2009 Annual Report
Genotyped 5,000 dairy cattle on the BovineSNP50 chip to further refine genome enhanced predictions of genetic merit across dairy breeds and identify signatures of selection in Holsteins. Another 1,000 genomic DNA samples were extracted from semen and blood. Completed commercial implementation of genotyping by guiding AIPL, service providers, NAAB members, and 3 breed associations in standardization of commercially-produced genotypes. Continued development of alternative methods for estimating genome-enhanced genetic predictions. Completed identification of genomic signatures of selection, and results show that selection for milk yield has led to an increase in alleles negatively affecting fertility. Mapped the osteopetrosis disease locus to a 7-Mbp region of Chr 4 using the SNP50 genotypes from ~60 Angus DNA samples. Developed a commercial diagnostic test for a genetic variant of the SLC4A2 gene that is the probable disease causing mutation in collaboration with USMARC, Univ. of Illinois, Univ. of Nebraska, and the Red Angus Association of America.
A systematic study of the cattle copy number variation (CNV) was completed using two oligonucleotide CGH arrays designed and fabricated from the bovine genome assemblies. Over 110 hybridizations identified approximately 229 CNV regions under stringent criteria. Selected CNV were confirmed by realtime qPCR and FISH.
With the bovine genome consortium, completed the first genome-wide analyses of segmental duplication (SD). Selected SD events were confirmed by FISH and we determined ~3.1% (92 Mbp) of the cattle genome consists of SD.
Developed a method based on previous work in primates to further classify and refine common repeat phylogeny in livestock. Initial testing in chicken identified 57 CR1 subfamilies and one novel turkey-specific CR1 subfamily. Results expand understanding of repeat evolution and potential function to the genome architecture. Led to development of an established software framework to further analyze the repeats in cattle. Done in collaboration with University of Maryland.
Completed mapping and expression analysis of >300 million digital gene expression (DGE) sequence tags representing a quantitative gene expression from 100 different tissues of the genome sequencing cow and her relatives. A Gbrowse database was created and made publicly available through AgBase under a specific cooperative agreement with Mississippi State University. Developed additional data visualization tools based on Shannon entropy plots and Mondrian. Done in collaboration with USMARC and LARRL.
Zhang, W., Ding, J., Qu, Y., Hu, H., Lin, M., Datta, A., Larson, A., Liu, G., Li, B. 2008. Genomic expression analysis by single-cell mRNA differential display of quiescent CD8 T cells from tumor-infiltrating lymphocytes obtained from in vivo liver tumours. Immunology. 127(1):83-90. Liu, G., Weirauch, M., Van Tassell, C.P., Li, R.W., Sonstegard, T.S., Matukumalli, L.K., Connor, E.E., Hanson, R.W., Yang, J. 2008. Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter. Genomics, Proteomics and Bioinformatics. 6(3-4):129-143. Yu, Y., Zhang, H.M., Byerly, M.S., Bacon, L.D., Porter, T.E., Liu, G.E., Song, J. 2009. Alternative Splicing Variants and DNA Methylation Status of BDNF in Inbred Chicken Lines. Brain Research. 1269(7):1-10. Liu, G., Alkan, C., Zhao, S., Eichler, E.E. 2009. Comparative Analysis of Alu Repeats in Primate Genomes. Genome Research. 19(5):876-885. Van Raden, P.M., Van Tassell, C.P., Wiggans, G.R., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Schenkel, F.S. 2009. Invited Review: Reliability of Genomic Predictions for North American Holstein Bulls. Journal of Dairy Science. 92(1):16-24. Wiggans, G.R., Sonstegard, T.S., Van Raden, P.M., Matukumalli, L.K., Schnabel, R.D., Taylor, J.F., Schenkel, F.S., Van Tassell, C.P. 2009. Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and Canada. Journal of Dairy Science. 92(7):3431-3436. Cole, J.B., Van Raden, P.M., O'Connell, J.R., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Wiggans, G.R. 2009. Distribution and Location of Genetic Effects for Dairy Traits. Journal of Dairy Science. 92(6):2931-2946. McDaneld, T.G., Smith, T.P., Doumit, M.E., Miles, J.R., Coutinho, L.L., Sonstegard, T.S., Matukumalli, L.K., Nonneman, D.J., Wiedmann, R.T. 2009. MicroRNA Transcriptome Profiles During Swine Skeletal Muscle Development. Biomed Central (BMC) Genomics. 10:77. Liu, G., Jiang, L., Tian, F., Zhu, B., Song, J. 2009. Calibration of mutation rates reveals diverse subfamily structure of galliform CR1 repeats. Genome Biology and Evolution. 2009:119-130. Wang, S., Sha, Z., Sonstegard, T.S., Liu, H., Xu, P., Somridhavej, B., Peatmen, E., Kucuktas, H., Liu, Z. 2008. Quality assessment parameters for EST-derived SNPs from catfish. Biomed Central (BMC) Genomics. 30(9):450. Liu, G. 2009. Applications and Case Studies of the Next-Generation Sequencing Technologies in Food, Mutrition and Agriculture. Recent Patents on Food, Nutrition & Agriculture. 1(1):75-79. Matukumalli, L.K., Lawley, C.T., Schnabel, R.D., Taylor, J.F., Allan, M.F., Heaton, M.P., O'Connell, J., Moore, S.S., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P. 2009. Development and Characterization of a High Density SNP Genotyping Assay for Cattle. PLoS One. 4(4):e5350. Available: http://dx.doi.org/10.1371/journal.pone.0005350. Elsik, C.G., Gibbs, R., Skow, L., Tellam, R., Weinstock, G., Worley, K., Kappes, S.M., Green, R.D., Alexander, L.J., Bennett, G.L., Carroll, J.A., Chitko Mckown, C.G., Hamernik, D.L., Harhay, G.P., Keele, J.W., Liu, G., Macneil, M.D., Matukumalli, L.K., Rijnkels, M., Roberts, A.J., Smith, T.P., Snelling, W.M., Stone, R.T., Waterman, R.C., White, S.N. 2009. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution. Science. 324:522-528. Liu, G., Li, R.W., Sonstegard, T.S., Matukumalli, L.K., Silva, M.V., Van Tassell, C.P. 2008. Characterization of a novel microdeletion polymorphism on BTA5 in cattle. Animal Genetics. 39(6):655-658. Gibbs, R., Van Tassell, C.P., Weinstock, G.M., Green, R.D., Hamernik, D.L., Kappes, S.M., Liu, G., Matukumalli, L.K., Matukumalli, A., Sonstegard, T.S., Silva, M.V. 2009. Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds. Science. 24:528-532. Regitano, L.C., Ibelli, A.M., Gasparin, G., Miyata, M., Azevedo, A.L., Coutinho, L.L., Teodoro, R.L., Machado, M.A., Silva, M.V., Nakata, L.C., Zaros, L.G., Sonstegard, T.S., Silva, A.M., Alencar, M.M., Oliveira, M.C. 2008. On the search for markers of tick resistance in bovines. Developments in Biologicals. 132:225-230. Mckay, S.E., Schnabel, R.D., Murdoch, B.M., Matukumalli, L.K., Aerts, J., Coppieters, W., Crews, D., Neto, E.D., Gill, C.A., Gao, C., Mannen, H., Wang, Z., Van Tassell, C.P., Williams, J.L., Taylor, J.F., Moore, S.S. 2008. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. Journal of Animal Breeding and Genetics. 20(9):37. Mckay, S.D., Schnabel, R.D., Murdoch, B.M., Matukumalli, L.K., Aerts, J., Coppieters, W., Crews, D., Neto, E.D., Gill, C.A., Gao, C., Mannen, H., Stothard, P., Wang, Z., Van Tassell, C.P., Williams, J.L., Taylor, J.F., Moore, S.S. 2007. Whole genome linkage disequilibrium maps in cattle. Journal of Animal Breeding and Genetics. 25(8):74. Tellam, R.L., Lemay, D.G., Van Tassell, C.P., Lewin, H.A., Worley, K.C., Elsik, C.G. 2009. Unlocking the bovine genome. BioMed Central (BMC) Genetics. 24(10):193. Zimin, A.V., Delcher, A.L., Florea, L., Kelley, D.R., Schatz, M.C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C.P., Sonstegard, T.S., Marcais, G., Roberts, M., Subramanian, P., Yorke, J.A., Salzberg, S.L. 2009. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology. 10(4):R42. Villa-Angulo, R., Matukumalli, L.K., Gill, C.A., Choi, J., Van Tassell, C.P., Grefenstette, J.J. 2009. High-resolution haplotype block structure in the cattle genome. Journal of Animal Breeding and Genetics. 24(10):19.