2011 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 along with collaborating institutions continued as global leaders for production of DNA sequence information from ruminant species. ARS directly contributed all the sequence for both international efforts to assembly genomes for tropical cattle (Bos indicus) and water buffalo. More details can be found in report for sub-projects 1265-3100-098-28T and 36T, respectively. ARS also generated additional sequence to improve the quality of the existing bovine genome assembly, re-sequence important Holstein patriarchs, and identify causative mutations underlying Weaver disease (a late-onset degenerative neuromuscular disease in dairy cattle) and Slick hair coat (heat tolerance) traits. The Holstein genome sequencing and Weaver mapping are also objectives in sub-projects.
ARS Scientists continued to develop research tools to better inform breed conservation, genetic improvement, and test parentage discovery for nations undergoing development of sustainable production systems. Multiple partnerships were initiated to develop inexpensive (<$10) single nucleotide polymorphism (SNP) assays available for parentage discovery (<1000 markers). A second effort included development of a new commercial beadchip assay for genetic prediction in dairy cattle containing approximately 6,000 markers. A third effort included redefining the gene space of the genome (2% of the genome) to develop targeted enrichment assays to discover new SNP in genes by resequencing. The gene space was identified by aligning RNAseq (gene sequence) data from cDNA onto the reference genome. This information is being provided to other publicly available databases (Bovine Genome Annotation, Gene Atlas, and InnateDB) to provide better annotations (definitions) of gene boundaries and expression patterns in cattle.
A systematic analysis of copy number variations (CNV) was performed using the Bovine HapMap SNP genotyping data. The analysis included more than 777,000 marker genotypes for each of 539 animals from 21 modern cattle breeds and 6 other ruminant species. This same HapMap SNP data was used to initiate studies to identify signatures of selection (genes fixed for milk, meat, coat color, horns, etc.) in these cattle breeds. The analysis was extended to look for SNP or CNV differences between tropical and temperate-adapted cattle in Africa, Brazil, and the U.S.
In conjunction with scientific partners in Brazil, ARS initiated a project to test whole genome selection for beef cattle raised in a tropical production environment. Initial activities included completion of experimental design and genotyping of the core population to determine the extent of admixture and linkage disequilibrium in Nellore cattle of Brazil.
We identified a 4.82 million base pair fragment of genome on Chr 4 containing the late onset degenerative neuro-muscular disease in dairy cattle called Weaver syndrome. This refined mapping of the locus better identifies animals, which carry this autosomal recessive disease. The methodologies used to better map Weaver have also led to creation of our first genomics unified schema (GUS) database: where phenotype, genotype, DNA genome sequence, and gene annotation information are combined to better analyze large complex data sets. Our new haplotype signature should provide a new diagnostic test that is more reliable than the previous single-marker test used by the industry for screening animals since 1995.
We identified 682 candidate copy number variations (CNV) regions, which represent 139.8 megabases (~4.60%) of the genome. Many CNV regions (~56%) overlap with cattle genes (1,263), which are significantly enriched for immunity, lactation, reproduction, and rumination. We also reported an initial analysis of CNV in cattle selected for resistance or susceptibility to intestinal nematodes. We identified 20 CNV in total, of which 12 were within known chromosomes harboring or adjacent to gains or losses. Pathway and transcription factor binding sites analyses indicated that annotated cattle genes within these variable regions are particularly enriched for immune function affecting receptor activities, signal transduction, and transcription. These results provide a valuable foundation for future studies gene variants underlying economically important health and production traits.
Supported genomics research at Beltsville, other ARS locations, EMBRAPA (Brazil) and Mississippi State University 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 have been highlighted by other researchers through the discovery of differential gene expression in soybeans, SNP discovery in catfish, metagenomic studies in swine and cattle, defining important gene locations for cattle, and genome sequence for water buffalo, cattle, and other important animal species. Access to these technologies for other scientists has catapulted genomics research in ARS and with its research partners at other institutions.
The results of our continued leadership in development of the commercial genotyping tools (BovineSNP50, BovineHD, Bovine3K-Illumina, and BOS1-Affymetrix) continue to have a major impact on livestock research and the dairy AI industry. Awareness of the success in genotype tool development and application to genomic research in cattle fueled development of an additional SNP beadchip (BovineLD-Illumina). We co-led development of this product, and its impact on the industry is anticipated to be high as it replaces the Bovine3K assay in the marketplace. We also developed the first sequence based genotyping tool (BovineExome-Agilent) for high-resolution genetic characterization. Because this product is not commercially available yet, its impact remains unknown. The BovineSNP50 assay continues to be the global de facto standard for cattle genomics research and genetic prediction use with sales having surpassed 700,000 samples.
Chung, H.Y., Mcclure, M.C. 2011. Effects of SNPs from the differentially expressed swine odorant binding protein (OBP) gene on average daily gain. Journal of Applied Animal Research. 39(1):1-4.
Flury, C., Tapio, M., Sonstegard, T.S., Drogemuller, C., Leeb, T., Simianer, H., Hanotte, O., Rieder, S. 2010. Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium. Journal of Animal Breeding and Genetics. 127:339-347.
Hou, Y., Liu, G., Bickhart, D.M., Cardone, M.F., Wang, K., Kim, E., Matukumalli, L., Ventura, M., Song, J., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P. 2011. Genomic characteristics of cattle copy number variations. Biomed Central (BMC) Genomics. 12:127.
Liu, G., Brown, T.E., Hebert, D.A., Cardone, M.F., Hou, Y., Choudhary, R.K., Shaffer, J.F., Amazu, C., Connor, E.E., Ventura, M., Gasbarre, L.C. 2010. Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes. Mammalian Genome. 22:111-121.
Dalloul, R.A., Long, J.A., Zimin, A.V., Reed, K.M., Blomberg, L., Van Tassell, C.P., Schroeder, S.G., Sonstegard, T.S., Aslam, L., Beal, K., Biedler, J., Burt, D.W., Crasta, O., Crooijmans, R.P., Cooper, K., Coulombe, R.A., De, S., Delany, M.E., Dodgson, J.B., Dong, J.J., Evans, C., Flicek, P., Florea, L., Folkerts, O., Groenen, M.A., Harkins, T.T., Herrero, J., Hoffmann, S., Megens, H., Jiang, A., Jong, P., Kaiser, P., Kim, H., Kim, K., Kim, S., Langenberger, D., Lee, M., Lee, T., Mane, S., Marcais, G., Marz, M., Mcelroy, A.P., Modise, T., Nefedov, M., Notredame, C., Paton, I.R., Payne, W.S., Pertea, G., Prickett, D., Puiu, D., Qioa, D., Raineri, E., Salzberg, S.L., Schatz, M.C., Scheuring, C., Schmidt, C.J., Schroeder, S.G., Smith, E.J., Smith, J., Sonstegard, T.S., Stadler, P.F., Tafer, H., Tu, Z., Van Tassell, C.P., Vilella, A.J., Williams, K., Yorke, J.A., Zhang, L., Zhang, H., Zhang, Z., Zhang, Y. 2010. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo) genome assembly and analysis. PLoS Biology. 8(9):e1000475.
Harhay, G.P., Smith, T.P.L., Alexander, L.J., Haudenschild, C.D., Keele, J.W., Matukumalli, L.K., Schroeder, S.G., Van Tassell, C.P., Gresham, C.R., Bridges, S.M., Burgess, S.C., Sonstegard, T.S. 2010. An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. Genome Biology [online serial]. 11:R102.
Kuehn, L.A., Keele, J.W., Bennett, G.L., Mcdaneld, T.G., Smith, T.P., Snelling, W.M., Sonstegard, T.S., Thallman, R.M. 2011. Predicting breed composition using breed frequencies of 50,000 markers from the U.S. Meat Animal Research Center 2,000 bull project. Journal of Animal Science. 89:1742-1750.