Signatures of selection in Nelore cattle revealed by whole-genome sequencing data
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1016/j.ygeno.2022.110304 http://hdl.handle.net/11449/234132 |
Resumo: | Nelore cattle breed was farmed worldwide due to its economic importance in the beef market and adaptation to the tropics. In Brazil, purebred Nelore animals (PO) receive a certificate from the breeders' association based on the animal's genealogy and morphological characterization. The top 20 to 30% of the superior animals are eligible to receive the Special Certificate of Identification and Production (CEIP), meaning animals from this category were selected and evaluated in a breeding program to improve economically important traits. We used whole-genome sequencing and approaches based on haplotype differentiation and allelic differentiation to detect regions of selection signatures in Nelore cattle by comparing animals from PO and CEIP categories. From a total of 150 animals, a hierarchical clustering analysis was performed to choose the more unrelated animals from each category (16 PO and 40 CEIP). The hapFLK statistic was performed, and extensions of hapFLK values were investigated considering continuous regions with significant q-values. The Weir and Cockerham's Fst estimator (wcFst) was computed using the GPAT++ software library. The total of 82,326 SNPs with hapFLK values passed the FDR control (q-value<0.05), and 718 segments were target as signatures of selection. A total of 1713 highly differentiated genomic regions were identified based on the segmentFst approach. The signatures of selection were spread across the genome. Annotation of overlapping selection signature regions between the two methods revealed 118 genes in common. A variant located within the 3′ region of the BOLA-DRB3 gene was found as a promising candidate polymorphism. Within genomic regions that deserves attention, we found genes previously associated with adaptation to tropical environments (HELB), growth and navel size (HMGA2), fat deposition and domestication (IRAK3), and feed efficiency and postmortem carcass traits (GABRG3). The genes BOLA-DQA2, BOLA-DQB, BOLA-DQA5, BOLA-DQA1, BOLA-DRB3, ENSBTAG00000038397 on chromosome 23 are part of the Bovine Major Histocompatibility Complex (MHC) Class II gene family, representing good candidates for immune response and adaptation to tropical conditions. The BoLA family genes and the interaction of ROBO1 with SLIT genes appeared in the enrichment results. Genomic regions located in intronic regions were also identified and might play a regulatory role in traits under selection in PO and CEIP subpopulations. The regions here identified contribute to our knowledge regarding genes and variants that have an important role in complex traits selected in this breed |
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Repositório Institucional da UNESP |
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Signatures of selection in Nelore cattle revealed by whole-genome sequencing dataAdaptationAllele frequencyBos indicusGenomicsHaplotypesSelective signaturesNelore cattle breed was farmed worldwide due to its economic importance in the beef market and adaptation to the tropics. In Brazil, purebred Nelore animals (PO) receive a certificate from the breeders' association based on the animal's genealogy and morphological characterization. The top 20 to 30% of the superior animals are eligible to receive the Special Certificate of Identification and Production (CEIP), meaning animals from this category were selected and evaluated in a breeding program to improve economically important traits. We used whole-genome sequencing and approaches based on haplotype differentiation and allelic differentiation to detect regions of selection signatures in Nelore cattle by comparing animals from PO and CEIP categories. From a total of 150 animals, a hierarchical clustering analysis was performed to choose the more unrelated animals from each category (16 PO and 40 CEIP). The hapFLK statistic was performed, and extensions of hapFLK values were investigated considering continuous regions with significant q-values. The Weir and Cockerham's Fst estimator (wcFst) was computed using the GPAT++ software library. The total of 82,326 SNPs with hapFLK values passed the FDR control (q-value<0.05), and 718 segments were target as signatures of selection. A total of 1713 highly differentiated genomic regions were identified based on the segmentFst approach. The signatures of selection were spread across the genome. Annotation of overlapping selection signature regions between the two methods revealed 118 genes in common. A variant located within the 3′ region of the BOLA-DRB3 gene was found as a promising candidate polymorphism. Within genomic regions that deserves attention, we found genes previously associated with adaptation to tropical environments (HELB), growth and navel size (HMGA2), fat deposition and domestication (IRAK3), and feed efficiency and postmortem carcass traits (GABRG3). The genes BOLA-DQA2, BOLA-DQB, BOLA-DQA5, BOLA-DQA1, BOLA-DRB3, ENSBTAG00000038397 on chromosome 23 are part of the Bovine Major Histocompatibility Complex (MHC) Class II gene family, representing good candidates for immune response and adaptation to tropical conditions. The BoLA family genes and the interaction of ROBO1 with SLIT genes appeared in the enrichment results. Genomic regions located in intronic regions were also identified and might play a regulatory role in traits under selection in PO and CEIP subpopulations. The regions here identified contribute to our knowledge regarding genes and variants that have an important role in complex traits selected in this breedFaculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista “Júlio de Mesquita Filho”, JaboticabalFaculdade de Medicina Veterinária Universidade Federal de Uberlândia, Minas GeraisUniversity of GuelphFaculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista “Júlio de Mesquita Filho”, JaboticabalUniversidade Estadual Paulista (UNESP)Universidade Federal de Uberlândia (UFU)University of GuelphMaiorano, Amanda Marchi [UNESP]Cardoso, Diercles FranciscoCarvalheiro, Roberto [UNESP]Júnior, Gerardo Alves Fernandes [UNESP]de Albuquerque, Lúcia Galvão [UNESP]de Oliveira, Henrique Nunes [UNESP]2022-05-01T13:41:34Z2022-05-01T13:41:34Z2022-03-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1016/j.ygeno.2022.110304Genomics, v. 114, n. 2, 2022.1089-86460888-7543http://hdl.handle.net/11449/23413210.1016/j.ygeno.2022.1103042-s2.0-85124430212Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengGenomicsinfo:eu-repo/semantics/openAccess2022-05-01T13:41:34Zoai:repositorio.unesp.br:11449/234132Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462022-05-01T13:41:34Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Signatures of selection in Nelore cattle revealed by whole-genome sequencing data |
title |
Signatures of selection in Nelore cattle revealed by whole-genome sequencing data |
spellingShingle |
Signatures of selection in Nelore cattle revealed by whole-genome sequencing data Maiorano, Amanda Marchi [UNESP] Adaptation Allele frequency Bos indicus Genomics Haplotypes Selective signatures |
title_short |
Signatures of selection in Nelore cattle revealed by whole-genome sequencing data |
title_full |
Signatures of selection in Nelore cattle revealed by whole-genome sequencing data |
title_fullStr |
Signatures of selection in Nelore cattle revealed by whole-genome sequencing data |
title_full_unstemmed |
Signatures of selection in Nelore cattle revealed by whole-genome sequencing data |
title_sort |
Signatures of selection in Nelore cattle revealed by whole-genome sequencing data |
author |
Maiorano, Amanda Marchi [UNESP] |
author_facet |
Maiorano, Amanda Marchi [UNESP] Cardoso, Diercles Francisco Carvalheiro, Roberto [UNESP] Júnior, Gerardo Alves Fernandes [UNESP] de Albuquerque, Lúcia Galvão [UNESP] de Oliveira, Henrique Nunes [UNESP] |
author_role |
author |
author2 |
Cardoso, Diercles Francisco Carvalheiro, Roberto [UNESP] Júnior, Gerardo Alves Fernandes [UNESP] de Albuquerque, Lúcia Galvão [UNESP] de Oliveira, Henrique Nunes [UNESP] |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (UNESP) Universidade Federal de Uberlândia (UFU) University of Guelph |
dc.contributor.author.fl_str_mv |
Maiorano, Amanda Marchi [UNESP] Cardoso, Diercles Francisco Carvalheiro, Roberto [UNESP] Júnior, Gerardo Alves Fernandes [UNESP] de Albuquerque, Lúcia Galvão [UNESP] de Oliveira, Henrique Nunes [UNESP] |
dc.subject.por.fl_str_mv |
Adaptation Allele frequency Bos indicus Genomics Haplotypes Selective signatures |
topic |
Adaptation Allele frequency Bos indicus Genomics Haplotypes Selective signatures |
description |
Nelore cattle breed was farmed worldwide due to its economic importance in the beef market and adaptation to the tropics. In Brazil, purebred Nelore animals (PO) receive a certificate from the breeders' association based on the animal's genealogy and morphological characterization. The top 20 to 30% of the superior animals are eligible to receive the Special Certificate of Identification and Production (CEIP), meaning animals from this category were selected and evaluated in a breeding program to improve economically important traits. We used whole-genome sequencing and approaches based on haplotype differentiation and allelic differentiation to detect regions of selection signatures in Nelore cattle by comparing animals from PO and CEIP categories. From a total of 150 animals, a hierarchical clustering analysis was performed to choose the more unrelated animals from each category (16 PO and 40 CEIP). The hapFLK statistic was performed, and extensions of hapFLK values were investigated considering continuous regions with significant q-values. The Weir and Cockerham's Fst estimator (wcFst) was computed using the GPAT++ software library. The total of 82,326 SNPs with hapFLK values passed the FDR control (q-value<0.05), and 718 segments were target as signatures of selection. A total of 1713 highly differentiated genomic regions were identified based on the segmentFst approach. The signatures of selection were spread across the genome. Annotation of overlapping selection signature regions between the two methods revealed 118 genes in common. A variant located within the 3′ region of the BOLA-DRB3 gene was found as a promising candidate polymorphism. Within genomic regions that deserves attention, we found genes previously associated with adaptation to tropical environments (HELB), growth and navel size (HMGA2), fat deposition and domestication (IRAK3), and feed efficiency and postmortem carcass traits (GABRG3). The genes BOLA-DQA2, BOLA-DQB, BOLA-DQA5, BOLA-DQA1, BOLA-DRB3, ENSBTAG00000038397 on chromosome 23 are part of the Bovine Major Histocompatibility Complex (MHC) Class II gene family, representing good candidates for immune response and adaptation to tropical conditions. The BoLA family genes and the interaction of ROBO1 with SLIT genes appeared in the enrichment results. Genomic regions located in intronic regions were also identified and might play a regulatory role in traits under selection in PO and CEIP subpopulations. The regions here identified contribute to our knowledge regarding genes and variants that have an important role in complex traits selected in this breed |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-05-01T13:41:34Z 2022-05-01T13:41:34Z 2022-03-01 |
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/10.1016/j.ygeno.2022.110304 Genomics, v. 114, n. 2, 2022. 1089-8646 0888-7543 http://hdl.handle.net/11449/234132 10.1016/j.ygeno.2022.110304 2-s2.0-85124430212 |
url |
http://dx.doi.org/10.1016/j.ygeno.2022.110304 http://hdl.handle.net/11449/234132 |
identifier_str_mv |
Genomics, v. 114, n. 2, 2022. 1089-8646 0888-7543 10.1016/j.ygeno.2022.110304 2-s2.0-85124430212 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Genomics |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
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 |
|
_version_ |
1799964845404061696 |