title: Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle.
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 (BTA) 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 (ROH), and identity by state (IBS) calculations were used to identify a 0.8 Mb (37.7-38.5 Mb) consensus region for the SLICK locus on BTA20 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. Principal component analysis (PCA) 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.
authors.affiliation: Department of Animal Science, Cornell University Ithaca, NY, USA ; Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA.
authors.forename: Heather J
authors.initials: HJ
authors.lastname: Huson
authors.affiliation: Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA ; Department of Animal Science, Iowa State University Ames, IA, USA.
authors.forename: Eui-Soo
authors.initials: ES
authors.lastname: Kim
authors.affiliation: Agricultural Experiment Station, University of the Virgin Islands St. Croix, Virgin Islands.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Godfrey
authors.affiliation: Department of Animal Science, University of Florida Gainsville, FL, USA.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Olson
authors.affiliation: Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA ; Irish Cattle Breeding Federation Cork, Ireland.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: McClure
authors.affiliation: Meat Animal Research Center, United States Department of Agriculture, Agricultural Research Services Clay Center, NE, USA.
authors.forename: Chad C
authors.initials: CC
authors.lastname: Chase
authors.affiliation: Department of Veterinary Medicine, Milan University Milan, Italy.
authors.forename: Rita
authors.initials: R
authors.lastname: Rizzi
authors.affiliation: Division of Livestock Sciences, BOKU University of Natural Resources and Life Sciences Vienna, Austria.
authors.forename: Ana M P
authors.initials: AM
authors.lastname: O'Brien
authors.affiliation: Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA.
authors.forename: Curt P
authors.initials: CP
authors.lastname: Van Tassell
authors.affiliation: Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista Brazil.
authors.forename: José F
authors.initials: JF
authors.lastname: Garcia
authors.affiliation: Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA.
authors.forename: Tad S
authors.initials: TS
authors.lastname: Sonstegard
keywords: Carora; Criollo; Romosinuano; SLICK; Senepol; thermo-tolerance