and RH methods in Dr. Tom Goldhammers laboratory (Research Institute for Biology of Farm Animals, Dummerstorf, Germany). Another 66 BACs from the Texas A&M library that have been previously mapped by FISH will also be integrated into the RH map. Through a collaboration of Utah State University and other members of the International Sheep Genome Consortium (ISGC), BAC-end sequences (BES) were obtained from the CHORI-243 library and a total of 258,650,691 bp sequence submitted to NCBI (http://www.ncbi.nlm.nih.gov/genome/guide/sheep/index.html). The BES have been used to create a whole genome BAC physical map of the CHORI-243 library and development of a virtual sheep genome (http://www.livestockgenomics.csiro.au/vsheep/). Another project being conducted by the ISGC, with contributions from Utah State University and Louisiana State University, is using a resequencing approach to identify SNPs in the sheep BAC end sequences and EST sequences contributed by AgResearch, New Zealand. The longer term goal of this project is to construct a 20K sheep SNP chip by late 2007. The SNP chip will also be used to produce a sheep haplotype map in 2007/2008 using a strategy similar to the bovine HapMap project.

    Swine New gene markers continue to be identified and mapped and some integration of the maps continues to have taken place as QTL maps are expanded. QTL have continued to be reported on all chromosomes for many traits. QTL studies continue to find imprinted QTL. Candidate gene analyses have proved successful with several gene tests being used in the industry for many traits including, fat, feed intake, growth, meat quality, litter size and coat color. The PigQTLdb is an excellent repository for all of these results. The Swine Genome Sequencing Consortium (SGSC) continued its efforts this past year and considerable advances have been made. USDA held a competitive grant program for $10 million and the grant was awarded to a team of international team led by the University of Illinois and the Sanger Center, UK and which included the Pig Genome Coordinator. Additional funding from a number of countries has helped to make this a real international effort.

    Progress toward Objective 2:

    Aquaculture Catfish: The Joint Genome Institute is sequencing 300,000 EST clones from catfish, of which 200,000 will be sequenced from channel catfish and 100,000 will be sequenced from blue catfish. Work in Lius lab was focused on the development of genome resources including 23 cDNA libraries from various tissues, and construction of four normalized cDNA libraries to support the JGI catfish EST project. Much effort was made to characterize innate immune genes and analyze their expression in resistant blue catfish as compared to expression in susceptible channel catfish after infection with the most serious bacterial disease enteric septicemia of catfish (ESC). A 28K gene array was constructed with the Nimblegen platform, and used to analyze differentially expressed genes. Wilsons group has completed the sequencing of 9 BACs covering part of the catfish immunoglobulin heavy chain locus and are continuing mapping of this important locus. Characterization and functional studies of catfish immune molecules are ongoing. Waldbiesers lab used microarrays for the analysis of catfish response to LPS injection. His lab has also conducted investigations on GH-IGF pathway and its interaction with the immune system, and prepared several cDNA libraries for the JGI EST project.

    Salmonids: The number of ESTs for rainbow trout increased 9% to 262,330 and Atlantic salmon increased 131% to 431,754. Several microarrays are available for functional genome research. These data have provided an excellent starting point for candidate gene investigation including uncoupling proteins, myostatins, pro-opiomelanocortins, and tapasins. Significant progress continues to be made in identifying genes which affect development rate, oxygen consumption, and sex determination.

    Tilapia: USDA-NRICGP has just approved a project to sequence 100,000 ESTs from a variety of tilapia cDNA libraries. These sequences will complement existing EST resources for related cichlid fish, allowing the production of 2nd generation microarrays for tilapia.

    Oysters: The Oyster Genome Consortium will sequence EST and BAC libraries for the Pacific oyster. JGI will do paired-end sequencing of 150,000 cDNAs. JGI will also sequence four BAC contigs containing genes identified by Cunningham et al. (2006), in order to assess levels of DNA polymorphism in coding and non-coding regions, which could ultimately influence whole genome shotgun sequencing strategy. A transcriptomic analysis of inbred and hybrid oysters (Hedgecock et al. 2007) revealed candidate genes for heterosis, several of which have been identified through BLAST searches. Work is in progress to find SNPs in these genes and to place them on the QTL map. For the Pacific oyster, Hedgecocks lab reported QTL-mapping results on the number, location, and mode of action of genes affecting yield in an F2 family derived from a naturalized C. gigas population in Dabob Bay (WA). Three dominant QTL for yield on three different chromosomes were detected. They also have mapped a recessive QTL for an abnormal "hook-hinge" condition segregating in this same family as well as an additive QTL for shell pigmentation. In the eastern oyster, Guos lab identified and mapped 12 putative disease-resistance QTLs. For the flat oyster, French researchers are in the process of mapping QTL of resistance to bonamiosis, a major disease for this species. Gaffneys lab is mapping SNPs using a F2 family segregating for resistance to summer mortality.

    Shrimps: Six high quality tissue specific cDNA libraries have been constructed and analyzed for depth and redundancy, with 1000 EST being collected from each library to date. JGI will perform full double pass sequencing. The first generation microarray has been printed and initial validation and QA/QC have been completed. These microarrays contain in excess of 3000 unigenes and are currently in use; the first experimental research work is in press. Studies on the effects of long dsRNA and RNAi in relation to viral challenge and WSSV in the Pacific Whiteleg Shrimp, Litopenaeus vannamei are ongoing. Continuing research in the area of antimicrobial peptides and their importance in shrimp immunity has yielded data on the structure of the Penaeidin gene family, its control elements, and specificity for microbial targets.

    Striped Bass: Significant progress was made in 2006 involving integration of genomic approaches toward better understanding of biological mechanisms underlying economically important traits in striped bass. Much of this work is described in three dissertations submitted to North Carolina State University (Couch, C.R., 2006; Garber, A.F., 2006) and Texas A&M University (Wang, X., 2006). Each of these dissertations studies used microsatellite markers to assess economically important traits such as growth, disease resistance, and carcass-quality in striped bass. These new studies will be important going forward as the genetic linkage map is produced for striped bass and will eventually aid in the identification of QTL for economically important traits.

    Cattle At the University of Wisconsin, mapping QTL for bovine twinning rate was continued by the Kirkpatrick laboratory. Efforts to fine-map previously identified QTL on BTA5 were initiated. Strong evidence for QTL based on combined effects of linkage and linkage disequilibrium were found in two separate locations on BTA5. As an initial step in a whole genome search for twinning rate QTL, 200 Holstein sires with high reliability twinning rate PTAs were genotyped using the ParAllele 10K SNP typing tool. The Kirkpatrick lab has also been mapping QTL for Johnes disease susceptibility. Significant evidence for a QTL was found only on BTA20 (chromosome-wise P<0.05). The Medrano laboratory is working to understand the biological mechanism underlying growth traits in animals and to define the architecture of genes interacting in the control of growth and body composition. To study these mechanisms they are utilizing mouse congenic strains as a powerful tool to isolate segregating QTL and to define the function of the underlying genes. They have characterized a unique mouse model (high growth, HG) that produces a 30-50% increase in post-weaning growth rate and mature body size, as well as a substantial increase in feed conversion efficiency during growth. In addition to the major effect of the hg deletion, the HG phenotype is influenced by genetic interactions with genes in Chr. 2, 9, 11 and 17. In order to fine map these regions they have developed a series of congenic and sub-congenic strains covering QTL in these chromosomes. Of particular interest has been the sex dependant expression of growth and obesity QTL, between the CAST/EiJ (CAST) and C57BL6/J-hg/hg (HG) strains, on distal mouse chromosomes 2 and 11. To confirm, fine map and further evaluate QTL X sex interactions, they constructed congenic by recipient F2 crosses for the HG2D and HG11 congenic strains. Of the 20 QTL identified, eight were sex-biased, sex-specific or sex-antagonistic.

    Poultry BAC libraries, prepared in part with NRSP-8 and NRI Tools & Reagent funding, were fingerprinted extensively and integrated with linkage and gene maps (mostly using the overgo mapping technique). These data were employed to generate a second generation BAC contig map comprised of 260 contigs, most of which have been anchored to the genetic linkage/chromosome map (Wallis et al., Nature 432:761-764, 2004). The BAC contig physical map was updated in parallel with the second build of the chicken genome sequence. Similar efforts applied to the turkey CHORI-260 library are underway in hopes of generating a BAC contig physical map of the turkey genome and a comparative chicken-turkey map. NCBIs dbEST (http://www.ncbi.nlm.nih.gov/dbEST/) presently lists almost 600,000 chicken ESTs. These have been critical in a variety of gene discovery efforts, especially in annotating the genome sequence and in array development. Radiation hybrid (RH) panels have been constructed by Vignal and colleagues at INRA (Morisson et al., Genet. Sel. Evol. 34:521-533, 2002), and a framework RH map has been constructed (e.g., Morisson et al., Genet Sel Evol. 37:229-251, 2005 and references therein). RH map data are being used to improve the new genome sequence build. The first assembly of the draft 6.6X chicken sequence was released on March 1, 2004. Additional sequence data, physical, RH and SNP data were used to assemble a second, improved build of the chicken genome, released in May, 2006. The second build moved a large portion of the previously unplaced sequence contigs into specific chromosomal locations and enhanced the general contiguity and accuracy of the sequence assembly. In addition, the NHGRI has approved funding that will allow additional directed sequencing to bring the chicken genome to a finished state (W. Warren, pers. comm.).

    Sheep Texas A&M has established a study to test the hypothesis that steroid hormones transiently induce expression of genes in the endometrial epithelium to make the uterine environment different between the earliest days of pregnancy. Using differential display-PCR, they identified NUDT16 as being strongly induced in ewes between day 3 and 6 of the estrous cycle. mRNA from this gene was elevated 10-fold in the endometrium of sheep from day 5 to 9 of the estrous cycle and returned to basal levels by day 11. A comparison of 15 tissues revealed NUDT16 was greatest in endometrium, and found exclusively in the endometrial epithelial cells of the glands and uterine lumen. A reciprocal backcross population has been created by crossing ewes from a Dorset population selected for aseasonality and prolificacy (Cornell University Sheep Farm) with rams from an East Friesian population known for high milk production. This population will be used by Oklahoma State University to conduct a whole-genome scan for QTL for the two traits using breeding values for milk yield and progesterone profiles, ultrasound readings, and lambing events for out of season breeding. Association studies will be conducted to investigate candidate genes for milk production (prolactin and b-lactoglobulin) and for out of season breeding (melatonin receptor and prolactin). A collaboration including Utah State University, Purdue University, USDA/ARS, and the University of Liége has identified a core cluster of imprinted genes (DLK1, GTL2, PEG11, and MEG8) located at the distal end of ovine chromosome 18. Using quantitative PCR, they have shown that the inheritance of the callipyge (CLPG) SNP in cis alters the expression of genes with a paternal allele-specific expression (DLK1 and PEG11) and maternal allele-specific expression (GTL2 and MEG8) in muscles that undergo hypertrophy in a genotype and age specific manner. The effects of age and genotype are also significant for expression of the CLPG1 RNA that is transcribed from the intergenic region between DLK1 and GTL2 and spans the CLPG SNP. A functional genomics approach is being used by Purdue University to study muscle growth in callipyge lambs using the Affymetrix Bovine Genome Expression Array. Microarray results were validated by quantitative PCR in a larger group of callipyge and normal lambs (six ages from 10 to 200d, N = 42 ). Differentially expressed genes included a transcription factor, a gene with similarity to a ribosomal protein methyltransferase, a cAMP phosphodiesterase and a muscle-specific metabolism enzyme. The transcription of the cAMP phosphodiesterase most closely mirrors the expression pattern of DLK1 (0.95 correlation), indicating it may play an important role in the early development of hypertrophy in callipyge muscle. Gastrointestinal parasites have a profound effect on sheep production. A sheep population segregating for parasite burden was constructed at Louisiana State University utilizing Gulf Coast Native (resistant) and Suffolk (susceptible) crosses. A genome-wide QTL scan has been implemented and QTLs significant at chromosome-wide levels (P < .05) were identified on OAR9 at 40 cM for FEC after natural challenge and at 95 cM for FEC and PCV after experimental challenge. Another QTL was identified on OAR19 at 20 cM for FEC and PCV after natural challenge. Fine mapping of these regions will more precisely locate the QTL and allow the identification of positional candidate genes. A large-scale EST sequencing project for goats has been implemented at Virginia State University. To date, sequences have been obtained from about 10,000 clones from a cDNA library from goat uterine/embryonic tissues collected between days 5 and 8 pregnancy. The cDNA is also being hybridized to human nylon arrays to examine gene expression during early embryonic development.

    Progress toward Objective 3:

    Aquaculture Catfish: Lius lab continues their efforts on development of comparative genome tools such as chromosome-anchored ESTs of catfish. Large scale informatic mining of microsatellites and SNPs are underway; The CGRU in 2006 will continue development and enhancement of microarray tools, and further use of arrays to identify candidate genes for disease resistance.

    Salmonids: The Atlantic salmon and rainbow trout gene indices have relocated to the Dana Farber Cancer Institute and have been updated to versions 3.0 and 6.0, respectively (http://compbio.dfci.harvard.edu/tgi/tgipage.html).

    Tilapia: Dr. Kochers group has implemented the Gbrowse software to facilitate viewing of tilapia sequences on the Tetraodon genome assembly (http://hcgs.unh.edu/gbrowse/).

    Oysters: Within the EU project Aquafirst, QTL data will be hosted by the Roslin Institute on ArkDB. EST data will be held on the INRA platform "Sigenae" in Toulouse.

    Shrimps: The marine genomics group at the Hollings Marine Laboratory and MUSC continues to maintain www.marinegenomics.org for the archiving of EST and microarray data, and as a resource for on-line tools that can be used in the analysis of genomic and transcriptomic data, which are being used to archive and analyze shrimp metagenomic and microarray data. In addition, contracting with Clemson University Genome Institute is underway to enhance EST analysis capabilities.

    Cattle At Texas A&M University, the Adelson laboratory has updated the Bovine QTL viewer (http://bovineqtl.tamu.edu/) and linked it to the 7.2x build (assembly version 3) of the bovine genome, to show existing SNPs and gene models. Development of a data model for SNP data and haplotype data has been performed and an initial SNP database has been created. The design of 24,000 long oligonucleotide probes by the Elsik laboratory at Texas A&M University comprising the first generation bovine whole genome expression array has been completed (http://bovineoligo.org). They have updated their EST gene family database by adding vertebrate proteins. The Livestock EST Gene Family Database now includes bovine and pig EST clusters, and is linked to the bovineoligo.org and pigoligoarray.org databases. They also continued development of the Bovine Genome Database (http://bovinegenome.org). They are organizing annotation of the bovine genome, and have developed an annotation submission website for bovine genome community members to upload gene models. Results from QTL experiments have been published in many journal articles. The enormity of this published research has made it very difficult for researchers to stay abreast of all published research. To alleviate this problem, the Reecy laboratory at Iowa State University have developed a Livestock QTL database (www.animalgenome.org/AnimalQTLdb). To date, they have curated, chicken, cattle and swine QTL. For the first time, researchers can go to a single source and evaluate published QTL for cattle, chickens and pigs. This resource should aid in the discovery of genetic variation that underlie quantitative trait loci.

    Poultry The sequence, along with a variety of options and tools, can be accessed at three different browsers: the UCSC Chicken Genome BrowserGateway, (http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chicken&db=0&hgsid=30948908); the NCBI Chicken Genome Resources, (http://www.ncbi.nlm.nih.gov/genome/guide/chicken/); and the EBI's Ensembl Chicken Genome Browser, (http://www.ensembl.org/Gallus_gallus/). The ChickFPC browser at http://www.bioinformatics.nl/gbrowse/cgi-bin/gbrowse/ChickFPC allows for various searches of the BAC contig map. The SNP data generated by the Beijing Genomics Institute (described above) can be accessed on the UCSC or Ensembl browsers, but more extensive descriptions are available at the BGI site at http://chicken.genomics.org.cn/index.jsp. A recent survey of chicken QTL was developed (Abasht et al., Poultry Science 85:2079-2096, 2006) and is made available through the NRSP-8 Bioinformatics team at http://www.animalgenome.org/QTLdb/chicken.html. The latest version of ChickGBASE developed by the Roslin Institute is at http://www.thearkdb.org/arkdb/do/getChromosomeDetails;jsessionid=B8A6A5EA698B84AF80EE99BE7530B04E?accession=ARKSPC00000004. US Poultry Genome Homepage: The homepage for the NRSP-8 U.S. Poultry Genome project (http://poultry.mph.msu.edu) provides a variety of genome mapping resources, including the latest EL maps and mapping data, descriptions of available resources, the latest cytogenetic map, and access to a host of other information relating to both genetic and physical maps, including our newsletter archive. Newsletter: The Poultry Genome Newsletter is published quarterly and is distributed through the Homepage, electronically on the angenmap email discussion group and via direct email to scientists worldwide. Recently, coordination funds were used to provide samples of a new 44,000 element long oligonucleotide chicken array made by Agilent to several NRSP-8 participants (http://www.operon.com/arrays/oligosets_chicken.php). A chicken whole genome long oligo array is also available (~$150 each) at the U. of Arizona, www.grl.steelecenter.arizona.edu and can also be purchased on a custom basis from Nimblegen, www.nimblegen.com. A 13K chicken spotted cDNA glass slide array remains available from the Array Facility at the Fred Hutchinson Cancer Research Center. See Burnside et al., BMC Genomics 6:13 (2005) (http://www.biomedcentral.com/bmcgenomics) for more details. Affymetrix, Inc. is marketing the GeneChip® Chicken Genome Array that measures levels of 32,773 chicken transcripts and 684 chicken viral transcripts (http://www.affymetrix.com/products/arrays/specific/chicken.affx).

    Sheep Sequences from the ovine CHORI-243 BES project are now publicly available at http://www.ncbi.nlm.nih.gov/genome/guide/sheep/index.html. Matches of the ovine BAC-end sequences to the bovine and human sequences and identity of clones can be obtained through a database established by CSIRO (Australia) at http://www.livestockgenomics.csiro.au/SheepGenomics/. An on-line, real-time comparative database will be developed for web-based transmission of mapping data generated from the ovine RH panel. Database displays will include ovine RH maps of each chromosome that are cross-referenced to homologous human and bovine chromosome segments, with lines between orthologous markers indicating internal rearrangements.

    Swine The Pig Genome Database has received considerable updating. News and updates were set up to report the genome sequencing progress (http://www.animalgenome.org/pigs/genomesequence/). New QTL continue to be curated into the Pig QTL Database. To date, there are 1,675 QTLs in the database representing 246 pig traits. In addition, new functions have been added to the PigQTLdb tools to align pig RH map-human comparative maps, and pig BAC physical maps, new microsatellite markers from Sino-Danish genome project, and pig SNPs from dbSNP, against pig QTL. It can be seen at http://www.animalgenome.org/QTLdb/pig.html. Database activities were transferred to the Bioinformatics Coordinator. Thanks to efforts of a number of groups and individuals we have developed a second generation novel 70-mer oligonucleotide microarray for profiling expression of the pig (Sus scrofa) genome. The Swine Protein-Annotated Oligonucleotide Microarray has been developed as an OPEN SOURCE collaboration between investigators and institutions with an interest in pig physiology. The sequences of the oligonucleotides, the consensus sequences they represent, and the annotation of the consensus sequences are provided at no cost to the entire research community. Microarrays spotted with already synthesized oligonucleotides can be purchased by going to: http://www.pigoligoarray.org/ or to http://www.animalgenome.org/pigs/resources/array_request.html to order them.

    Impact Statements:
    1. The genetic linkage maps of aquaculture species and cattle, chicken, equine, sheep and swine have provided a framework for numerous QTL and other mapping experiments and a platform on which genome sequences have been assembled and linked to chromosomes.
    2. The rapid expansion of SNP data for chicken, cattle, equine and sheep will provide high density linkage maps and should aid numerous on-going attempts to identify the causative genetic changes involved in many QTL.
    3. A whole genome ovine BAC physical map was developed along with a virtual sheep genome (http://www.livestockgenomics.csiro.au/vsheep/), and an ovine haplotype map was initiated.
    4. The understanding of the genetic process controlling animal growth in a model organism allows the isolation and study of homologous genes in livestock that could be used to select faster growing and more efficient animals.
    5. Long oligo arrays for gene expression analyses are now available for chicken, cattle and swine.
    Last Modified: 14-Aug-2007

    Date of Annual Report: 05/27/2008

    Report Information:
  • Annual Meeting Dates: 01/12/08 to 01/15/08
  • Period the Report Covers: 10/2006 to 09/2007

    • Participants:
    Brief Summary of Minutes of Annual Meeting:
    Brief Summary of Minutes of the Annual Meeting:

    OLD BUSINESS A. Call to Order 3:40 pm - Mary Delany, NRSP-8 2007 Chair. Motion to approve minutes from January 14, 2007 meeting by C Ashwell, NCSU; 2nd J Reecy, ISU; approval by acclimation.

    B. Species Coordinator Reports 1. Sheep/Goat Report - Noelle Cockett, Sheep Genome Coordinator. NRSP8 funds have been used to leverage other funding for the International Sheep Genome Consortium. BAC end sequencing of the CHORI-243 ovine BAC library was completed under a USDA-NRICGP project, and the BAC end sequences were used to develop a sheep whole genome physical map. Combined data was compared to reference genomes, including human, cattle and horse, to give the final product, the virtual sheep genome map. A 1536 SNP array has been used for typing multiple populations, including the sheep reference population used for linkage map and the USU RH panel. New sets of primers have been generated for 1800 genes and are being typed across the RH panel. The RH and linkage maps are used to confirm the virtual sheep genome map. These primers may be useful for the planned goat RH panel. The push for a whole genome sequence for sheep will be discussed at the ISGC meeting on Monday, 1/14/08 at PAG. Several new members have been added to the NRSP8 sheep and goat committee. NRSP-8 coordinator funds are an important incentive for travel to the meeting. 2. Cattle - James Womack, Cattle Genome Coordinator. NRSP8 funds were used for travel for workshop speakers and students. Primers originally developed for RH panel are now being used successfully for RH map in other bovids. Bovine sequencing assembly is still continuing, much more effort will be required for full sequence assembly. 3. Equine - Ernest Bailey, Equine Genome Coordinator. Whole genome sequencing has already been completed for horse in 2007 at Broad Institute, MIT, MA. Plans are underway for development of new Illumina 60K SNP chip with support by Morris Animal Foundation. A major update of the horse genome webpage has been completed. It includes added information for scientists as well as for members of the horse industry. Ernie urged all species to evaluate their websites for utility by the general public and stakeholders. 4. Poultry - Jerry Dodgson / Hans Cheng, Poultry Genome Co-Coordinators. Chicken genome sequencing has been accomplished, two iterations, 2004 and 2006, even though not representative of a truly completed assembly nor fully annotated. However, the sequence availability has opened up major areas for future work including SNP efforts, comparative studies in turkeys, copy number variant investigations. There are currently no funds, but clear need and hope, for developing more comprehensive SNP chips for chickens. It is now much more evident that breeding companies have invested in genomics and are actively using tools developed by NRSP-8 scientists for their chicken work. 5. Swine - Max Rothschild, Swine Genome Coordinator. NRSP-8 funds have been used to support development and use of new expression arrays using long oligos. Slides printed at Univ. AZ are being validated at MSU, UMN and BARC in 2008 with NRSP-8 support. Swine genome sequencing is continuing at Sanger; it is coming together but not expected to be finished until mid-2009. It is currently at 2x coverage with 4-6x final coverage expected. A new swine SNP chip with 40-60K SNPs is being developed. Purchase of 700-1000 chips is planned for US labs using specifically stockpiled funds from the NRSP8 Swine Coordinator. 6. Aquaculture - John Liu, Aquaculture Genomes Coordinator. Currently 6 aquaculture species are covered under NRSP-8; at PAG 30 aquaculture species reported their research results. WGS of tilapia is scheduled by the Broad Institute. Genome BC is planning WGS for Atlantic salmon; the community is working on funding for that. New Co-Coordinator for Aquaculture is Caird Rexroad, ARS, Leetown, WV. 7. Database - James Reecy, Database Lead Coordinator. There has been recent funding for animal bioinformatics projects, e.g., Shane Burgess for GO annotation, Carl Schmidt for GallusGBrowse; Chris Elsik for bovine annotation, and Jim Reecy for expanding the web viewer to be used for many species. Jim Reecy is working with rat and mouse genome groups to develop comparative applications. Expertise and computer structure is available for developing needed relational databases; if want to pursue could take advantage of ISU supercomputers for different applications. There was a general email message with 2 surveys for NRSP-8 web tools. Please respond to provide input.

    C. Administrator Reports 1. Lead Administrative Advisor - Colin Kaltenbach. There has been good progress by all the species Coordinators with improvements at both basic plus applied levels. The most important current issue is the NRSP-8 renewal. Note that the annual report must be submitted within 60 days. The writing for the new project has progressed very well, thanks to the leadership of NRSP-8 Chair, Mary Delany. Reviews to date have been very good. New species Coordinators are expected to be selected before Oct.1 2008, the start date for a new project. All scientists should remember to sign up for the new NRSP-8 project. Participation does not role over. Please contact your Experiment Station Director to add members for the new project (Appendix E form). All levels of participants are welcome, PIs, postdocs, and students. 2. Other Administrative Advisors - Eric Young and Bert Stromberg. Each affirmed the impact of the current NRSP-8 project and the importance of the efforts to renew it. It was noted that industry partners are allowed; contact Colin Kaltenbach for further information. Scientists from other countries are also welcome to participate in NRSP-8. 3. USDA-CSREES National Program Leader - Muquarrab Qureshi. NRSP-8 is a high impact project. It is impressive how many species sequencing have been completed since 2003. In 2008 numerous species sequencing are underway or being completed. These efforts are viewed as very important to the US government and its PMA and OSTP. This is viewed nationally as one of the best NRSP programs. The revised project has paid attention to USDA Animal Genome Blueprint www.csrees.usda.gov/nea/animals/pdfs/animal_genomics_blueprint.pdf Animal genomics are valued at CSREES as evidenced by NRI grant rfps. Thanks to the bioinformatics efforts, to the QTL group, for its impact for industry. Approval of the NRS-P8 rewrite is underway. Once completed CSREES will expedite Coordinators selection. The aim is for a mid-June deadline. Remember to email species leadership changes to NRSP-8 Secretary, Joan Lunney so she can send the updates to Muquarrab Qureshi.

    D. NRSP-8 Project Re-write  Mary Delany The new NRSP8 project objectives were each reviewed and approved.

    NEW BUSINESS 1. Election of officers for 2008. Jerry Dodgson nominated Joan Lunney, USDA BARC, for chair and Ernie Bailey nominated Cecilia Penedo, UC Davis, for secretary. Both nominations were approved by acclamation. 2. Selection of next meeting location and date. Jerry Dodgson suggested the meeting be held next year at PAG on Sunday; approved by acclamation. 3. Meeting format. Jerry Dodgson noted that the Poultry group suggested a modification of the format of the NRSP-8 PAG meeting stating a need for joint species sessions at PAG for common animal genome related topics. Its difficult to move between the separate species meetings. The suggestion is for the species meetings to end by lunch on Sunday. This would open up time for a common scientific meeting for general topics for all species, e.g., SNPs would have been good this year. Motion: Jerry Dodgson moved that NRSP-8 scientists consider a Sunday afternoon joint animal session; 2nd by Sue Lamont. Discussion: Qureshi noted that this would improve cross-species communication. Liu said many scientists only stay the weekend so a larger session on Sunday is a good idea. Reecy asked why not go for earlier Sunday for this NRSP-8 plenary session? Cassady noted that now it is difficult to go to other species sessions; it is important particularly for people working on multiple species. There had been a previous agreement for swine meeting on Saturday and cattle on Sunday. This year cattle had a 2 day meeting Saturday and Sunday. Change in meeting schedule will depend on room availability; Cheng will check possibilities and ask Scherago for options. Species chairs will plan this session with the NRSP8 leadership and with Coordinators. All present approved the motion that NRSP-8 scientists consider a Sunday afternoon joint animal session. Motion was made by Qureshi to thank Mary Delany and Joan Lunney (2007 Secretary) for a good job with this NRSP8 meeting. Meeting adjourned at 5:30 pm.

    Accomplishments:
    Progress toward Objective 1. Aquaculture. Catfish. Over 300 microsatellite markers derived from ESTs were mapped. To integrate the linkage and physical maps hundreds of microsatellites derived from BAC-end sequence were genotyped. Two BAC contig-based physical maps of the channel catfish were generated using fingerprints; combined contig size was about 931 and 961 Mb. Some 48,275 BAC end sequences were generated with 12,586 microsatellites identified. Salmonids. Eighty percent of the NCCCWA Swanson 10x BAC library clones were fingerprinted and BAC end-sequencing of 100,000 clones was completed by a collaborative partnership (Genoscope and INRA). Assignments of 27 Atlantic salmon linkages groups were made to the 29 chromosomes pairs. BACs were assigned to 46 of the 50 rainbow trout chromosome arms using FISH. Centromere assignments were made to the trout genetic maps. Tilapia. About 20,000 BAC clones were sequenced (Genoscope). The sequencing project was assigned by NIH-NHGRI to the Broad Institute. Oysters. A JGI/Standford project to sequence 58 BAC clones progressed. A BAC-based physical map was constructed of the Pacific oyster genome from a single inbred male. The library was fingerprinted (Genome Sciences Ctr). A project that progressed was the deep-sequencing of Pacific oysters ESTs from tissue and age-specific libraries. Work also continued for the eastern oyster in marker development. Shrimps. First order genetic maps have been published, marker development continues. Striped bass. New microsatellite markers were developed (~500) and creation of the first genetic linkage map is underway.

    Bioinformatics. Work focused on linking QTL data to the human and livestock genome sequences for researchers to transfer information between maps; in addition minor allele frequencies and microarray features have been included as available.

    Cattle. Contributions were made to the NIHGR bovine genome sequencing project technical committee.

    Equine. A first assembly of the horse genome was accomplished (Broad Institute) and the sequence was analyzed by the horse genome group; this involved sharing amongst numerous national and international lab from previously completed RH maps, linkage maps, and FISH markers. Comparative genomic questions can now be addressed between equine, other sequenced animal genomes and human.

    Pig New gene markers were identified, mapped and map integration continued with expansion of QTL map and physical maps. The sequencing consortium continued its fund raising efforts and a review of progress was published; sequencing continues to advance with significant coverage of all chromosomes.

    Poultry The chicken linkage map provides a framework for QTL and other mapping research and the platform on which the sequences have been assembled and linked to chromosomes. Prior SNP research was built upon by USDA NRI support of an US and EU consortium to genotype thousands of birds and utilizing the EL and W linkage families further enhancing the linkage map. A second SNP study was supported by coordination funds re-using SNP genotyping information and reagents  combined this SNP data improve the linkage map and contributes to numerous on-going research to find causative genes involved in many chicken QTL.

    Sheep/Goats An ovine whole-genome RH 5,000-rad panel consisting of 88 clones was generated and used to construct map with 1306 markers. The result was 95 RH linkage groups over26 autosome. Progress continued with NRSP-8 collaboration in the International Sheep Genome Consortium to create new resources which includes a high coverage BAC library, end-sequencing, integrated ovine map, BAC physical map, development of the virtual sheep genome (http://www.livestockgenomics.csiro.au/vsheep ) and a 1,536 SNP chip.

    Progress toward Objective 2. Aquaculture. Catfish. About 300,000 EST clone sequences (200K from catfish, 100K from blue catfish) have been generated (project with Joint Genome Institute and NRSP-8 members). Salmonids. The community continues to identify ESTs from tissues and physiological conditions from a number of salmonids. Functional genomics involving global gene expression with respect to proteolysis and toxicological responses are producing candidate genes for further analysis. Two QTL were found in a study using clonal lines (WSU) and stress analysis with opposing effects. A growth QTL analysis found 22 QTL across 11 linkage groups with effects on numerous growth parameters. Tilapia. A major EST study was approved by the USDA-NRICGP to sequence 100,00 ESTs from a variety of tilapia libraries. Oysters. Deep sequencing of 16,000 Pacific oyster clones derived from multiple tissues and age-specific libraries has been completed and working is continuing. Shrimps. About 130,000 white shrimp EST clone sequences (from both ends) are being checked (Joint Genome Institute) against the physical library; these will be used to create a microarray. Striped bass. A new inter-disciplinary program of graduate education in aquaculture genomics was developed at NCSU with funding from the USDA  CSREES Food and Agricultural Sciences National Needs Grants Program. This group has been very active in collaborative efforts for improved breeding and development of specialized stocks, with an emphasis on enhancing genetic diversity and commercially important traits.

    Bioinformatics. Focus was on curation of cattle, chicken and swine QTL information generated from hundred of manuscripts describing QTL or association tests for these species. The database was expanded to include sheep QTL information.

    Equine Numerous studies were conducted and published related to QTL analyses and also diseases involving bone, muscle, skin as well as coat color variants and aspects of performance and infectious disease. The work involved use of the genetic marker maps previously developed by NRSP-8.

    Pig QTL are reports in all chromosomes for numerous traits; imprinted QTLs continue to be discovered. Candidate gene analysis was successful with several gene tests used by the industry for traits including fat, feed intake, growth, meat quality, litter size and coat color.

    Poultry BAC libraries were extensively fingerprinted and integrated with linkage and gene maps and used to generate a second generation contig map updated in parallel with the second build of the chicken genome sequence. Similar efforts were undertaken for the turkey CHORI-260 library to generate a BAC contig physical map of the turkey genome and a comparative chicken-turkey map. Over 21,000 BAC end sequences and 15,200 BAC overgo hybridization assignments were made to 1248 markers or genes. More tha 40,000 turkey BAC fingerprints were generated allowing a first generation physical map for turkey of about 5.6x coverage.

    Sheep/Goats A resource population was created by crossing Dorset ewes with East Friesian rams, with an F1 backcross to both parental populations. Phenotyping was initiated. Microsatellites will be used for genotyping. Research on the callipyge trait continued by analysis of gene expression (using bovine arrays). A QTL scan was initiated of a sheep population segregating parasite burden. A large scale EST sequencing project of 10,000 clones from a cDNA library from goat uterine/embryonic tissues was initiated.

    Progress toward Objective 3: Aquaculture. Catfish. Work progressed on creating chromosome-anchored ESTs with large sale informatic mining of microsatellites and SNPs Salmonids. Atlantic salmon and rainbow trout gene indices can be found at http://compbio.dfci.harvard.edu/tgi/tgipage.html Tilapia. The Gbrowse software has migrated to the University of Maryland, www.cichlidgenome.org . Shrimps. Archiving of EST and microarray can be found at www.marinegenomics.org .

    Bioinformatics. Extensive communication was held with curators of other relevant livestock-genomics databases, along with compilation of database information and assessment of content and function, to allow for US coordination efforts to focus on development in areas of high priority and utility. In addition alignment and display of microarray data was successful. On line tools were developed to generate PCR primers across species, a GO term counter and also graphing tools are accessible. An Animal Trait Ontology was developed. A bovine genome annotation meeting was co-hosted.

    Cattle Web site was maintained for on-line radiation hybrid mapping for investigators using the 5000 rad bovine RH panel available from the coordinator. Distribution of bovine reference family panel DNA (IBRP) was continued. Microsatellite primers were purchased and were distributed by the coordinator (quality tested by coordinator lab). Other tools are also available: RH panels of (5,000 and 12,000 rad)), BAC libaries, panel of 31 hybrid somatic cells.

    Equine Sharing of resources continued including reference families DNAs, primers, RH mapping resources, BAC clones (CHORI). Contributions were made to database develop for genetic data, BAC map data, SNP data.

    Pig The PigQTLdb serves as a repository for QTL related studies. There are 1,675 QTL in the database representing 246 pig trais. New functions have been added including tools to align pig RH map-human comparative maps, BAC physical maps, new microsatellite markers, pig SNPs from various sources and micro array elements  against pig QTL. News and updates are communicated to membership routinely. A second generation novel 7-mer oligo microarray for profiling expression was developed. The informational materials are available to the community (no cost); the array can be purchased via the coordination unit. Validation is ongoing through a collaborative venture.

    Poultry The sequence is available on three browsers (UCSC, NCBI, Ensembl). Numerous unique and resource-packed databases and browsers are available and maintained by researchers supported by USDA-NRI funds along with the NRSP-8 Bioinformatics coordination site(s), all can be accessed by the NRSP-8 poultry genome website (http://poultry.mph.msu.edu ).

    Sheep/Goats Sequences from the CHORI-243 BES project are available via NCBI. Matches of the ovine to bovine and human sequences and clone identity are available through CSIRO (http://www.livestockgenomics.csiro.au/SheepGenomics ). Virtual sheep genome information and mammalian comparisons are available through the site.

    Impact Statements:
    1. Cutting-edge genomic tools continue to be generated for the community in the form of reagents, high throughput assay systems, bioinformatic resources, and sequence data for all species designated which serves national and international researchers at very economical terms.
    2. Sequence analysis is contributing to our understanding of comparative vertebrate biology, making it possible to understand genome organization and evolution in the context of production animal systems, model organisms and human.
    3. Analysis of expression data is creating new information of molecular pathways and networks previously unexplored and highly relevant to commercial productivity and success with a continued focus on growth, reproduction and disease.
    Last Modified: 27-May-2008
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