Genome-wide association study and functional analysis of feet and leg conformation traits in Nellore cattle
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1093/jas/sky079 http://hdl.handle.net/11449/176267 |
Resumo: | Feet and leg conformation is evaluated as a subset of conformational structure traits in dairy and beef cattle and is related to the feet and leg quality that can compromise the animals’ productive performance and longevity. The aim of this study was to perform a genome-wide association study (GWAS) of two traits related to feet and leg conformation in Nellore cattle to identify chromosomal regions related to the expression of these traits. Phenotypic and pedigree data from 104,725 animals and genotypes from 1,435 animals and 407,730 SNPs were used. Feet and leg structure was evaluated as a binary trait (FL1) to identify yearling animals with feet and leg problems or as categorical score (FL2) to assess the overall quality of their feet and leg. The top ten 1-Mb windows that explained the largest proportion of the total genetic variance were identified and functional enrichment analyses were performed. The 10 windows with large effects obtained for FL1 are located on chromosomes 1, 2, 6, 7, 8, 10, and 14, and together explained 8.96% of the additive genetic variance. For FL2, these windows are located on chromosomes 1, 7, 10, 11, 18, 20, 22, 28, and 29, explaining 8.98% of the additive genetic variance. Several candidate genes were identified, including DLX2 which is associated with osteogenic differentiation, IL-1β and IL-1A associated with some properties of articular cartilage, PiT1 which plays an important role in bone physiology, and CTSL associated with rheumatoid arthritis. The results presented here should contribute to a better understanding of the genetic and physiologic mechanisms regulating both traits, and identifies candidate genes for future investigation of causal mutations. |
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Genome-wide association study and functional analysis of feet and leg conformation traits in Nellore cattleBeef cattleBos taurus indicusCandidate genesWeighted single step GBLUPFeet and leg conformation is evaluated as a subset of conformational structure traits in dairy and beef cattle and is related to the feet and leg quality that can compromise the animals’ productive performance and longevity. The aim of this study was to perform a genome-wide association study (GWAS) of two traits related to feet and leg conformation in Nellore cattle to identify chromosomal regions related to the expression of these traits. Phenotypic and pedigree data from 104,725 animals and genotypes from 1,435 animals and 407,730 SNPs were used. Feet and leg structure was evaluated as a binary trait (FL1) to identify yearling animals with feet and leg problems or as categorical score (FL2) to assess the overall quality of their feet and leg. The top ten 1-Mb windows that explained the largest proportion of the total genetic variance were identified and functional enrichment analyses were performed. The 10 windows with large effects obtained for FL1 are located on chromosomes 1, 2, 6, 7, 8, 10, and 14, and together explained 8.96% of the additive genetic variance. For FL2, these windows are located on chromosomes 1, 7, 10, 11, 18, 20, 22, 28, and 29, explaining 8.98% of the additive genetic variance. Several candidate genes were identified, including DLX2 which is associated with osteogenic differentiation, IL-1β and IL-1A associated with some properties of articular cartilage, PiT1 which plays an important role in bone physiology, and CTSL associated with rheumatoid arthritis. The results presented here should contribute to a better understanding of the genetic and physiologic mechanisms regulating both traits, and identifies candidate genes for future investigation of causal mutations.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Departamento de Zootecnia Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias, Câmpus de JaboticabalGensys Associated ConsultantsDepartamento de Zootecnista Universidade Federal da Bahia (UFBA)Departamento de Ciências Exatas Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias, Câmpus de JaboticabalConselho Nacional de Desenvolvimento Científico e TecnológicoDepartamento de Zootecnia Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias, Câmpus de JaboticabalDepartamento de Ciências Exatas Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias, Câmpus de JaboticabalFAPESP: 2013/25312-5CAPES: 303606/2009-6Universidade Estadual Paulista (Unesp)Gensys Associated ConsultantsUniversidade Federal da Bahia (UFBA)Conselho Nacional de Desenvolvimento Científico e TecnológicoVargas, Giovana [UNESP]Neves, Haroldo H. R.Camargo, Gregório Miguel F.Cardoso, VâniaMunari, Danísio P. [UNESP]Carvalheiro, Roberto [UNESP]2018-12-11T17:19:52Z2018-12-11T17:19:52Z2018-05-04info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article1617-1627application/pdfhttp://dx.doi.org/10.1093/jas/sky079Journal of Animal Science, v. 96, n. 5, p. 1617-1627, 2018.1525-31630021-8812http://hdl.handle.net/11449/17626710.1093/jas/sky0792-s2.0-850464464702-s2.0-85046446470.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal of Animal Science0,848info:eu-repo/semantics/openAccess2023-12-29T06:19:55Zoai:repositorio.unesp.br:11449/176267Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-12-29T06:19:55Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Genome-wide association study and functional analysis of feet and leg conformation traits in Nellore cattle |
title |
Genome-wide association study and functional analysis of feet and leg conformation traits in Nellore cattle |
spellingShingle |
Genome-wide association study and functional analysis of feet and leg conformation traits in Nellore cattle Vargas, Giovana [UNESP] Beef cattle Bos taurus indicus Candidate genes Weighted single step GBLUP |
title_short |
Genome-wide association study and functional analysis of feet and leg conformation traits in Nellore cattle |
title_full |
Genome-wide association study and functional analysis of feet and leg conformation traits in Nellore cattle |
title_fullStr |
Genome-wide association study and functional analysis of feet and leg conformation traits in Nellore cattle |
title_full_unstemmed |
Genome-wide association study and functional analysis of feet and leg conformation traits in Nellore cattle |
title_sort |
Genome-wide association study and functional analysis of feet and leg conformation traits in Nellore cattle |
author |
Vargas, Giovana [UNESP] |
author_facet |
Vargas, Giovana [UNESP] Neves, Haroldo H. R. Camargo, Gregório Miguel F. Cardoso, Vânia Munari, Danísio P. [UNESP] Carvalheiro, Roberto [UNESP] |
author_role |
author |
author2 |
Neves, Haroldo H. R. Camargo, Gregório Miguel F. Cardoso, Vânia Munari, Danísio P. [UNESP] Carvalheiro, Roberto [UNESP] |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Gensys Associated Consultants Universidade Federal da Bahia (UFBA) Conselho Nacional de Desenvolvimento Científico e Tecnológico |
dc.contributor.author.fl_str_mv |
Vargas, Giovana [UNESP] Neves, Haroldo H. R. Camargo, Gregório Miguel F. Cardoso, Vânia Munari, Danísio P. [UNESP] Carvalheiro, Roberto [UNESP] |
dc.subject.por.fl_str_mv |
Beef cattle Bos taurus indicus Candidate genes Weighted single step GBLUP |
topic |
Beef cattle Bos taurus indicus Candidate genes Weighted single step GBLUP |
description |
Feet and leg conformation is evaluated as a subset of conformational structure traits in dairy and beef cattle and is related to the feet and leg quality that can compromise the animals’ productive performance and longevity. The aim of this study was to perform a genome-wide association study (GWAS) of two traits related to feet and leg conformation in Nellore cattle to identify chromosomal regions related to the expression of these traits. Phenotypic and pedigree data from 104,725 animals and genotypes from 1,435 animals and 407,730 SNPs were used. Feet and leg structure was evaluated as a binary trait (FL1) to identify yearling animals with feet and leg problems or as categorical score (FL2) to assess the overall quality of their feet and leg. The top ten 1-Mb windows that explained the largest proportion of the total genetic variance were identified and functional enrichment analyses were performed. The 10 windows with large effects obtained for FL1 are located on chromosomes 1, 2, 6, 7, 8, 10, and 14, and together explained 8.96% of the additive genetic variance. For FL2, these windows are located on chromosomes 1, 7, 10, 11, 18, 20, 22, 28, and 29, explaining 8.98% of the additive genetic variance. Several candidate genes were identified, including DLX2 which is associated with osteogenic differentiation, IL-1β and IL-1A associated with some properties of articular cartilage, PiT1 which plays an important role in bone physiology, and CTSL associated with rheumatoid arthritis. The results presented here should contribute to a better understanding of the genetic and physiologic mechanisms regulating both traits, and identifies candidate genes for future investigation of causal mutations. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-12-11T17:19:52Z 2018-12-11T17:19:52Z 2018-05-04 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1093/jas/sky079 Journal of Animal Science, v. 96, n. 5, p. 1617-1627, 2018. 1525-3163 0021-8812 http://hdl.handle.net/11449/176267 10.1093/jas/sky079 2-s2.0-85046446470 2-s2.0-85046446470.pdf |
url |
http://dx.doi.org/10.1093/jas/sky079 http://hdl.handle.net/11449/176267 |
identifier_str_mv |
Journal of Animal Science, v. 96, n. 5, p. 1617-1627, 2018. 1525-3163 0021-8812 10.1093/jas/sky079 2-s2.0-85046446470 2-s2.0-85046446470.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Journal of Animal Science 0,848 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
1617-1627 application/pdf |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
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1797790144379486208 |