Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle
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-t...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2014-04-01
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| Series: | Frontiers in Genetics |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00101/full |
| _version_ | 1819206769830789120 |
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| author | Heather Jay Huson Heather Jay Huson Eui-Soo eKim Eui-Soo eKim Robert W Godfrey Timothy A Olson Matthew eMcClure Matthew eMcClure Chad C Chase Rita eRizzi Ana Maria Perez O'Brien Curtis eVan Tassell Jose Fernando eGarcia Tad Stewart Sonstegard |
| author_facet | Heather Jay Huson Heather Jay Huson Eui-Soo eKim Eui-Soo eKim Robert W Godfrey Timothy A Olson Matthew eMcClure Matthew eMcClure Chad C Chase Rita eRizzi Ana Maria Perez O'Brien Curtis eVan Tassell Jose Fernando eGarcia Tad Stewart Sonstegard |
| author_sort | Heather Jay Huson |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-23T05:12:52Z |
| format | Article |
| id | doaj.art-8039830634f24e67a371ae9d762c05c2 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-23T05:12:52Z |
| publishDate | 2014-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-8039830634f24e67a371ae9d762c05c22022-12-21T17:58:56ZengFrontiers Media S.A.Frontiers in Genetics1664-80212014-04-01510.3389/fgene.2014.0010179498Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattleHeather Jay Huson0Heather Jay Huson1Eui-Soo eKim2Eui-Soo eKim3Robert W Godfrey4Timothy A Olson5Matthew eMcClure6Matthew eMcClure7Chad C Chase8Rita eRizzi9Ana Maria Perez O'Brien10Curtis eVan Tassell11Jose Fernando eGarcia12Tad Stewart Sonstegard13Cornell UniversityUnited States Department of AgricultureIowa State UniversityUnited States Department of AgricultureUniversity of Virgin IslandsUniversity of FloridaIrish Cattle Breeding FederationUnited States Department of AgricultureUnited States Department of AgricultureMilan UniversityUniversity of Natural Resources and Life SciencesUnited States Department of AgricultureUNESP Universite Estadual PaulistaUnited States Department of AgricultureThe 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.http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00101/fullGenome-wide association studies (GWAS)SLICKCriolloSenepolCaroraRomosinuano |
| spellingShingle | Heather Jay Huson Heather Jay Huson Eui-Soo eKim Eui-Soo eKim Robert W Godfrey Timothy A Olson Matthew eMcClure Matthew eMcClure Chad C Chase Rita eRizzi Ana Maria Perez O'Brien Curtis eVan Tassell Jose Fernando eGarcia Tad Stewart Sonstegard Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle Frontiers in Genetics Genome-wide association studies (GWAS) SLICK Criollo Senepol Carora Romosinuano |
| title | Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle |
| title_full | Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle |
| title_fullStr | Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle |
| title_full_unstemmed | Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle |
| title_short | Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle |
| title_sort | genome wide association study and ancestral origins of the slick hair coat in tropically adapted cattle |
| topic | Genome-wide association studies (GWAS) SLICK Criollo Senepol Carora Romosinuano |
| url | http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00101/full |
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