Progress 10/01/08 to 09/30/13

Outputs
Target Audience: Researchers Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? NRSP-8 species coordinators and chairs are organizing a meeting in Spring, 2014 to discuss Ag-ENCODE. Program managers from USDA, NIH and NSF as well as representatives from other countries will be invited. A strategy will be developed for funding the project while avoiding redundancies across agencies. Discussion of appropriate methods and samples will also occur. How have the results been disseminated to communities of interest? The NRSP-8 Sheep Genome Coordinator will provide travel support for members of the NRSP-8 Sheep/Goat Committee to attend the annual NRSP-8 meeting held in conjunction with the Plant and Animal Genome (PAG) meeting in San Diego, CA in January. The annual meeting of the ISGC will also be held at PAG; NRSP-8 members are encouraged to attend. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Objective 1 (Develop high resolution genome maps): An ongoing project of the ISGC is development of a whole genome reference assembly. In 2010, sequence data were generated at two sequencing facilities (Beijing Genomics Institute and the Roslin Institute) from DNA of a Texel ewe and a Texel ram, respectively. The first step of the reference sequence assembly involved de novo assembly of 75X reads from the Texel ewe into contigs and scaffolds. Once that was completed, sequences from both animals were used for gap filling. Version 2.0 of the ovine whole-genome reference sequence (Oar v2.0) was publicly released in February, 2011 and Oar v3.1 was released in October, 2012 through NCBI GenBank. For chromosome assemblies go to http://www.ncbi.nlm.nih.gov/assembly/GCA_000298735.1/ and for the full assembly, including scaffolds and contigs not assigned to chromosomes, go to http://www.livestockgenomics.csiro.au/cgi-bin/gbrowse/oarv3.1/. To allow annotation by Ensembl, the ISGC has agreed not to release a new version of the assembly until late 2015, although update patches for some regions will likely be released before then. The RNA dataset produced by Roslin Institute and submitted to Ensembl is the largest transcriptome analysis of any species in Ensembl, including man. A manuscript describing the whole genome assembly (Oar v3.1), the RH map, and the linkage map is in preparation. Highlights of differences between the genome structure of sheep, cattle and goats are included in the manuscript. The analysis of about a terabite of data on the transcriptome is also included. Variation of alleles, allelic imbalance and copy number variation have been included in the manuscript as points of interest. Biological stories include reproduction, digestive tract enzymes, evolution of the rumen, lipid metabolism and evolution of wool. Kim Worley (BCM-HGSC) received funding from a 2013 USDA/AFRI grant to fill gaps in the sheep assembly using PacBio data with PBJelly (scaffolding and gap filling) and Honey (structural variation identification and assembly QC). For sheep, this approach has produced 19x long read data (40 kb max, 8.5 kb N50, and 6 kb mean). Using three rounds of PBJelly 2, analysis has moved the assembly contig N50 from 41.7 kb to over 500 kb and closed 89% of gaps. However, there was only a minor shift in scaffold N50 (from 100.1Mb to 101.2Mb). Improvement of the Y chromosome, which is full of repetitive sequence, will not be possible with this method. The PacBio work will be in Oar v4. Objective 2 (Provide genome mapping resources): An ovine HD (600K) SNP chip was released by Illumina in 2013. Parameters for inclusion of SNPs on the chip were equal spacing (80% of the SNPs), functional, GBS (genotyping by sequencing), literature and 50K chip SNPs (that were not already included under equal spacing). There is still 6K “head room” which can be added by users. The final design provides about 12 SNPs every 50K. There should be little ascertainment bias across breeds; however, there will be bias within breeds. There are a lot of low MAF SNPs on the HD chip so users should not create a cluster file, and instead use the cluster file created with ~3,500 animals and available from Illumina. The SNPs will be deposited in dbSNP by March, 2014. The chip should be useful for GWAS and evolutionary studies, and be moderately useful for imputation.

Publications

Progress 01/01/13 to 09/30/13

Outputs
Target Audience: Researchers Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? NRSP-8 species coordinators and chairs are organizing a meeting in Spring, 2014 to discuss Ag-ENCODE. Program managers from USDA, NIH and NSF as well as representatives from other countries will be invited. A strategy will be developed for funding the project while avoiding redundancies across agencies. Discussion of appropriate methods and samples will also occur. How have the results been disseminated to communities of interest? The NRSP-8 Sheep Genome Coordinator will provide travel support for members of the NRSP-8 Sheep/Goat Committee to attend the annual NRSP-8 meeting held in conjunction with the Plant and Animal Genome (PAG) meeting in San Diego, CA in January. The annual meeting of the ISGC will also be held at PAG; NRSP-8 members are encouraged to attend. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Objective 1 (Develop high resolution genome maps): An ongoing project of the ISGC is development of a whole genome reference assembly. In 2010, sequence data were generated at two sequencing facilities (Beijing Genomics Institute and the Roslin Institute) from DNA of a Texel ewe and a Texel ram, respectively. The first step of the reference sequence assembly involved de novo assembly of 75X reads from the Texel ewe into contigs and scaffolds. Once that was completed, sequences from both animals were used for gap filling. Version 2.0 of the ovine whole-genome reference sequence (Oar v2.0) was publicly released in February, 2011 and Oar v3.1 was released in October, 2012 through NCBI GenBank. For chromosome assemblies go to http://www.ncbi.nlm.nih.gov/assembly/GCA_000298735.1/ and for the full assembly, including scaffolds and contigs not assigned to chromosomes, go to http://www.livestockgenomics.csiro.au/cgi-bin/gbrowse/oarv3.1/. To allow annotation by Ensembl, the ISGC has agreed not to release a new version of the assembly until late 2015, although update patches for some regions will likely be released before then. The RNA dataset produced by Roslin Institute and submitted to Ensembl is the largest transcriptome analysis of any species in Ensembl, including man. A manuscript describing the whole genome assembly (Oar v3.1), the RH map, and the linkage map is in preparation. Highlights of differences between the genome structure of sheep, cattle and goats are included in the manuscript. The analysis of about a terabite of data on the transcriptome is also included. Variation of alleles, allelic imbalance and copy number variation have been included in the manuscript as points of interest. Biological stories include reproduction, digestive tract enzymes, evolution of the rumen, lipid metabolism and evolution of wool. Kim Worley (BCM-HGSC) received funding from a 2013 USDA/AFRI grant to fill gaps in the sheep assembly using PacBio data with PBJelly (scaffolding and gap filling) and Honey (structural variation identification and assembly QC). For sheep, this approach has produced 19x long read data (40 kb max, 8.5 kb N50, and 6 kb mean). Using three rounds of PBJelly 2, analysis has moved the assembly contig N50 from 41.7 kb to over 500 kb and closed 89% of gaps. However, there was only a minor shift in scaffold N50 (from 100.1Mb to 101.2Mb). Improvement of the Y chromosome, which is full of repetitive sequence, will not be possible with this method. The PacBio work will be in Oar v4. Objective 2 (Provide genome mapping resources): An ovine HD (600K) SNP chip was released by Illumina in 2013. Parameters for inclusion of SNPs on the chip were equal spacing (80% of the SNPs), functional, GBS (genotyping by sequencing), literature and 50K chip SNPs (that were not already included under equal spacing). There is still 6K “head room” which can be added by users. The final design provides about 12 SNPs every 50K. There should be little ascertainment bias across breeds; however, there will be bias within breeds. There are a lot of low MAF SNPs on the HD chip so users should not create a cluster file, and instead use the cluster file created with ~3,500 animals and available from Illumina. The SNPs will be deposited in dbSNP by March, 2014. The chip should be useful for GWAS and evolutionary studies, and be moderately useful for imputation.

Publications

Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: The NRSP-8 sheep coordinator is a participant in the International Sheep Genome Consortium (ISGC), a multi-institutional group developing resources needed for genomic research in sheep. The ISGC is now contributing to development of a whole genome reference assembly. In 2010, sequence data were generated at two sequencing facilities (Beijing Genomics Institute and the Roslin Institute) from DNA of a Texel ewe and a Texel ram, respectively. The first step of the reference sequence assembly involved de novo assembly of 75X reads from the Texel ewe into contigs and scaffolds. Once that was completed, sequences from both animals were used for gap filling. PARTICIPANTS: CSIRO Livestock Industries, AgResearch New Zealand, Beijing Genome Institute TARGET AUDIENCES: Researchers PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Several important discoveries in sheep genomics research have been made possible through collaborations established within the NRSP-8 organization. For example, the ovine whole genome reference sequence, which has been supported by NRSP-8 scientists, has been used by several researchers to explore genetic regions of interest that influence the efficiency of sheep production. The whole genome reference sequence is also contributing to studies that use sheep as a biomedical model for diseases in humans.

Publications

• No publications reported this period

Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: The NRSP-8 sheep coordinator is a participant in the International Sheep Genome Consortium (ISGC), a multi-institutional group developing resources needed for genomic research in sheep. The ISGC is now contributing to development of a whole genome reference assembly. In 2010, sequence data were generated at two sequencing facilities (Beijing Genomics Institute and the Roslin Institute) from DNA of a Texel ewe and a Texel ram, respectively. The first step of the reference sequence assembly involved de novo assembly of 75X reads from the Texel ewe into contigs and scaffolds. Once that was completed, sequences from both animals were used for gap filling. PARTICIPANTS: CSIRO Livestock Industries, AgResearch New Zealand, Beijing Genome Institute TARGET AUDIENCES: Researchers PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Version 2.0 of the ovine whole-genome reference sequence (Oar v2.0) was publicly released in February, 2011 and contains 2.71 Gb of sequence. It covers 93.1% of the sheep genome, with 2.57 Gb placed onto chromosomes. This version contains 145K intra-scaffold gaps of 0-2000 bp, 13K intra-scaffold gaps of 2 kb - 20 Kb, and 4,400 inter-scaffold gaps. Of particular concern are gaps in the 5' ends of ~2,000 genes (high GC-content regions). There are also ~100 split scaffolds and ~ 1% inverted contigs. Around 140 Mb of sequence is in unmapped scaffolds.

Publications

• No publications reported this period

Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: The latest release of the sheep genetic linkage map (SM5) contains 2,528 loci across 3,800 cM, with 1,420 unique locations and average marker spacing of 2.5 cM. About 1,100 loci on SM5 were contributed from the 1.5K SNP pilot chip and the rest are primarily microsatellites. Genotypes from the ovine SNP 50K BeadChip generated across the IMF are being analyzed, with over 44,000 SNPs currently assigned to a chromosomal location. The 50K SNP chip has also been typed on two ovine radiation hybrid panels, specifically the 12,000 rad INRA panel and the 5,000 rad USUo5000RH panel. An analysis of these data are ongoing. Reports of this updated linkage map, as well as the current status of the ovine radiation hybrid map, were presented at the NRSP-8, Plant and Animal Genome XIX, and the International Sheep Genomics Consortium (ISGC) meetings in January, 2011. Strategies for publication and recognition of efforts for the sheep genome assembly and whole genome reference sequence were also discussed at the ISGC meeting. PARTICIPANTS: University of New England, Armidale, Genesis Faraday, CSIRO Livestock Industries, AgResearch, University of Melbourne, Purdue University, Oklahoma State University, Washington State University, University of California-Davis, Prairie View A&M, Virginia Tech, USDA-ARS Sheep Experiment Station. TARGET AUDIENCES: Researchers, including members of the NRSP-8 Sheep Committee and the International Sheep Genome Consortium, as well as sheep producers, including those involved with the American Sheep Industry and sheep breed associations. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Updated genetic and radiation hybrid (RH) maps for the sheep were publicly released in 2010. The sheep genetic map contains over 2,450 loci covering 3,800 centimorgans. The current RH map contains 2,167 markers spaced 1.0 to 1.5 megabases apart. The two maps will be applied in studies that use the sheep as a biomedical model or in experiments on economically important traits in sheep. The information contained in these maps is contributing independent and complementary information to the ongoing assembly of the ovine whole genome reference sequence.

Publications

• No publications reported this period

Progress 01/01/09 to 12/31/09

Outputs
OUTPUTS: The International Sheep Genomics Consortium (ISGC), which includes members of the NRSP-8 Sheep Committee, has had noteworthy success in collaboratively developing and distributing resources that advance research in sheep genomics. The first of these resources is the ovine CHORI-243 BAC library, constructed using DNA from a Texel ram. The library contains 202,752 clones with an average insert size of 184 kb and 10-fold genome coverage. BAC end-sequences (BESs) were subsequently generated from the CHORI-243 library, resulting in 376,493 sequences from 193,073 BAC clones. The average BAC end-sequence length is 687 bp, with a range of 64 to 1044 bp. A total of 258,650,691 bp sequence (approximately 6% of the genome) is publicly available. These sequence data were used to develop a comprehensive whole genome physical map for sheep. Specifically, the paired end sequences from the BACs were incorporated into a "virtual sheep genome". Alignment of 84,624 ovine BACs with paired end sequences in the correct orientation and spacing to bovine (bosTau2), human (hg17), and dog (canFam2) genome sequences resulted in 1,172 BAC mega-contigs (BAC-comparative genome contigs or BAC-CGCs). Another ~55K BACs were mapped with lower confidence. Further extension of the virtual genome, using inter-chromosomal breaks and the sheep marker map to orientate the BAC-CGC into their most likely order, resulted in 70% coverage of the sheep genome. A high-density ovine SNP array was released in January, 2009, as the Illumina Ovine SNP50 BeadChip; 3064 sheep from 64 breeds and strains, seven species of wild sheep and nine outgroup species were typed with the BeadChip as part of the world-wide ovine HapMap project, as well as two ovine RH panels and the International Mapping Flock. PARTICIPANTS: University of New England, Armidale, Genesis Faraday, CSIRO Livestock Industries, AgResearch, University of Melbourne, Purdue University, Oklahoma State University, Washington State University, University of California-Davis, Prairie View A&M, Virginia Tech, USDA-ARS Sheep Experiment Station. TARGET AUDIENCES: Researchers, including members of the NRSP-8 Sheep Committee and the International Sheep Genome Consortium, as well as sheep producers, including those involved with the American Sheep Industry and sheep breed associations. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Substantial leveraging of funds and expertise from the International Sheep Genomics Consortium, combined with technological and computational advances in the area of de novo sequence assembly, has contributed significantly to the development of genomics resources that are used by scientists around the world. It is not just the agricultural research community that has benefited from these research tools. The sheep is widely used in biomedical research as a model organism for heart, lung and musculoskeletal diseases. Thus, biomedical researchers are keenly interested in these resources as well.

Publications

• Cockett, N.E., B. P. Dalrymple, J. McEwan, C. Wu, J. Kijas, J. F. Maddox, F. Nicholas, H. Oddy, H. Raadsma, C. Wade, T. Goldammer, A. A 2009. Assembly of the ovine whole genome reference sequence. . Gene Nomenclature Across Species. Cambridge, UK. 2009.

Progress 01/01/08 to 12/31/08

Outputs
OUTPUTS: The NRSP-8 project has been established to promote research in food animal genomics by providing resources and coordination across U.S. researchers, with facilitation provided by the NRSP-8 Species Coordinators. As NRSP-8 Species Coordinator for the Sheep Committee, I facilitate the efforts of sheep genome researchers by seeking the development of genome resources. I also provide updates to the sheep industry on advances and needs within the sheep genome research community. Within the last year, over 9.7 Gbp of sequence from the six sheep has been generated using 454 FLX genome sequencing technology and over 160,000 SNPs have been identified to date using several robust selection criteria, with 180,000 more SNPs expected from the remaining analyses. An additional 180,000 SNPs will be obtained from a Solexa Genome Analyzer sequencing project using reduced representational libraries created from pooled DNA of 60 sheep, with 58,000 SNPs identified so far from those sequence data. The design of an Illumina iSelect Infinium BeadChip containing 60K SNPs has been completed, and the chip is anticipated to be commercially available in January, 2009. Samples from at least 23 sheep breeds from around the world, including 100 Gulf Coast Natives and 100 Rambouillets submitted by Utah State University, will be genotyped with the 60K SNP chip and analyzed for estimates of genome-wide linkage disequilibrium. More details on the SNP project can be found at http://www.sheephapmap.org/. PARTICIPANTS: University of New England, Armidale, Genesis Faraday, CSIRO Livestock Industries, AgResearch, University of Melbourne, Purdue University, Oklahoma State University, Washington State University, University of California-Davis, Prairie View A&M, Virginia Tech, USDA-ARS Sheep Experiment Station. TARGET AUDIENCES: Researchers, including members of the NRSP-8 Sheep Committee and the International Sheep Genome Consortium, as well as sheep producers, including those involved with the American Sheep Industry and sheep breed associations. PROJECT MODIFICATIONS: 1. Create shared genomic tools and reagents and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest. 2. Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes. 3. Develop, integrate and implement bioinformatics resources to support the discovery of genetic mechanisms that underlie traits of interest.

Impacts
Many researchers are establishing projects to identify economic trait loci (ETL) in livestock, including sheep. The development of genomic resources for sheep will greatly enhance the identification of genetic regions influencing economically important traits.

Publications

• Oddy, H., B. Dalrymple, J. McEwan, J. Kijas, B. Hayes, J. van der Werf, D. Emery, P. Hynd, T. Longhurts, T. Fischer, D. Ferguson, R. Fo 2007. SheepGenomics and the International Sheep Genomics Consortium. Proc., 17th AAABG Conference, Armidale, NSW, Australia.
• Notter, D. R., L. Baker, and N. E. Cockett 2007. The outlook for quantitative and molecular genetic applications in improving sheep and goats. Small Ruminant Research 70:1-13.

Progress 01/01/07 to 12/31/07

Outputs
OUTPUTS: The International Sheep Genomics Consortium used Sanger re-sequencing to search for single nucleotide polymorphisms within the sheep genome. A total of 3000 genomic targets were selected from available BAC end sequence (2294) or ESTs (706). Re-sequencing of each was performed using a panel of nine individuals, each drawn from a different breed. The average target size was 510 bp meaning approximately 1.5 Mb of the ovine genome was scanned for the presence of SNP. A total of 6022 SNP were independently identified using two SNP-calling packages. The location of each SNP within the virtual sheep genome, accompanied by access to the aligned sequence reads, is available at www.livestockgenomics.csiro.au/vsheep/. A subset of 1,536 SNPs were selected based on their predicted chromosome positions for genotyping using Illumina's BeadArray platform. SNPs were selected to represent every ovine chromosome (OAR) with an average of 56 SNPs per chromosome ranging from one SNP on OARY to 151 SNPs on OAR1. The SNP markers were evaluated for Mendelian inheritance, and genotyping was performed on the International Mapping Flock and the USUoRH5000 radiation hybrid panel in order to integrate the SNPs into the ovine linkage reference and radiation hybrid maps. PARTICIPANTS: University of New England, Armidale, NSW 2351, Australia; Genesis Faraday, Roslin BioCentre, Roslin, Midlothian, EH25 9PS, UK; CSIRO Livestock Industries, Brisbane, Queensland 4067, Australia; AgResearch, Invermay Agricultural Centre PB 50034, Mosgiel, NZ; Department of Veterinary Science, University of Melbourne, Victoria 3010, Australia. TARGET AUDIENCES: Researchers PROJECT MODIFICATIONS: A renewal of the NRSP-8 project has been submitted.

Impacts
The International Sheep Genome Consortium (ISGC) is composed of scientists, commodity organizations and funding agencies from Australia, France, Kenya, New Zealand, United Kingdom and United States, including the NAGRP Sheep Genome Coordinator. The ISGC emphasizes the development of public genome resources that contribute to the sheep genome map and ultimately lead to a completely sequenced ovine genome.

Publications

• Oddy, H., B. Dalrymple, J. McEwan, J. Kijas, B. Hayes, J. van der Werf, D. Emery, P. Hynd, T. Longhurts, T. Fischer, D. Ferguson, R. Fo 2007. SheepGenomics and the International Sheep Genomics Consortium. .. Proc., 17th AAABG Conference, Armidale, NSW, Australia.
• Notter, D. R., L. Baker, and N. E. Cockett 2007. The outlook for quantitative and molecular genetic applications in improving sheep and goats. . Small Ruminant Research 70:1-13.
• Cockett, N. E., T. S. Hadfield, C. H. Wu and K. Nomura 2006. Resources available for sheep genomics research. Amer. Soc. Anim. Science, A231.
• Cockett, N. E. 2006. The Sheep Genome. In: Structure and Evolution of Vertebrate Genomics. Editor: J. N. Volff. Karger, 78-85.
• Qin, Y., J. Wetherall, K. Munyard, N. Cockett and D. Groth 2006. Polymorphic loci within the ovine MHC central region. 30th International Conference on Animal Genetics, B490.

Progress 01/01/06 to 12/31/06

Outputs
Identification of specific genes and genetic markers associated with economically important traits will have a significant impact on U.S. livestock production. In addition, many aspects of livestock genome projects will contribute to human genetic research. The NRSP-8 project has been established to promote research in this area by providing resources and coordination. Through partnership with the International Sheep Genomics Consortium (ISGC), the NRSP-8 Species Coordinator for Sheep has contributed to genome resources in sheep, including a high coverage BAC library, end-sequencing of 100% of the BAC library, high and moderate resolution radiation hybrid panels, full coverage linkage maps, an integrated ovine genetic map, a whole genome BAC physical map, and development of a virtual sheep genome (http://www.livestockgenomics.csiro.au/vsheep/). In addition, over 180,000 ESTs have been generated and assembled into expressed sequence contigs (McEwan et al. personal communication). Information collated to date is currently being used to generate SNPs and a sheep HapMap through a resequencing approach (http://www.sheephapmap.org/). All information has been placed in the public domain through NCBI (http://www.ncbi.nlm.nih.gov/genome/guide/sheep/index.html).

Impacts
The role of NAGRP and the U.S. Sheep Genome Coordinator is to facilitate development of genomic resources in sheep, leading to the identification of economic trait loci (ETL) in sheep. Increased efficiency of sheep production in the US, including around 7 million sheep, is expected.

Publications

• Bidwell, C. A., N. E. Cockett, J. F. Maddox, and J. E. Beever (2007) Genome Mapping in Sheep. In: Genome Mapping in Animals: Food and Fiber Animals. Editors: C. Kole and N. E. Cockett. Springer Publishers, Germany (accepted).

Progress 01/01/05 to 12/31/05

Outputs
Identification of specific genes and genetic markers associated with economically important traits will have a significant impact on U.S. livestock production. In addition, many aspects of livestock genome projects will contribute to human genetic research. The NRSP-8 project has been established to promote research in this area by providing resources and coordination. The purpose of the NRSP-8 Species Coordinator for Sheep is to enhance and promote research in sheep genome mapping. In the coming year, support of the sheep coordinator activities will continue and development of new resources will be funded. Ovine radiation hybrid panel: Coordination funds have contributed to the development of an ovine radiation hybrid panel by Texas A&M University. Markers are now being typed on the panel at Utah State University as well in four other international laboratories. Ovine BAC library: Funds from the Coordinator have been used to construct the CHORI-243 ovine BAC library. Arrayed filters suitable for screening the BAC library are available from the coordinator. Ovine BAC end sequences: Over 376,000 BAC-end sequences (BES) have been obtained from 193,073 of the clones within the CHORI-243 library. The sequences are now being ordered against the bovine and human genome sequences. These sequence data, publicly available at http://www.ncbi.nlm.nih.gov/genome/guide/sheep/index.html, will be used to develop a whole genome physical map for sheep.

Impacts
The role of the NRSP-8 Sheep Genome Coordinator is to facilitate development of genomic resources in sheep, leading to the identification of economic trait loci (ETL) in sheep. Increased efficiency of sheep production in the US, including around 7 million sheep, is expected.

Publications

• Brenig, B., T. E. Broad, N. E. Cockett and A. Eggen (2004) Achievements of Research in the Field of Molecular Genetics. In: The World Association for Animal Production, Book of the Year for 2003. Wageningen Academic Publishers, The Netherlands pp. 73-84.

Progress 01/01/04 to 12/31/04

Outputs
Identification of specific genes and genetic markers associated with economically important traits will have a significant impact on U.S. livestock production. In addition, many aspects of livestock genome projects will contribute to human genetic research. The NRSP-8 project has been established to promote research in this area by providing resources and coordination. The purpose of the NRSP-8 Species Coordinator for Sheep is to enhance and promote research in sheep genome mapping. In the current year, support of the sheep coordinator activities will continue and development of new resources will be funded. Informational database: SheepBase contains an up-to-date compilation of published data from sheep genome mapping projects. Coordinator funds have been used to continue curation of the database. Genetic markers: A collection of 450 ovine and bovine microsatellite primer pairs that have been mapped to specific ovine chromosomes have been selected by the Coordinator for distribution to researchers mapping traits in sheep. Ovine radiation hybrid panel: Coordination funds have contributed to the development of an ovine radiation hybrid panel by Texas A&M University. Markers are now being typed on the panel at Utah State University. Ovine BAC library: Funds from the Coordinator have been used to construct an ovine BAC library suitable for BAC end sequencing, which will commence in the coming year.

Impacts
Many researchers are establishing projects to identify economic trait loci (ETL) in livestock. The development of a genome map for sheep will greatly enhance the identification of genetic regions influencing economically important traits in sheep. The role of NAGRP and the U.S. Sheep Genome Coordinator is to facilitate the development of the ovine genome map, leading to the identification of ETL in sheep.

Publications

• No publications reported this period

Progress 01/01/03 to 12/31/03

Outputs
Identification of specific genes and genetic markers associated with economically important traits will have a significant impact on U.S. livestock production. In addition, many aspects of livestock genome projects will contribute to human genetic research. The NRSP-8 project has been established to promote research in this area by providing resources and coordination. The purpose of the NRSP-8 Species Coordinator for Sheep is to enhance and promote research in sheep genome mapping. In the current year, support of the sheep coordinator activities will continue and development of new resources will be funded. Informational database: SheepBase contains an up-to-date compilation of published data from sheep genome mapping projects. Coordinator funds have been used to continue curation of the database. Genetic markers: A collection of 450 ovine and bovine microsatellite primer pairs that have been mapped to specific ovine chromosomes have been selected by the Coordinator for distribution to researchers mapping traits in sheep. Ovine radiation hybrid panel: Coordination funds have contributed to the development of an ovine radiation hybrid panel by Texas A&M University. Markers are now being typed on the panel at Utah State University. Ovine BAC library: Funds from the Coordinator have been used to construct an ovine BAC library suitable for fingerprinting and BAC end sequencing.

Impacts
Many researchers are establishing projects to identify economic trait loci (ETL) in livestock. The development of a genome map for sheep will greatly enhance the identification of genetic regions influencing economically important traits in sheep. The role of NAGRP and the U.S. Sheep Genome Coordinator is to facilitate the development of the ovine genome map, leading to the identification of ETL in sheep.

Publications

• Liu, W-S., C. W. Beattie, N. E. Cockett and F. A. Ponce de Leon (2004) Comparative analysis of 38 bovine Y-chromosome microsatellites in cattle, sheep and goats. Proc., Plant and Animal Genome XII (abstract).

Progress 01/01/02 to 12/31/02

Outputs
Identification of specific genes and genetic markers associated with economically important traits will have a significant impact on U.S. livestock production. In addition, many aspects of livestock genome projects will contribute to human genetic research. The NRSP-8 project has been established to promote research in this area by providing resources and coordination. The purpose of the NRSP-8 Species Coordinator for Sheep is to enhance and promote research in sheep genome mapping. In the current year, support of the sheep coordinator's past activities will continue and development of new resources will be funded. Informational database: SheepBase contains an up-to-date compilation of published data from sheep genome mapping projects. Coordinator funds have been used to continue curation of the database. Genetic markers: A collection of 450 ovine and bovine microsatellite primer pairs that have been mapped to specific ovine chromosomes have been selected by the Coordinator for distribution to researchers mapping traits in sheep. Ovine radiation hybrid panel: Coordination funds have contributed to the development of an ovine radiation hybrid panel by Texas A&M University. Characterization of the panel will be done at Utah State University. Ovine BAC library: Funds from the Coordinator have been used to construct an ovine BAC library suitable for BAC fingerprinting and eventual sequencing of the ovine genome.

Impacts
Many researchers are establishing projects to identify economic trait loci (ETL) in livestock. The development of a genome map for sheep will greatly enhance the identification of genetic regions influencing economically important traits in sheep. The role of NAGRP and the U.S. Sheep Genome Coordinator is to facilitate the development of the ovine genome map, leading to the identification of ETL in sheep.

Publications

• Bidwell, C. A., T. L. Shay, M. Georges and N. E. Cockett (2002) Expression of PEG11 transcripts in the muscles of normal and callipyge lambs (Ovis aries). Proc., 27th International Conference on Animal Genetics p. 51.
• Cockett, N. E., T. L. Shay, C. A. Bidwell and M. Georges (2002) Genetics of obesity: studies in sheep. Intern. J. Obesity 26(Suppl. 1): S105.

Progress 01/01/01 to 12/31/01

Outputs
Identification of specific genes and genetic markers associated with economically important traits will have a significant impact on U.S. livestock production. In addition, many aspects of livestock genome projects will contribute to human genetic research. The NRSP-8 project has been established to promote research in this area by providing resources and coordination. The purpose of the NRSP-8 Species Coordinator for Sheep is to enhance and promote research in sheep genome mapping. In the current year, support of the sheep coordinator's past activities will continue and development of new resources will be funded. Informational database: SheepBase contains an up-to-date compilation of published data from sheep genome mapping projects. Coordinator funds have been used to continue curation of the database. Genetic markers: A collection of 450 ovine and bovine microsatellite primer pairs that have been mapped to specific ovine chromosomes have been selected by the Coordinator for distribution to researchers mapping traits in sheep. Ovine radiation hybrid panel: Coordination funds have contributed to the development of an ovine radiation hybrid panel by Texas A&M University. Characterization of the panel will be done at Utah State University.

Impacts
Many researchers are establishing projects to identify economic trait loci (ETL) in livestock. The development of a genome map for sheep will greatly enhance the identification of genetic regions influencing economically important traits in sheep. The role of NAGRP and the U.S. Sheep Genome Coordinator is to facilitate the development of the ovine genome map, leading to the identification of ETL in sheep.

Publications

• Cockett, N. E., T. L. Shay and M. A. Smit. 2001. Analysis of the sheep genome. Physiol. Genomics (in press).
• Cockett, N. E. and G. D. Snowder. 2001. Genetic influences on carcass merit of sheep. J. Anim. Sci. 79 (Suppl. 1): 99.

Progress 01/01/00 to 12/31/00

Outputs
Identification of specific genes and genetic markers associated with economically important traits will have a significant impact on U.S. livestock production. In addition, many aspects of livestock genome projects will contribute to human genetic research. The NRSP-8 project has been established to promote research in this area by providing resources and coordination. The purpose of the NRSP-8 Species Coordinator for Sheep is to enhance and promote research in sheep genome mapping. In the current year, support of the sheep coordinator's past activities will continue and development of new resources will be funded. Distributed markers: Distribution of microsatellite markers will continue. The panel of markers will be expanded to provide 10 cM coverage of the ovine genome. Ovine BAC library: Additional clones will be added to the ovine BAC library recently constructed, in order to increase genome coverage (currently at 1.5 genome equivalents). Distribution and screening of the library will occur as requested by researchers. A physical mapping project using the BAC library is ongoing. A panel of chromosome-specific clones will soon be available for those doing physical mapping experiments. Ovine radiation hybrid panel: A radiation hybrid (RH) panel specific to sheep will be constructed. While the currently available bovine RH panels are often used in sheep projects, many ovine-derived STSs do not amplify bovine DNA and therefore, cannot be incorporated into a radiation hybrid map. An ovine-specific RH panel would allow the development of ovine RH maps without loss of information. Databases: The informational database, SheepBase, will be enhanced by adding links to various species databases.

Impacts
Many researchers are establishing projects to identify economic trait loci (ETL) in livestock. The development of a genome map for sheep will greatly enhance the identification of genetic regions influencing economically important traits in sheep. The role of NAGRP and the U.S. Sheep Genome Coordinator is to facilitate the development of the ovine genome map, leading to the identification of ETL in sheep.

Publications

• No publications reported this period

Progress 01/01/99 to 12/31/99

Outputs
Identification of specific genes and genetic markers associated with economically important traits will have a significant impact on U.S. livestock production. In addition, many aspects of livestock genome projects will contribute to human genetic research. During the last five years, advances in livestock genome mapping have been remarkable. The NRSP-8 project has been established to promote research in this area by providing resources and coordination. The purpose of the NRSP-8 Species Coordinator for Sheep is to enhance and promote research in sheep genome mapping. In the current year, support of the sheep coordinator's past activities will continue and development of new resources will be funded. Distributed markers: Distribution of microsatellite markers will continue. The panel of markers will be expanded to provide 10 cM coverage of the ovine genome. Ovine ESTs: To facilitate the development of ovine ESTs, construction of normalized cDNA libraries and sequencing of individual clones will be funded. Emphases will be placed on tissues that are of economical importance in the sheep, such as muscle, reproductive organs and mammary gland. A centralized database will be established for collection of EST mapping data. Ovine BAC library: Additional clones will be added to the ovine BAC library recently constructed, in order to increase genome coverage (currently at 1.5 genome equivalents). Distribution and screening of the library will occur as requested by researchers. A physical mapping project using the BAC library is ongoing. A panel of chromosome-specific clones will soon be available for those doing physical mapping experiments. Databases: The informational database, SheepBase, will be enhanced by adding links to various species databases.

Impacts
The development of a genome map for sheep will greatly enhance the Identification of genetic regions influencing economically important traits in sheep. The role of NAGRP and the U.S. Sheep Genome Coordinator is to facilitate the development of the ovine genome map, leading to the identification of economically important loci in sheep.

Publications

• Cockett, N.E. 1999. Genomics of sheep. AgBiotech Net 1:1-3.

Progress 01/01/98 to 12/31/98

Outputs
Identification of specific genes and genetic markers associated with economically important traits will have a significant impact on U.S. livestock production. In addition, many aspects of livestock genome projects will contribute to human genetic research. During the last five years, advances in livestock genome mapping have been remarkable. In order to continue these advancements, it is imperative that livestock mapping research be supported. The NRSP-8 project has been established to promote research in this area by providing resources and coordination to enhance and promote research in sheep genome mapping. Distributed markers: Distribution of microsatellite markers will continue. The panel of markers will be expanded to provide 10 cM coverage of the ovine genome. Also, m13-29 base extensions will be added to a subset of the markers, to allow for labeling of the markers that will be used in automated genotyping systems. Ovine ESTs: To facilitate the development of ovine ESTs, construction of normalized cDNA libraries and sequencing of individual clones will be funded. Emphases will be placed on tissues that are of economical importance in the sheep, such as muscle, reproductive organs and mammary gland. A centralized database will be established for collection of EST mapping data. Ovine BAC library: Additional clones will be added to the ovine BAC library recently constructed, in order to increase genome coverage (currently at 1.5 genome equivalents). Distribution and screening of the library will occur as requested by researchers. A physical mapping project using the BAC library is ongoing. A panel of chromosome-specific clones will soon be available for those doing physical mapping experiments. Databases: The informational database, SheepBase, will be enhanced by adding links to various species databases.

Impacts
(N/A)

Publications

• Gill, C. A., Davis, S.K., Taylor, J.D., Cockett, N.E. and Bottema, C.D.K. 1998. A set of ovine bacterial artificial chromosomes for accurate physical mapping in Bovidae. Proc., XXVI Inter. Conf. Anim. Genet. p. 57.

Progress 01/01/97 to 12/31/97

Outputs
To date, about 555 loci have been mapped to all 26 autosomal chromosomes and both sex chromosomes of sheep. Of these assignments, about 167 loci have been done through physical mapping and about 388 through family linkage analyses. In the current linkage map, 15% are candidate genes and 85% are random markers. The current sheep map spans nearly 2700 centiMorgans. The SheepBase informational database is now available, containing an up-to-date compilation of published data from sheep genome mapping projects, along with both physical and linkage maps of the sheep genome, together with information on individual loci and associated references. Information is presented using the WWW interface and can be accessed through a number of nodes (e.g., http://dirk.invermay.cri.nz). A collection of 223 ovine and bovine microsatellite primer pairs that have been mapped to specific ovine chromosomes have been selected for distribution. These markers were selected because of their coverage of the sheep genome. To date, the markers have been distributed to 17 laboratories world-wide and used in projects investigating wool traits, carcass composition, parasite resistance, growth characteristics and single-gene defects. For more information on these primers, contact fanoelle@cc.usu.edu.

Impacts
(N/A)

Publications

• COCKETT, N.E. 1997. Chapter 10. Developmental genetics. pp. 413- 436. IN: L. Piper and A. Ruvinsky (eds.) The genetics of the sheep. CAB International, Wallingford, United Kingdom.

Progress 01/01/96 to 12/30/96

Outputs
In summarizing the current ovine genome map, about 555 loci have been mapped to all 26 autosomal chromosomes and both sex chromosomes of sheep. Of these assignments, about 167 loci (31% of all assignments) have been done through physical mapping (in situ hybridization and somatic cell hybrids) and about 388 (69%) through family linkage analyses. In the current linkage map, 57 (15%) are candidate genes and 331 (85%) are random markers. The current sheep map spans 2662 centiMorgans. About 185 markers are shared between the sheep and cattle linkage maps. An informational database that includes mapped loci in sheep is now available. SheepBase contains an up-to-date compilation of published data from sheep genome mapping projects and provides both physical and linkage maps of the sheep genome, together with information on individual loci and associated references. Information is presented using the WWW interface and can be accessed through a number of nodes: AgResearch (New Zealand): (http://dirk.invermay.cri.nz), the Roslin Institute (United Kingdom): (http://www.ri.bbsrc.ac.uk/genome-mapping.html), and the National Agricultural Library (U.S.): (http://tetra.gig.usda.gov:8400/). The current version of SheepBase contains about 467 loci gathered from 114 publications. There are about 173 Type I loci, 269 Type II loci and 25 other loci (such as blood group polymorphisms) currently in the database.

Impacts
(N/A)

Publications

• COCKETT, N.E. 1996. Developmental Genetics. In: Genetics of the Sheep. L. Piper and A. Ruvinsky (Eds.). CAB International, UK. (accepted).
• COCKETT, N.E. AND MEDRANO, J. 1996. Development and use of the sheep genome map.In: Biotech. Role in the Genetic Improvement of Farm Animals. R.H. Miller, G. Pursel and D. Norman. Amer. Soc. of A. Sci., Savoy, IL. pp. 81-90.
• COCKETT, N.E. 1996. Use of genetic markers for characterization of single gene traits. Proceed., National Sheep Genetics Symposium, pp. 161-165.

Progress 01/01/95 to 12/30/95

Outputs
Investigators on the NRSP-8 Sheep Technical Committee have emphasized the fat content and lean composition of lamb products. A collaborative project between Utah State University and the U.S. Sheep Experiment Station has studied the callipyge gene that affects both the production efficiency and quality of meat in sheep. In addition to the identification of a genetic marker linked to this gene, several markers were assigned to ovine chromosome 18 in their study. The University of California research team has demonstrated that the RAPD assay is a powerful approach for identifying polymorphisms useful for constructing a sheep genetic linkage map. Laboratory and data analysis protocols established in this project will facilitate applications to other livestock and domestic animal species. This research team is also investigating the high growth (hg) locus in mice. The region encompassing hg maps to bovine chromosome 5, pig chromosome 5 and sheep chromosome 3. The fine map of hg should enable studies of these homologous regions in domestic animal species and may lead to identification of important growth genes. Previous studies have established that the Gulf Coast Native sheep breed is more resistant to Haemonchus contortus infection than the Suffolk breed. The goal of the Louisiana State University study is to identify genetic markers that are associated with this resistance, which in turn will place loci responsible for the resistance on the sheep genome map.

Impacts
(N/A)

Publications

• COCKETT, N.E. AND MEDRANO, J. 1995. Development and use of the sheep genome map. Beltsville Symposium XX: Biotechnology's Role in the Genetic Improvement of Farm Animals (in press).

Progress 01/01/94 to 12/30/94

Outputs
A sheep reference population has been established at the USDA/ARS U.S. Meat Animal Research Center (MARC). Four large half-sib families have produced 247 offspring and include two Romanov x Rambouillet rams mated to 21 Romanov ewes, producing 135 lambs, and two Romanov x Suffolk rams mated to 22 Romanov ewes, producing 112 offspring. The RAPD-PCR methodology has been optimized to analyze sheep DNA, with polymorphisms detected in 142 RAPD markers. During the next year, a laboratory will run 50 of these RAPD markers. Construction of an ovine YAC library is ongoing. A genetic region that will be targeted within the YAC library is the telomeric end of ovine chromosome 21. It has been demonstrated that the callipyge gene, which is responsible for muscle hypertrophy in sheep, maps to this region. Several projects characterizing traits of sheep carrying the callipyge mutation are being conducted. A project has been initiated using techniques for in situ hybridization and physical mapping in sheep. Dynamic and G-banding methods suitable for prometaphase/metaphase chromosomes have been established.

Impacts
(N/A)

Publications

• COCKETT, N. E., BUNCH, T. D., MEDRANO, J. F., SNOWDER, G. D., KEELE, J., LEYMASTER, K. AND BEATTIE, C. (1994) Current status of the ovine genome map. J. Anim. Sci. 72(Suppl. 1):102.