Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle
Open Access
- 29 April 2014
- journal article
- Published by Frontiers Media SA in Frontiers in Genetics
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.Keywords
This publication has 29 references indexed in Scilit:
- The UCSC Genome Browser database: 2014 updateNucleic Acids Research, 2013
- A Quasi-Exclusive European Ancestry in the Senepol Tropical Cattle Breed Highlights the Importance of the slick Locus in Tropical AdaptationPLOS ONE, 2012
- rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structureBioinformatics, 2012
- Enhancements to the ADMIXTURE algorithm for individual ancestry estimationBMC Bioinformatics, 2011
- Fast model-based estimation of ancestry in unrelated individualsGenome Research, 2009
- Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chickenBMC Genomics, 2008
- Genetic diversity among Angus, American Brahman, Senepol and Romosinuano cattle breedsAnimal Genetics, 2007
- Haploview: analysis and visualization of LD and haplotype mapsBioinformatics, 2004
- Heat tolerance in Tuli-, Senepol-, and Brahman-sired F1 Angus heifers in Florida.Journal of Animal Science, 1998
- Heat tolerance in two tropically adapted Bos taurus breeds, Senepol and Romosinuano, compared with Brahman, Angus, and Hereford cattle in Florida.Journal of Animal Science, 1996