Multitrait meta-analysis identified genomic regions associated with sexual precocity in tropical beef 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/sky289 http://hdl.handle.net/11449/188193 |
Resumo: | Multitrait meta-analyses are a strategy to produce more accurate genome-wide association studies, especially for complex phenotypes. We carried out a meta-analysis study for traits related to sexual precocity in tropical beef cattle (Nellore and Brahman) aiming to identify important genomic regions affecting these traits. The traits included in the analyses were age at first calving (AFC), early pregnancy (EP), age at first corpus luteum (AGECL), first postpartum anoestrus interval (PPAI), and scrotal circumference (SC). The traits AFC, EP, and SCN were measured in Nellore cattle, while AGECL, PPAI, and SCB were measured in Brahman cattle. Metaanalysis resulted in 108 significant single-nucleotide polymorphisms (SNPs), at an empirical threshold P-value of 1.39 × 10-5 (false discovery rate [FDR] < 0.05). Within 0.5 Mb of the significant SNP, candidate genes were annotated and analyzed for functional enrichment. Most of the closest genes to the SNP with higher significance in each chromosome have been associated with important roles in reproductive function. They are TSC22D2, KLF7, ARHGAP29, 7SK, MAP3K5, TLE3, WDR5, TAF3, TMEM68, PPP1R15B, NR2F2, GALR1, SUFU, and KCNU1. We did not observe any significant SNP in BTA5, BTA12, BTA17, BTA18, BTA19, BTA20, BTA22, BTA23, BTA25, and BTA28. Although the majority of significant SNPs are in BTA14, it was identified significant associations in multiple chromosomes (19 out of 29 autosomes), which is consistent with the postulation that reproductive traits are complex polygenic phenotypes. Five proposed association regions harbor the majority of the significant SNP (76%) and were distributed over four chromosomes (P < 1.39 × 10-5, FDR < 0.05): BTA2 (5.55%) from 95 to 96 Mb, BTA4 (5.55%) from 94.1 to 94.8 Mb, BTA14 (59.26%) from 24 to 25 Mb and 29 to 30 Mb, and BTA21 (5.55%) from 6.7 Mb to 11.4 Mb. These regions harbored key genes related to reproductive function. Moreover, these genes were enriched for functional groups associated with immune response, maternal-fetal tolerance, pregnancy maintenance, embryo development, fertility, and response to stress. Further studies including other breeds and precocity traits could confirm the importance of these regions and identify new candidate regions for sexual precocity in beef cattle. |
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Multitrait meta-analysis identified genomic regions associated with sexual precocity in tropical beef cattleBos indicusBrahmanEarly pubertyGWASMeta-analysisNelloreMultitrait meta-analyses are a strategy to produce more accurate genome-wide association studies, especially for complex phenotypes. We carried out a meta-analysis study for traits related to sexual precocity in tropical beef cattle (Nellore and Brahman) aiming to identify important genomic regions affecting these traits. The traits included in the analyses were age at first calving (AFC), early pregnancy (EP), age at first corpus luteum (AGECL), first postpartum anoestrus interval (PPAI), and scrotal circumference (SC). The traits AFC, EP, and SCN were measured in Nellore cattle, while AGECL, PPAI, and SCB were measured in Brahman cattle. Metaanalysis resulted in 108 significant single-nucleotide polymorphisms (SNPs), at an empirical threshold P-value of 1.39 × 10-5 (false discovery rate [FDR] < 0.05). Within 0.5 Mb of the significant SNP, candidate genes were annotated and analyzed for functional enrichment. Most of the closest genes to the SNP with higher significance in each chromosome have been associated with important roles in reproductive function. They are TSC22D2, KLF7, ARHGAP29, 7SK, MAP3K5, TLE3, WDR5, TAF3, TMEM68, PPP1R15B, NR2F2, GALR1, SUFU, and KCNU1. We did not observe any significant SNP in BTA5, BTA12, BTA17, BTA18, BTA19, BTA20, BTA22, BTA23, BTA25, and BTA28. Although the majority of significant SNPs are in BTA14, it was identified significant associations in multiple chromosomes (19 out of 29 autosomes), which is consistent with the postulation that reproductive traits are complex polygenic phenotypes. Five proposed association regions harbor the majority of the significant SNP (76%) and were distributed over four chromosomes (P < 1.39 × 10-5, FDR < 0.05): BTA2 (5.55%) from 95 to 96 Mb, BTA4 (5.55%) from 94.1 to 94.8 Mb, BTA14 (59.26%) from 24 to 25 Mb and 29 to 30 Mb, and BTA21 (5.55%) from 6.7 Mb to 11.4 Mb. These regions harbored key genes related to reproductive function. Moreover, these genes were enriched for functional groups associated with immune response, maternal-fetal tolerance, pregnancy maintenance, embryo development, fertility, and response to stress. Further studies including other breeds and precocity traits could confirm the importance of these regions and identify new candidate regions for sexual precocity in beef cattle.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Department of Animal Science School of Agricultural and Veterinarian Sciences FCAV/ UNESP - Sao Paulo State UniversityThe University of Queensland School of Chemistry and Molecular BiosciencesThe University of Queensland Queensland Alliance for Agriculture and Food InnovationNational Council for Scientific and Technological Development (CNPq)Department of Animal Science School of Agricultural and Veterinarian Sciences FCAV/ UNESP - Sao Paulo State UniversityCNPq: 559631/2009-0Universidade Estadual Paulista (Unesp)School of Chemistry and Molecular BiosciencesQueensland Alliance for Agriculture and Food InnovationNational Council for Scientific and Technological Development (CNPq)Melo, Thaise P. [UNESP]Fortes, Marina R.S.Bresolin, Tiago [UNESP]Mota, Lucio F.M. [UNESP]Albuquerque, Lucia G. [UNESP]Carvalheiro, Roberto [UNESP]2019-10-06T16:00:13Z2019-10-06T16:00:13Z2018-09-29info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article4087-4099http://dx.doi.org/10.1093/jas/sky289Journal of Animal Science, v. 96, n. 10, p. 4087-4099, 2018.1525-31630021-8812http://hdl.handle.net/11449/18819310.1093/jas/sky2892-s2.0-85054751460Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal of Animal Scienceinfo:eu-repo/semantics/openAccess2021-10-23T19:23:20Zoai:repositorio.unesp.br:11449/188193Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462021-10-23T19:23:20Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Multitrait meta-analysis identified genomic regions associated with sexual precocity in tropical beef cattle |
title |
Multitrait meta-analysis identified genomic regions associated with sexual precocity in tropical beef cattle |
spellingShingle |
Multitrait meta-analysis identified genomic regions associated with sexual precocity in tropical beef cattle Melo, Thaise P. [UNESP] Bos indicus Brahman Early puberty GWAS Meta-analysis Nellore |
title_short |
Multitrait meta-analysis identified genomic regions associated with sexual precocity in tropical beef cattle |
title_full |
Multitrait meta-analysis identified genomic regions associated with sexual precocity in tropical beef cattle |
title_fullStr |
Multitrait meta-analysis identified genomic regions associated with sexual precocity in tropical beef cattle |
title_full_unstemmed |
Multitrait meta-analysis identified genomic regions associated with sexual precocity in tropical beef cattle |
title_sort |
Multitrait meta-analysis identified genomic regions associated with sexual precocity in tropical beef cattle |
author |
Melo, Thaise P. [UNESP] |
author_facet |
Melo, Thaise P. [UNESP] Fortes, Marina R.S. Bresolin, Tiago [UNESP] Mota, Lucio F.M. [UNESP] Albuquerque, Lucia G. [UNESP] Carvalheiro, Roberto [UNESP] |
author_role |
author |
author2 |
Fortes, Marina R.S. Bresolin, Tiago [UNESP] Mota, Lucio F.M. [UNESP] Albuquerque, Lucia G. [UNESP] Carvalheiro, Roberto [UNESP] |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) School of Chemistry and Molecular Biosciences Queensland Alliance for Agriculture and Food Innovation National Council for Scientific and Technological Development (CNPq) |
dc.contributor.author.fl_str_mv |
Melo, Thaise P. [UNESP] Fortes, Marina R.S. Bresolin, Tiago [UNESP] Mota, Lucio F.M. [UNESP] Albuquerque, Lucia G. [UNESP] Carvalheiro, Roberto [UNESP] |
dc.subject.por.fl_str_mv |
Bos indicus Brahman Early puberty GWAS Meta-analysis Nellore |
topic |
Bos indicus Brahman Early puberty GWAS Meta-analysis Nellore |
description |
Multitrait meta-analyses are a strategy to produce more accurate genome-wide association studies, especially for complex phenotypes. We carried out a meta-analysis study for traits related to sexual precocity in tropical beef cattle (Nellore and Brahman) aiming to identify important genomic regions affecting these traits. The traits included in the analyses were age at first calving (AFC), early pregnancy (EP), age at first corpus luteum (AGECL), first postpartum anoestrus interval (PPAI), and scrotal circumference (SC). The traits AFC, EP, and SCN were measured in Nellore cattle, while AGECL, PPAI, and SCB were measured in Brahman cattle. Metaanalysis resulted in 108 significant single-nucleotide polymorphisms (SNPs), at an empirical threshold P-value of 1.39 × 10-5 (false discovery rate [FDR] < 0.05). Within 0.5 Mb of the significant SNP, candidate genes were annotated and analyzed for functional enrichment. Most of the closest genes to the SNP with higher significance in each chromosome have been associated with important roles in reproductive function. They are TSC22D2, KLF7, ARHGAP29, 7SK, MAP3K5, TLE3, WDR5, TAF3, TMEM68, PPP1R15B, NR2F2, GALR1, SUFU, and KCNU1. We did not observe any significant SNP in BTA5, BTA12, BTA17, BTA18, BTA19, BTA20, BTA22, BTA23, BTA25, and BTA28. Although the majority of significant SNPs are in BTA14, it was identified significant associations in multiple chromosomes (19 out of 29 autosomes), which is consistent with the postulation that reproductive traits are complex polygenic phenotypes. Five proposed association regions harbor the majority of the significant SNP (76%) and were distributed over four chromosomes (P < 1.39 × 10-5, FDR < 0.05): BTA2 (5.55%) from 95 to 96 Mb, BTA4 (5.55%) from 94.1 to 94.8 Mb, BTA14 (59.26%) from 24 to 25 Mb and 29 to 30 Mb, and BTA21 (5.55%) from 6.7 Mb to 11.4 Mb. These regions harbored key genes related to reproductive function. Moreover, these genes were enriched for functional groups associated with immune response, maternal-fetal tolerance, pregnancy maintenance, embryo development, fertility, and response to stress. Further studies including other breeds and precocity traits could confirm the importance of these regions and identify new candidate regions for sexual precocity in beef cattle. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-09-29 2019-10-06T16:00:13Z 2019-10-06T16:00:13Z |
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/sky289 Journal of Animal Science, v. 96, n. 10, p. 4087-4099, 2018. 1525-3163 0021-8812 http://hdl.handle.net/11449/188193 10.1093/jas/sky289 2-s2.0-85054751460 |
url |
http://dx.doi.org/10.1093/jas/sky289 http://hdl.handle.net/11449/188193 |
identifier_str_mv |
Journal of Animal Science, v. 96, n. 10, p. 4087-4099, 2018. 1525-3163 0021-8812 10.1093/jas/sky289 2-s2.0-85054751460 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Journal of Animal Science |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
4087-4099 |
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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1799965471765692416 |