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United States Department of Agriculture

Agricultural Research Service

Research Project: Enhancing Genetic Merit of Ruminants Through Genome Selection and Analysis

Location: Animal Genomics and Improvement Laboratory

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

The JH1 Haplotype-a newly discovered marker for infertility in the jersy breed - (Popular Publication)
(18-Jun-14)
The SLICK Locus derived from Senepol cattle confers thermotolerance to Intensively-Managed lactating Holstein cows - (Peer Reviewed Journal)
(20-May-14)
Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions - (Book / Chapter)
(14-May-14)
The identification of a putative mutation for SLICK hair coat in Senepol cattle - (Abstract Only)
(05-May-14)
Genome-wide identification of signatures of positive selection in African admixed zebu cattle - (Abstract Only)
(02-May-14)
Using genomics for genetic improvement and discovery of adaptive traits for climate change - (Abstract Only)
(02-May-14)
Recent advances in studying of copy number variation and gene expression - (Peer Reviewed Journal)
Liu, G., Xu, L., Huang, K.S. 2014. Recent advances in studying of copy number variation and gene expression. Gene Expression. 7:1-5 DOI:10.4137/GGG.S14286.
MicroRNA content in milk exosomes as a phenotypic indicator of Staphylococcus aureus infection in the bovine mammary gland - (Abstract Only)
Jiajie, S., Kshama, A., Schroeder, S.G., Reinhardt, T.A., Lippolis, J.D., Sonstegard, T.S. 2014. MicroRNA content in milk exosomes as a phenotypic indicator of Staphylococcus aureus infection in the bovine mammary gland. BARC Poster Day, Poster 61, pp. 73.
Computational analysis of bovine milk exosomal miRNAs profiles derived from uninfected and Streptococcus uberis infected mammary gland - (Abstract Only)
Aswath, K., Jiajie, S., Schroeder, S.G., Reinhardt, T.A., Lippolis, J.D., Sonstegard, T.S. 2014. Computational analysis of bovine milk exosomal miRNAs profiles derived from uninfected and Streptococcus uberis infected mammary gland. BARC Poster Day, Poster 62, pp. 74.
Assessment of inbreeding depression in Nellore cows (Bos indicus) through high-density SNP genotypes - (Abstract Only)
Zavarez, L.B., Utsunomiya, Y.T., Sonstegard, T.S., Garcia, J.F. 2014. Assessment of inbreeding depression in Nellore cows (Bos indicus) through high-density SNP genotypes. BARC Poster Day, Poster 59, pp. 71.
Genome-Wide scans for carcass and meat traits in nellore cattle - (Abstract Only)
Pereira, A.G., Utsunomiya, Y.T., Sonstegard, T.S., Castilli, C., Garcia, J.F. 2014. Genome-Wide scans for carcass and meat traits in nellore cattle. BARC Poster Day, Poster 34, pp. 46.
Evidence of common signatures of selection in the genomes of West African cattle and the Yoruba human population - (Abstract Only)
Utsunomiya, Y.T., Sonstegard, T.S., Hanotte, O., Van Tassell, C.P., Garcia, J.F. 2014. Evidence of common signatures of selection in the genomes of West African cattle and the Yoruba human population. BARC Poster Day, Poster 66, pp.78.
Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins - (Abstract Only)
Xu, L., Cole, J.B., Bickhart, D.M., Hou, Y., Song, J., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2014. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. BARC Poster Day. BARC Poster Day.p.67, abstract 54.
Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle - (Peer Reviewed Journal)
Huson, H., Eui-Soo, K., Godfrey, R.W., Olson, T.A., Mcclure, M., Chase, C.C., Rizzi, R., Perez O'Brien, A., Van Tassell, C.P., Garcia, J., Sonstegard, T.S. 2014. Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle. Frontiers in Livestock Genomics. 5:101.
Population sequencing reveals breed and sub-species specific CNVs in cattle - (Abstract Only)
Bickhart, D.M., Xu, L., Hutchison, J.L., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Fernando Garcia, J., Taylor, J.F., Schnabel, R.D., Lewin, H.A., Liu, G. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. CONFERENCE ON THE BIOLOGY OF GENOMES. Conference on the Biology of Genomes, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. p199.
Progress report – African goat genome and genetic improvement project - (Other)
(01-Apr-14)
Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle - (Peer Reviewed Journal)
Cesar, A., Regitano, L., Tullio, R.R., Lannal, D., Nassu, R.T., Mudado, M.A., Oliveira, P., Nascimento, M., Chaves, A., Alencar, M.M., Sonstegard, T.S., Garrick, D., Reecy, J.M., Coutinho, L.L. 2014. Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle. BioMed Central (BMC) Genetics. 15(1):39.
Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects HH2, HH3, and BH1 reveals causative mutation in SMC2 for HH3     Reprint Icon - (Peer Reviewed Journal)
Mc Clure, M., Bickhart, D.M., Null, D.J., Van Raden, P.M., Xu, L., Wiggans, G.R., Liu, G., Schroeder, S.G., Glasscock, J., Armstrong, J., Cole, J.B., Sonstegard, T.S., Van Tassell, C.P. 2014. Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects HH2, HH3, and BH1 reveals causative mutation in SMC2 for HH3. PLoS One. 9(3):e92769.
Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu (EASZ) - (Peer Reviewed Journal)
Mbole-Kariuki, M., Sonstegard, T.S., Orth, A., Thumbi, S.M., Bronsvoort, B.S., Kiara, H., Toye, P., Conradie, I., Jennings, A., Coetzer, K., Woolhouse, M.J., Hanotte, O., Tapio, M. 2014. Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu (EASZ). Heredity. DOI:10.1038/hdy.2014.31.
An atlas of DNA methylation in diverse bovine tissues - (Abstract Only)
Liu, G. 2013. An atlas of DNA methylation in diverse bovine tissues. Meeting Abstract. The Clinical Epigenome Conference Program Guide. p.17.
A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle - (Peer Reviewed Journal)
Xu, L., Hou, Y., Bickhart, D.M., Song, J., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2014. A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle. Functional and Integrative Genomics. DOI: 10.1007/s10142-014-0371-6.
Gene expression profiles of bovine mammary epithelial cells and association with milk composition traits using RNA-seq - (Peer Reviewed Journal)
Cui, X., Hou, Y., Sun, D., Zhang, S., Lv, X., Liu, G., Zhang, Y., Zhang, Q. 2014. Gene expression profiles of bovine mammary epithelial cells and association with milk composition traits using RNA-seq. Biomed Central (BMC) Genomics 15:226.
Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle - (Peer Reviewed Journal)
Decker, J.E., Mckay, S.D., Rolf, M.M., Kim, J., Alcala, A., Sonstegard, T.S., Hanotte, O., Gotherstrom, A., Seabury, C.M., Praharani, L., Babar, M., Regitano, L. ., Yildiz, M., Heaton, M.P., Lui, W., Lei, C., Reecy, J.M., Saif-Ur-Rehman, M., Schnabel, R.D., Taylor, J.F. 2014. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genetics. 10(3):e1004254.
Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle - (Peer Reviewed Journal)
Perez O'Brien, A.M., Utsunomiya, Y.T., Meszaros, G., Bickhart, D.M., Liu, G., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Solkner, J. 2014. Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle. Genetics Selection Evolution. 46:19.
Genome-wide mapping of loci explaining variance in scrotal circumference in Nellore cattle     Reprint Icon - (Peer Reviewed Journal)
Utsunomiya, Y.T., Do Carmo, A.S., Neves, H.H., Carvalheiro, R., Matos, M.C., Zavarez, L.B., Rauschkolb Katsuda I, P., Perez Obrien, A.M., Solkner, J., Porto Neto, L.R., Schenkel, F.S., Mcewan, J., Cole, J.B., Da Silva, M., Van Tassell, C.P., Sonstegard, T.S., Garcia, J. 2014. Genome-wide mapping of loci explaining variance in scrotal circumference in Nellore cattle. PLoS One. 9(2):e88561.
The USDA Feed the Future Initiative for genetic improvement of African goats: an update on genomic resources and genetic characterization of indigenous breeds - (Abstract Only)
Sonstegard, T.S. 2014. The USDA Feed the Future Initiative for genetic improvement of African goats: an update on genomic resources and genetic characterization of indigenous breeds. Plant Animal Genome XXII, paper W430, pp. 161.
Population sequencing reveals breed and sub-species specific CNVs in cattle - (Abstract Only)
Liu, G., Bickhart, D.M., Xu, L., Hutchison, J.L., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Garcia, J., Taylor, J.F., Schnabel, R.D., Lewin, H.A. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. Meeting Abstract. Advances in Genome Biology & Technology Conference Meeting Abstract. p.58.
Genome-wide detection of signatures of selection in Korean Hanwoo cattle - (Peer Reviewed Journal)
Porto-Neto, L., Lee, S., Sonstegard, T.S., Van Tassell, C.P., Lee, H., Gondro, C. 2014. Genome-wide detection of signatures of selection in Korean Hanwoo cattle. Animal Genetics. 45(2):180-190.
Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression - (Peer Reviewed Journal)
Murray, G., Woolhouse, M., Tapio, M., Mbole-Kariuki, M.N., Sonstegard, T.S., Thumbi, S., Jennings, A., Conradie Van Wyk, I., Kiara, H., Toye, P., Coetzer, K., Bronsvoort, B.S., Hanotte, O. 2013. Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression. Heredity. 13:246.
Identification and characterization of MicroRNAs expressed in chicken skeletal muscle - (Peer Reviewed Journal)
Andreote, A., Rosario, M.F., Ledur, M.C., Jorge, E.C., Sonstegard, T.S., Matukumalli, L., Countinho, L.L. 2014. Identification and characterization of MicroRNAs expressed in chicken skeletal muscle. Genetics and Molecular Research. 13(1):1465-1479.
Effect of artificial selection on runs of Homozygosity in U.S. Holstein cattle     Reprint Icon - (Peer Reviewed Journal)
Kim, E., Cole, J.B., Huson, H.J., Wiggans, G.R., Van Tassell, C.P., Crooker, B.A., Liu, G., Da, Y., Sonstegard, T.S. 2013. Effect of artificial selection on runs of Homozygosity in U.S. Holstein cattle. PLoS One. PLoS One.2013 Nov 14;8(11):e80813.
A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle - (Abstract Only)
Liu, G., Xu, L., Hou, Y., Bickhart, D.M., Song, J., Van Tassell, C.P., Sonstegard, T.S. 2013. A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle. BA-UMD Symposium. The University of Maryland/Beltsville ARS 3rd Annual Symposium.
Accuracy of genomic predictions in Nellore beef cattle - (Proceedings)
Carvalheiro, R., Mcewan, J.C., Neves, H., Utsunomiya, Y.T., Perez O'Brien, A.M., Boison, A., Solkner, J., Schenkel, F., Van Tassell, C.P., Sonstegard, T.S., Garcia, F. 2013. Accuracy of genomic predictions in Nellore beef cattle. Genetics Selection Evolution. 20:171-174.
A genome scan for meat quality in Nelore beef cattle - (Peer Reviewed Journal)
Tizioto, P.C., Decker, J.E., Taylor, J.F., Schnabel, R.D., Mudadu, M.A., Silva, F.L., Mourao, G.B., Coutinho, L.L., Tholon, P., Sonstegard, T.S., Rosa, A.N., Alencar, M.M., Tullio, R.R., Medeiros, S.R., Nassu, R.T., Feijo, G., Silva, L., Torres, R.A., Siqueira, F., Higa, R.H., Regitano, L. 2013. A genome scan for meat quality in Nelore beef cattle. Physiological Genomics. 45(21):1012-1020.
Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds - (Peer Reviewed Journal)
Mcclure, M.C., Sonstegard, T.S., Wiggans, G.R., Van Eenennaam, A., Weber, K., Penedo, M., Berry, D.P., Flynn, J., Garcia, J., Santana Do Carmo, A., Regitano, L., Albuquerque, M., Silva, M.V., Machado, M.A., Coffey, M., Moore, K., Boscher, M., Genestout, L., Mazza, R., Taylor, J.F., Schnabel, R., Simpson, B., Marques, E., Mc Ewan, J., Cromie, A., Lehmann Coutinho, L., Kuehn, L.A., Keele, J.W., Piper, E., Cook, J., Williams, R., Hap Map Consortium, B., Van Tassell, C.P. 2013. Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds. Frontiers in Genetics. 4:176. DOI.10.3389/fgene.2013.00176.
Goat breeding in the tropics: development and application of the genomic tools in a USAID "Feed the Future" program - (Proceedings)
Sayre, B.L., Sonstegard, T.S., Silverstein, J., Huson, H.J., Woodward-Greene, J., Rothschild, M., Nene, V., Denis Mujibi, F., Masiga, C., Fernando Garcia, J., Solkner, J., Van Tassell, C.P. 2013. Goat breeding in the tropics: development and application of the genomic tools in a USAID "Feed the Future" program. Meeting Proceedings. 1983-4357.
Structural and functional impacts of copy number variations on the cattle genome - (Abstract Only)
Liu, G., Bickhart, D.M. 2013. Structural and functional impacts of copy number variations on the cattle genome (abstract). Lecture. p.3.
What have we learned from the current state of genomics in livestock? - (Other)
(05-Jun-13)
Genome-wide association study for birth weight Brazilian Nellore cattle (Bos primigenuis indicus) points to previously described orthologous genes affecting human and bovine height     Reprint Icon - (Peer Reviewed Journal)
Utsunomiya, Y.T., Carmo, A.S., Carvalheiro, R., Neves, H.H., Matos, M.C., Zavarez, L.B., O'Brien, A.M., Solkner, J., Mcewan, J., Cole, J.B., Van Tassell, C.P., Schenkel, F.S., Silva, M.V., Porto Neto, L., Sonstegard, T.S., Garcia, J.F. 2013. Genome-wide association study for birth weight Brazilian Nellore cattle (Bos primigenuis indicus) points to previously described orthologous genes affecting human and bovine height. BioMed Central (BMC) Genetics. 13:14-52.
Comparative analysis of CNV calling algorithms: literature survey and a case study using bovine high-density SNP data - (Review Article)
Xu, L., Hou, Y., Bickhart, D.M., Jiuzhou, S., Liu, G. 2013. Comparative analysis of CNV calling algorithms: literature survey and a case study using bovine high-density SNP data. Microarrays. 2(3):171-185.
Applied genomics: Tools ranging from genomic prediction to bioconservation - (Other)
(06-May-13)
Applied Genomics in Cattle – Identification of the SLICK locus in tropically adapted cattle - (Other)
(02-May-13)
African goat improvement project: a Feed the Future initiative harnessing genetic diversity for conservation, disease resistance, and improved productivity - (Abstract Only)
(05-Apr-13)
Analysis of population structure and genetic history of cattle breeds based on high-density SNP data - (Abstract Only)
Xu, L., Huson, H.J., Hou, Y., Bickhart, D.M., Song, J., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2013. Analysis of population structure and genetic history of cattle breeds based on high-density SNP data. BARC Poster Day. p.55 Abstract 48.
Adaptmap: International Coordinated Data Resource for Improving Goat Production Effiency - (Other)
(27-Mar-13)
High overlap of CNVs and selection signatures revealed by varLD analyses of taurine and zebu cattle - (Abstract Only)
Perez O'Brien, A., Meszaros, G., Utsunomiya, Y., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Solkner, J. 2013. High overlap of CNVs and selection signatures revealed by varLD analyses of taurine and zebu cattle. Book of Abstracts of the 64th Annual Meeting of the European Association for Animal Production, Nantes, France 2013 pp.604.
Applied genomics in ruminants-new discoveries and model for predictive medicine - (Other)
(04-Mar-13)
Genomic divergence of indicine and taurine cattle identified through high-density SNP genotyping - (Abstract Only)
Porto-Neto, L.R., Sonstegard, T.S., Mcclure, M.C., Bickhart, D.M., Gondro, C., Da Silva, M., Utsunomiya, Y.T., Garcia, J.F., Van Tassell, C.P. 2013. Genomic divergence of indicine and taurine cattle identified through high-density SNP genotyping. J. Anim. Sci. Vol. 91, E-Suppl. 2/J. Dairy Sci. Vol. 96, E-Suppl. 1, paper 314, pp. 314.
Mapping cattle copy number variations in water buffalo - (Abstract Only)
Liu, G., Bickhart, D.M. 2013. Mapping cattle copy number variations in water buffalo. Meeting Abstract. W115.
Combined arms: a full spectrum approach to structural variant discovery in livestock populations - (Abstract Only)
Bickhart, D.M., Liu, G. 2013. Combined arms: a full spectrum approach to structural variant discovery in livestock populations. Meeting Abstract. W145.
African goat improvement project: A feed the future initiative harnessing genetic diversity for conservation, disease resistance, and improved productivity - (Other)
(10-Jan-13)
Progress report- African goat genome and genetic improvement project - (Other)
(10-Jan-13)
African goat improvement project: A feed the future initiative harnessing geneticdiversity for conservation, disease resistance, and improved productivity - (Abstract Only)
Huson, H.J., Sonstegard, T.S., Silverstein, J., Sayre, B., Woodward Greene, M.J., Rothschild, M., Nene, V., Mujibi, D., Kemp, S., Masiga, C., Mubiru, S., Garcia, F., Soelkner, J., Van Tassell, C.P. 2013. African goat improvement project: A feed the future initiative harnessing geneticdiversity for conservation, disease resistance, and improved productivity. Plant ANimal Genome XXI, paper W416, pp. 171.
Admixture and linkage disequilibrium analysis of meat goat breeds - (Abstract Only)
Sayre, B., Soelkner, J., Van Tassell, C.P., Sonstegard, T.S. 2013. Admixture and linkage disequilibrium analysis of meat goat breeds. Plant Animal Genome XXI, paper PO711, pp. 251.
Microsatellite Imputation for parental verification from SNP across multiple Bos taurus and indicus breeds - (Abstract Only)
Mcclure, M.C., Sonstegard, T.S., Van Tassell, C.P., Wiggans, G.R., Van Eenennaam, A., Weber, K., Penedo, C., Berry, D., Flynn, J., Fernando Garcia, J., Santa, A., Regitano, L., Albuquerque, M., Silva, M., Coffey, M., Moore, K., Boscher, M., Genestout, L., Mazza, R., Taylor, J., Schnabel, R., Machado, M.A., Simpson, B., Mcewan, J., Cromie, A., Countinho, L.L., Kuehn, L.A., Keele, J.W., Piper, E., Cook, J., Marques, E. 2013. Microsatellite Imputation for parental verification from SNP across multiple Bos taurus and indicus breeds. Plant Animal Genome XXI, paper PO132, pp. 206.
Population analysis of 60 worldwide cattle breeds using high-density (700k)SNP genotyping - (Abstract Only)
Huson, H.J., Sonstegard, T.S., Soelkner, J., Mustafa, H., Mukasa, C., Nash, O., Bradely, D., Van Tassell, C.P. 2013. Population analysis of 60 worldwide cattle breeds using high-density (700k)SNP genotyping. Plant Animal Genome XXI, paper PO524, pp. 237.
Multi-platform next generation sequencing of a high quality genome assembly for the goat - (Abstract Only)
Sonstegard, T.S., Smith, T.P., Schroeder, S.G., Huson, H.J., Zimin, A., Woodward Greene, M.J., Mujibi, D.F., Mcclure, M.C., Silverstein, J., Van Tassell, C.P., Sayre, B.L. 2013. Multi-platform next generation sequencing of a high quality genome assembly for the goat. Plant Animal Genome XXI, paper W417, pp. 171.
Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads - (Abstract Only)
Schroeder, S.G., Zimin, A., Bickhart, D.M., Sonstegard, T.S., Van Tassell, C.P., Garcia, F.J. 2013. Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads. Poster P0523, pp.237.
Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping - (Peer Reviewed Journal)
Porto-Neto, L.R., Sonstegard, T.S., Liu, G., Bickhart, D.M., Gondro, C., Silva, M., Machado, M., Utsunomiya, Y.T., Garcia, J.F., Van Tassell, C.P. 2013. Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping. Biomed Central (BMC) Genomics. DOI:10.1186/1471-2164-14-876.
Genomics and parentage identification/verification - (Other)
(03-Dec-12)
Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads - (Abstract Only)
(27-Nov-12)
Last Modified: 10/23/2014
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