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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Research Project #423740


Location: Animal Genomics and Improvement Laboratory

2014 Annual Report

The long-term objective of this project is to enhance selection in target ruminant populations by integrating traditional, quantitative-based selection methods with DNA marker-based tools. To successfully meet this objective and better understand the underlying gene networks affecting phenotypic variation, basic research to characterize both genome structure and activity must be done as a complementary effort. Objective 1: Develop biological resources and computational tools to enhance characterization of ruminant genomes. De novo reference genome assemblies will be developed for Zebu cattle (Bos indicus), goat (Capra hircus), and water buffalo (Bos bubalis). In addition, improvements will be made to the existing reference assembly for Bos taurus cattle. These reference genome resources are essential for discovery of single nucleotide polymorphisms (SNP) and copy number variation (CNV) polymorphisms commonly segregating in target populations. Objective 2: Utilize novel genotypic and environmental data to enhance genetic improvement of food animals across a spectrum of ruminant production systems,including the following: SNP markers or haplotype information to identify signatures of natural and artificial selection; novel marker array panels to generate adapted goat genetic lines for extreme environments that improve animal survival, fertility and growth; and "whole herd" molecular pedigree information to further increase the accuracy and speed of genetic improvement for animal populations. Objective 3: Characterize functional genetic variation for improved fertility and environmental sustainability of ruminants.

Completion of the objectives is expected, in the short term, to improve methods of genome-wide selection in the U.S. dairy industry as well as initiate new genome-enhanced breeding strategies to bring economic and genetic stability to various ruminant value chains in developing nations. Ultimately, longer term objectives to identify and understand how causative genetic variation affects livestock biology will require a combination of genome resequencing and comparative genome alignment and annotation, quantitative genetics, and gene expression analyses, all of which are components of this project plan and areas of expertise in the group. Efforts to characterize genome activity and structural conservation/variation are an extension of the current ARS/BA research program in applied genomics. This project plan completely leverages the resources derived from the Bovine and Caprine Genomes and HapMap and ADAPTmap projects and genotypic data derived from both the official USDA genome enhanced genetic evaluations for North American dairy cattle and African Goat Improvement Network under the Feed the Future Initiative.

Progress Report
Under Objective 1, ARS scientists in Beltsville, MD continued as global leaders for production of genome sequence information from ruminant species by completing a de novo genome assembly of Bos indicus and attempting the first mammalian genome assembly based solely on caprine sequence data from a third generation sequence platform (PacBio). Relative to objective 2, ARS scientists continued to use genomic tools to better understand natural and artificial selection in cattle and goats. ARS scientists developed methods in determining runs of homozygosity to detect signatures of artificial selection in contemporary Holsteins compared to an unselected control line. Analysis of signatures from natural selection will continue using more than 1500 indigenous cattle from Brazil, Venezuela, and Turkey using newly generated data derived from the 700K SNP (single nucleotide polymorphism) beadchip assay (Illumina’s BovineHD) and 600 indigenous goats Ethiopia, Nigeria, Kenya, Uganda, Turkey, and Egypt using Illumina’s Caprine50K assay. To date, regions of the genome under natural selection for thermotolerance (second SLICK mutation), resistance to diseases endemic to Africa, and signatures of selection for carcass traits and fertility have been detected in cattle. This effort also includes a comprehensive screen for candidate regions under positive selection across Holstein, Angus, Charolais, Brahman, Nelore, and N'Dama as results of geographic adaptation and human selection. Other efforts included additional sampling of indigenous goat populations in Mali, Madagascar, Burundi, Tanzania, Egypt, and the Sudan. ARS scientists continued development of a digital-based system for collecting goat phenotypes, and initiated three community breeding programs in Uganda and Malawi. Under Objective 3, ARS scientists performed genome-wide association studies (GWAS) between Copy number variations (CNV) and parasite resistance traits in Angus cattle and between copy number variations (CNV) and milk traits in Holsteins, and are finishing an integrated tool/algorithm to merge CNV results derived from various discovery platforms. ARS scientists also generated and analyzed additional whole-genome sequence to identify potential causative mutations affecting fertility haplotype BH2 in Brown Swiss and two different SLICK loci in Senepol and Limonero cattle. Validation genotyping of 900 tropically adapted cattle was completed to confirm the causative variant for thermo-tolerance from the Senepol-derived SLICK allele.

1. Identified mutations affecting thermo-tolerance in cattle. Genotyping and sequencing of Criollo cattle populations revealed that there are at least two different mutations with major effects on skin morphology and hair growth in cattle. One of these mutations derived from Senepol cattle was confirmed as a frameshift mutation in the prolactin receptor (PRLR), which truncates the encoded protein by 120 amino acids. Loss of this encoded domain is associated with maintenance of a cooler body temperature under tropical heat conditions. Results from this study are being used by producers to guide future mating decisions (diagnostic DNA marker for SLICK), and by researchers to better understand the gene pathways involved in adaptation to climate change.

2. Identified signatures of selection for differences in fertility, stature (frame size), carcass quality, milk production, and natural selection among global cattle populations. Within these signatures, identified and validated PLAG1 is a major locus controlling growth potential, while a variety of novel and lesser-known genes like LAP3 and SAR1B affect differences in meat quality and milk production, respectively. Population genetics analyses further revealed that genetic hitchhiking and recombination are two major evolutionary mechanisms involved in natural selection in cattle. These results provided a glimpse into geographic adaptation and human selection during cattle domestication, breed formation, and recent genetic improvement. Deep sequencing of 27 Nelore, 10 Criollo, and 10 West African cattle also was completed, and these data will be used as a resource to identify the actual genetic variants underlying phenotypic differences among temperate and tropically adapted cattle. This information will assist genetic improvement of cattle in nations undergoing rapid economic development and population growth and facing challenges of limited resources and predicted climate change.

3. Completed the first genome-wide association studies using copy number variation (CNV) as the source of genotypic information. For Angus, ARS scientists identified one associated deletion CNV on Chromosome 7 for gastrointestinal parasite resistance near immune-related genes such as ZNF496 and NLRP3. For Holsteins, ARS scientists proved that while 75% of all CNV can be tagged by neighboring single nucleotide polymorphisms (SNP) for association testing, the remaining 25% of CNV provided new trait association information not captured by neighboring SNP. The resultant CNV could be used as additional markers for animal selection for traits like production, parasite resistance, fertility, and feed efficiency. These findings will facilitate genome-assisted breeding to improve animal production and health.

Review Publications
Zhao, C., Zan, L., Wang, Y., Updike, M., Liu, G., Bequette, B.J., Baldwin, R.L., Song, J. 2013. Functional proteomic and interactome analysis of proteins associated with beef tenderness in angus cattle. Livestock Science. 161:201-209.
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.
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.
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:14(2):333-9.
Bickhart, D.M., Liu, G. 2014. The challenges and importance of structural variation detection in livestock. Frontiers in Genetics. 5:37.
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.
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.
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.
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. 113(4):297-305.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Lawless, N., Reinhardt, T.A., Bryan, K., Baker, M., Pesch, B.A., Zimmerman, D.R., Zuelke, K.A., Sonstegard, T.S., O'Farrelly, C., Lippolis, J.D., Lynn, D.J. 2014. MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model. Genes, Genomes, Genetics. 4(6):957-971. DOI: 10.1534/g3.113.009936.