2012 Annual Report
1a.Objectives (from AD-416):
Objective 1: Develop biological resources and computational tools to enhance characterization of the bovine genome sequence.
Objective 2: Use genotypic data and resulting bovine haplotype map to enhance genetic improvement in dairy cattle through development and implementation of whole genome selection and enhanced parentage verification approaches.
Objective 3: Characterize conserved genome elements and identify functional genetic variation.
1b.Approach (from AD-416):
Completion of our objectives is expected, in the short term, to result in development and implementation of genome-wide selection. Ultimately the longer term objective of QTN discovery to better understand livestock biology will require a combination of quantitative genetics, LD-MAS, genome annotation, and gene expression analyses, all of which are components of this proposal and areas of expertise in our group. Efforts to characterize genome activity and structure conservation and variation are an extension of our current research program in QTL mapping and bioinformatics. This proposal completely leverages the resources derived from the Bovine Genome and HapMap projects, for which the authors of this proposal have played prominent roles. As more of the genetic variation for a specific trait is explained, a better understanding of pleiotropic and epistatic gene action will be needed. This knowledge will be developed through characterizing changes at a very fine level combined with studies of animals with known genotype associated with phenotypes resulting from selection programs. Tools used in this characterization are likely to include, but not be limited to, gene expression patterns, protein expression or structural changes, or regulatory changes.
ARS scientists continued as global leaders for production of DNA sequence information from ruminant species contributing all the sequence for international efforts to assemble genomes and single nucleotide polymorphism (SNP) discovery for Bos indicus cattle and water buffalo. ARS generated and analyzed additional whole-genome sequence to identify causative mutations affecting fertility haplotypes HH1 in Holsteins, JH1 in Jerseys, and Weaver disease in Brown Swiss.
ARS Scientists continued to develop and use new genomic tools for selection. One effort included development of a new 9K SNP assay for genetic prediction (Neogen’s GGP) of dairy genomic breeding values, imputation of parentage microsatellite markers, and testing of multiple genetic diseases. A third effort included testing commercial assays that collect sequence information from the gene space (exome) of the cattle genome. Exome sequence from the genome-sequencing cow was contributed to improving the genome assembly. Exome sequence was generated to find mutations for lethal haplotypes HH2 and HH3 in Holsteins and BH1 in Brown Swiss.
ARS continued to characterize tropical adaptation by genotyping more than 400 cattle from Africa and SW Asia and more than 1,400 improved beef lines of tropically adapted cattle using 700K SNP genotypes. This effort included searching for the causal mutation affecting the dominant trait for SLICK hair coat, which has a phenotype for greater tolerance to heat stress. The mutation is within a 1 Mbp portion of Chromosome 20, and sequencing has identified 38 candidate mutations in this region. Using a computational approach based on next-generation sequencing, genome-wide copy number variation (CNV) differences among 1 indicine (tropically adapted) and 5 taurine animals. We identified 1,265 CNV regions comprising ~56 Mbp of sequence, and 38% were not reported previously. We validated these findings (82%) using 3 other laboratory methods. Some genes related to pathogen and parasite resistance were highly duplicated in the indicine animal relative to the taurine cattle, while genes involved in lipid transport and metabolism were highly duplicated in the beef breeds. These results suggest there are CNV underlying breed-specific differences in adaptation, health, and production traits.
Over the life of this project, significant progress was made to develop genomic tools in cattle that could be applied to increase the rate of genetic improvement. This included the first implementation of genome selection, which revolutionized the way genetic progress is made in the dairy industry on a global scale. ARS scientists also developed novel methods for SNP discovery from next-generation sequencing data and SNP assay design for selection tools that were used by others in multiple species of agricultural importance. Finally, ARS scientists revealed the power of genomic data on finding lethal recessive mutations that affect fertility. In conclusion, this work points out the importance of genomic tools for genetic improvement. The next phase is to develop these tools for other ruminant production paradigms to help secure the global food supply.
Developed low-cost genotyping tools for genomic predictions of genetic merit. Better low-cost tools for genotyping were needed to improve efficiency for genomic predictions from less SNP information and to encompass parentage and other important DNA tests for the industry in a single genotyping tool. The results of our continued leadership in development of two new, low-cost commercial genotyping tools (BovineLD-Illumina and Neogen’s GGP) continue to have a major impact on livestock research and the dairy AI industry. These tools also have the capabilities of helping producers to transition from “old” parentage markers to SNP-based parentage through imputation of microsatellite genotypes. Combined, the North American dairy industry used these new products and the BovineSNP50 that we developed in 2007 at a rate of more than 12,000 assays per month to generate genome-based predictions of genetic merit on young animals. The BovineSNP50 and BovineHD assays developed over the duration of this project continue to the global de facto standard for cattle genomics genetic prediction and research, respectively.
Created a highly accurate DNA test for Weaver. Weaver is a neurodegenerative disease afflicting mostly Brown Swiss cattle, and a previously designed diagnostic test was not completely accurate. ARS scientists identified a 67 thousand base-pair fragment of the genome on bovine chromosome 4 containing the mutation causing Weaver syndrome. This refined mapping of the locus identified more than 10 “normal” animals that carry this autosomal recessive disease. The SNP-based haplotype signature will be used by breeders in the U.S. and Italy to more reliably screen animals for this disease.
Discovered genome copy number variation (CNV) potentially affecting tropical adaptation and metabolism. Previously, no tangible links between CNV and phenotype differences in cattle were known. ARS scientists, using complex next-generation sequences for the whole genomes of six animals, completed the first comprehensive discovery of CNV. The methods used to find these CNV were validated to be highly accurate. Comparison of CNV regions between indicine and taurine DNA samples were linked to genes associated with health and production traits including fertility, parasite resistance, and feed efficiency. These results are a major step forward in basic research to identify some of the components affecting genetic variance beyond SNP, which are not accounted for in current genetic evaluation systems.
Led genomic research and support within ARS. Sequence-based approaches to genetics and biological discovery are important methods for ground-breaking discoveries in agricultural research. BFGL scientists supported genomics research within ARS and with national and international collaborators in a multitude of species and applications. We provided scientific, computing, labor, and bioinformatic support for projects at various locations that wanted to incorporate next-generation sequencing applications into their investigations. Over the past year, our efforts were highlighted by other researchers through genome sequence for water buffalo, cattle, catfish, catfish pathogens, wood rot fungus, and other important animal species. Access to these technologies for other scientists has catapulted genomics research within ARS and other research institutions.
Identified mutations affecting dairy cow fertility. Extensive genotyping of U.S. dairy populations has revealed portions of the genome that appear to contain lethal mutations causing embryonic death during pregnancy. ARS scientists discovered the causative mutations underlying two of these recessive lethal mutations in the Holstein and Jersey cattle breeds. The mutation in Holsteins known as HH1 caused a knock-out of a gene necessary for normal neural tube development. Loss of this gene causes spontaneous abortion after the first trimester. This work was done in conjunction with the University of Illinois. The mutation in Jerseys known as JH1 caused a knock-out of a gene important in regulating proper RNA splicing. Loss of this gene causes spontaneous abortion during the first trimester of pregnancy. DNA tests for both mutations are now available to producers. Results are being used to guide future mating decisions in both breeds, thus lowering the rate of infertility caused by embryonic loss.
Partipilo, G., D'Addabbo, P., Lacalandra, G.M., Liu, G., Rocchi, M. 2011. Refinement of Bos taurus sequence assembly based on BAC-FISH experiments. Biomed Central (BMC) Genomics. 12:639.
Cole, J.B., Wiggans, G.R., Ma, L., Sonstegard, T.S., Lawlor, T.J., Crooker, B.A., Van Tassell, C.P., Yang, J., Wang, S., Matukumalli, L.K., Da, Y. 2011. Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows. Biomed Central (BMC) Genomics. Online, 12:408.
Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L.K., Song, J., Schnabel, R.D., Ventura, M., Taylor, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Eichler, E.E., Liu, G. 2012. Copy number variation of individual cattle genomes using next-generation sequencing. Genome Research. 22(4):778-90.
Tang, J.D., Perkins, A.D., Sonstegard, T.S., Schroeder, S.G., Burgess, S.C., Diehl, S.V. 2012. Short read sequencing for Genomic Analysis of the brown rot fungus Fibroporia radiculosa. Applied and Environmental Microbiology. 78(7):2272-81.
McDaneld, T.G., Kuehn, L.A., Thomas, M.G., Snelling, W.M., Sonstegard, T.S., Matukumalli, L.K., Smith, T.P., Pollak, E.J., Keele, J.W. 2012. Y are you not pregnant: identification of Y chromosome segments in female cattle with decreased reproductive efficiency. Journal of Animal Science. 90(7):2142-2151.
Boichard, D., Chung, H., Dassonneville, R., David, X., Eggen, A., Fritz, S., Gietzen, K.J., Hayes, B.J., Lawley, C.T., Sonstegard, T.S., Van Tassell, C.P., Van Raden, P.M., Viaud, K., Wiggans, G.R. 2012. Design of a bovine low-density SNP array optimized for imputation. PLoS One. 7(3):e34130.
Veneroni- Gouveia, G., Meirelles, S.L., Grossi, D.A., Santiago, A.C., Sonstegard, T.S., Yamagishi, M.B., Matukumalli, L.K., Coutinho, L.L., Alencar, M.M., Oliveira, H.N., Regitano, L.A. 2011. Whole genome analysis for backfat thickness in a tropically adapted, composite cattle breed from Brazil. Animal Genetics. DOI: 10.1111/j.1365-2052.2011.02286.x.