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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

Title: Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle

Authors
item Huson, Heather -
item Eui-Soo, Kim -
item Godfrey, Robert -
item Olson, Timothy -
item Mcclure, Matthew -
item Chase, Chadwick
item Rizzi, Rita -
item Perez O'Brien, Ana Maria -
item Van Tassell, Curtis
item Garcia, Jose Fernando -
item Sonstegard, Tad

Submitted to: Frontiers in Livestock Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 8, 2014
Publication Date: April 25, 2014
Citation: 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.

Interpretive Summary: The slick hair coat (SLICK) is a dominantly inherited trait typically associated with tropically adapted cattle that are from Criollo descent through Spanish colonization of cattle into the New World. The trait is of interest relative to climate change, due to its association with improved thermo-tolerance and subsequent increased productivity under these conditions compared to normal haired cattle. These findings raise the possibility that introgression of the SLICK locus into otherwise normally haired breeds can be used as a way to improve production in animals in tropical regions. In order to introgress SLICK efficiently into other breeds, high resolution map information or discovery of the underlying mutation causing the short hair phenotype is necessary. The current study compares three slick-haired Criollo-derived breeds including Senepol, Carora, and Romosinuano and three additional slick-haired cross-bred lineages to non-slick ancestral breeds to better map SLICK. In brief, the genome interval containing SLICK was refined from 4 to 0.8 million bases on bovine chromosome 20. We also identified three diagnostic haplotypes for the SLICK locus. In summary, this study has identified potential diagnostic markers for breed management, and given insight as to ancestral origins of the mutation, all of which will help in the identification of the causative genetic mechanism controlling this phenotype.

Technical Abstract: The slick hair coat (SLICK) is a dominantly inherited trait typically associated with tropically adapted cattle that are from Criollo descent through Spanish colonization of cattle into the New World. The trait is of interest relative to climate change, due to its association with improved thermo-tolerance and subsequent increased productivity. Previous studies localized the SLICK locus to a 4 cM region on chromosome (Chr) 20 and identified signatures of selection in this region derived from Senepol cattle. The current study compares three slick-haired Criollo-derived breeds including Senepol, Carora, and Romosinuano and three additional slick-haired cross-bred lineages to non-slick ancestral breeds. Genome-wide association (GWA), haplotype analysis, signatures of selection, runs of homozygosity, and identity by state (IBS) calculations were used to identify a 0.8Mb (37.7-38.5Mb) consensus region for the SLICK locus on Chr 20 in which contains SKP2 and SPEF2 as possible candidate genes. Three specific haplotype patterns are identified in slick individuals, all with zero frequency in non-slick individuals. Admixture analysis identified common genetic patterns between the three slick breeds at the SLICK locus. Principle component analysis and admixture results show Senepol and Romosinuano sharing a higher degree of genetic similarity to one another with a much lesser degree of similarity to Carora. Variation in GWA, haplotype analysis, and IBS calculations with accompanying population structure information supports potentially two mutations, one common to Senepol and Romosinuano and another in Carora, effecting genes contained within our refined location for the SLICK locus.

Last Modified: 10/25/2014
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