Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus).

Detalhes bibliográficos
Autor(a) principal: CORTEZ, T.
Data de Publicação: 2022
Outros Autores: MONTENEGRO, H., COUTINHO, L. L., REGITANO, L. C. de A., ANDRADE, S. C. S.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
Texto Completo: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1152197
Resumo: Evolutionary history leads to genome changes over time, especially for species that have experienced intense selective pressures over a short period. Here, we investigated the genomic evolution of Bos species by searching for potential selection signatures, focusing on Nelore, an economically relevant cattle breed in Brazil. We assessed the genomic processes determining the molecular evolution across Nelore and thirteen other related taxa by evaluating (i) amino acid sequence conservation, (ii) the dN/dS ratio, and (iii) gene families? turnover rate (lambda. Low conserved regions potentially associated with fatty acid metabolism seem to reflect differences in meat fat content in taxa with different evolutionary histories. All Bos species presented genes under positive selection, especially B. indicus and Nelore, which include transport protein cobalamin, glycolipid metabolism, and hormone signaling. These findings could be explained by constant selective pressures to obtain higher immune resistance and efficient metabolism. The gene contraction rate across the Nelore + B. indicus branch was almost nine times higher than that in other lineages (lambda = 0.01043 vs. 0.00121), indicating gene losses during the domestication process. Amino acid biosynthesis, reproductive and innate immune system-related pathways were associated with genes recognized within the most frequent rapidly evolving gene families and in genes under positive selection, supporting the substantial relevance of such traits from a domestication perspective. Our data provide new insights into how the genome may respond to intense artificial selection in distinct taxa, and reinforces the presence of selective pressures on traits potentially relevant for future animal breeding investments.
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spelling Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus).Genomic evolution of Bos speciesAmino acid biosynthesisIntense artificial selection in distinct taxaGado NeloreEvolutionary history leads to genome changes over time, especially for species that have experienced intense selective pressures over a short period. Here, we investigated the genomic evolution of Bos species by searching for potential selection signatures, focusing on Nelore, an economically relevant cattle breed in Brazil. We assessed the genomic processes determining the molecular evolution across Nelore and thirteen other related taxa by evaluating (i) amino acid sequence conservation, (ii) the dN/dS ratio, and (iii) gene families? turnover rate (lambda. Low conserved regions potentially associated with fatty acid metabolism seem to reflect differences in meat fat content in taxa with different evolutionary histories. All Bos species presented genes under positive selection, especially B. indicus and Nelore, which include transport protein cobalamin, glycolipid metabolism, and hormone signaling. These findings could be explained by constant selective pressures to obtain higher immune resistance and efficient metabolism. The gene contraction rate across the Nelore + B. indicus branch was almost nine times higher than that in other lineages (lambda = 0.01043 vs. 0.00121), indicating gene losses during the domestication process. Amino acid biosynthesis, reproductive and innate immune system-related pathways were associated with genes recognized within the most frequent rapidly evolving gene families and in genes under positive selection, supporting the substantial relevance of such traits from a domestication perspective. Our data provide new insights into how the genome may respond to intense artificial selection in distinct taxa, and reinforces the presence of selective pressures on traits potentially relevant for future animal breeding investments.THAINÁ CORTEZ, Universidade de São Paulo; HORÁCIO MONTENEGRO, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo; LUIZ L. COUTINHO, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; SÔNIA C. S. ANDRADE, Universidade de São Paulo.CORTEZ, T.MONTENEGRO, H.COUTINHO, L. L.REGITANO, L. C. de A.ANDRADE, S. C. S.2023-03-08T17:50:33Z2023-03-08T17:50:33Z2023-03-082022info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article19 p.Plos One, v. 17, n. 12, e0279091, 2022.http://www.alice.cnptia.embrapa.br/alice/handle/doc/115219710.1371/journal.pone.0279091enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2023-03-08T17:50:33Zoai:www.alice.cnptia.embrapa.br:doc/1152197Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542023-03-08T17:50:33Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false
dc.title.none.fl_str_mv Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus).
title Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus).
spellingShingle Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus).
CORTEZ, T.
Genomic evolution of Bos species
Amino acid biosynthesis
Intense artificial selection in distinct taxa
Gado Nelore
title_short Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus).
title_full Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus).
title_fullStr Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus).
title_full_unstemmed Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus).
title_sort Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus).
author CORTEZ, T.
author_facet CORTEZ, T.
MONTENEGRO, H.
COUTINHO, L. L.
REGITANO, L. C. de A.
ANDRADE, S. C. S.
author_role author
author2 MONTENEGRO, H.
COUTINHO, L. L.
REGITANO, L. C. de A.
ANDRADE, S. C. S.
author2_role author
author
author
author
dc.contributor.none.fl_str_mv THAINÁ CORTEZ, Universidade de São Paulo; HORÁCIO MONTENEGRO, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo; LUIZ L. COUTINHO, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; SÔNIA C. S. ANDRADE, Universidade de São Paulo.
dc.contributor.author.fl_str_mv CORTEZ, T.
MONTENEGRO, H.
COUTINHO, L. L.
REGITANO, L. C. de A.
ANDRADE, S. C. S.
dc.subject.por.fl_str_mv Genomic evolution of Bos species
Amino acid biosynthesis
Intense artificial selection in distinct taxa
Gado Nelore
topic Genomic evolution of Bos species
Amino acid biosynthesis
Intense artificial selection in distinct taxa
Gado Nelore
description Evolutionary history leads to genome changes over time, especially for species that have experienced intense selective pressures over a short period. Here, we investigated the genomic evolution of Bos species by searching for potential selection signatures, focusing on Nelore, an economically relevant cattle breed in Brazil. We assessed the genomic processes determining the molecular evolution across Nelore and thirteen other related taxa by evaluating (i) amino acid sequence conservation, (ii) the dN/dS ratio, and (iii) gene families? turnover rate (lambda. Low conserved regions potentially associated with fatty acid metabolism seem to reflect differences in meat fat content in taxa with different evolutionary histories. All Bos species presented genes under positive selection, especially B. indicus and Nelore, which include transport protein cobalamin, glycolipid metabolism, and hormone signaling. These findings could be explained by constant selective pressures to obtain higher immune resistance and efficient metabolism. The gene contraction rate across the Nelore + B. indicus branch was almost nine times higher than that in other lineages (lambda = 0.01043 vs. 0.00121), indicating gene losses during the domestication process. Amino acid biosynthesis, reproductive and innate immune system-related pathways were associated with genes recognized within the most frequent rapidly evolving gene families and in genes under positive selection, supporting the substantial relevance of such traits from a domestication perspective. Our data provide new insights into how the genome may respond to intense artificial selection in distinct taxa, and reinforces the presence of selective pressures on traits potentially relevant for future animal breeding investments.
publishDate 2022
dc.date.none.fl_str_mv 2022
2023-03-08T17:50:33Z
2023-03-08T17:50:33Z
2023-03-08
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 Plos One, v. 17, n. 12, e0279091, 2022.
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1152197
10.1371/journal.pone.0279091
identifier_str_mv Plos One, v. 17, n. 12, e0279091, 2022.
10.1371/journal.pone.0279091
url http://www.alice.cnptia.embrapa.br/alice/handle/doc/1152197
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 19 p.
dc.source.none.fl_str_mv reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
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