Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.

The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

Funding priorities in animal reproduction at the United States Department of Agriculture's Cooperative State Research, Education, and Extension Service.

The National Research Initiative (NRI) Competitive Grants Program is the U.S. Department of Agriculture's major competitive grants program and is administered by the Cooperative State Research, Education, and Extension Service (CSREES). Since its inception in 1991, the NRI has funded competitive grants in the discipline of animal reproduction. Previously, this program provided funding for a broad range of projects encompassing almost every subdiscipline in reproductive biology of farm animals, including aquatic species important to the aquaculture industry. During fiscal year 2004, the NRI Animal Reproduction Program narrowed the focus of funding priorities to the topics of infertility, basic mechanisms regulating fertility, cryopreservation of gametes, reducing the postpartum interval to conception, and sterilization methods or development of monosex populations. In response to a directive to further narrow the focus of funding priorities for fiscal year 2005 and beyond, CSREES conducted a Stakeholder Workshop on Funding Priorities in Animal Reproduction at the 37th Annual Meeting of the Society for the Study of Reproduction in Vancouver, Canada. More than 75 stakeholder scientists from a cross section of federal, public, and private institutions from across the United States participated in the workshop and provided recommendations to CSREES for future NRI-funding priorities in Animal Reproduction. The recommendations provided by stakeholders included continuing efforts to focus funding priorities into fewer high-impact areas relevant to animal agriculture and aquaculture. Recommendations also included movement back toward subdisciplines of animal reproduction that cut across all applicable species. The three funding priorities that consistently emerged as recommendations from the workshop participants were 1) gonadal function and production of gametes, 2) pituitary-hypothalamic function, and 3) embryo and conceptus development, including interaction between the conceptus and uterus. These funding priorities were considered when preparing the fiscal year 2006 NRI Request for Applications.

Allerton III. Beyond livestock genomics.

Throughout the Allerton III Conference, several consistent research needs were identified across scientific disciplines. First, additional basic research is needed to identify genomic mechanisms and novel genes/proteins in a variety of tissues under different conditions. Second, expansion of the infrastructure of the scientific community is needed. This can best be accomplished by additional competitive grants programs for training grants, program project grants, and multidisciplinary research projects. Third, the need for improved tools for animal bioinformatics was emphasized. Fourth, competitive grants programs for extension/outreach efforts and application of genomic technologies to production systems are needed. Finally, efforts to publicize and document the benefits of animal genomics for improved human health and animal production systems to members of Congress and the general public should be enhanced.

USDA Stakeholder Workshop on Animal Bioinformatics: Summary and Recommendations.

An electronic workshop was conducted on 4 November-13 December 2002 to discuss current issues and needs in animal bioinformatics. The electronic (e-mail listserver) format was chosen to provide a relatively speedy process that is broad in scope, cost-efficient and easily accessible to all participants. Approximately 40 panelists with diverse species and discipline expertise communicated through the panel e-mail listserver. The panel included scientists from academia, industry and government, in the USA, Australia and the UK. A second 'stakeholder' e-mail listserver was used to obtain input from a broad audience with general interests in animal genomics. The objectives of the electronic workshop were: (a) to define priorities for animal genome database development; and (b) to recommend ways in which the USDA could provide leadership in the area of animal genome database development. E-mail messages from panelists and stakeholders are archived at http://genome.cvm.umn.edu/bioinfo/. Priorities defined for animal genome database development included: (a) data repository; (b) tools for genome analysis; (c) annotation; (d) practical application of genomic data; and (e) a biological framework for DNA sequence. A stable source of funding, such as the USDA Agricultural Research Service (ARS), was recommended to support maintenance of data repositories and data curation. Continued support for competitive grants programs within the USDA Cooperative State Research, Education and Extension Service (CSREES) was recommended for tool development and hypothesis-driven research projects in genome analysis. Additional stakeholder input will be required to continuously refine priorities and maximize the use of limited resources for animal bioinformatics within the USDA.