Capra hircus outliers markers in Brazil: searching for genomic regions under the action of natural selection.
Autor(a) principal: | |
---|---|
Data de Publicação: | 2023 |
Outros Autores: | , , , , |
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/1157489 https://doi.org/10.1590/1678-4685-GMB-2023-0084 |
Resumo: | Identifying genome regions subject to selection in local breeds of Brazil is an opportunity to elucidate the C. hircus genome plasticity, flowing the colonization history of the country. Using SNP Bead Chip Illumina 50K genotyping of Brazilian Anglo-Nubian (standardized breed) and Marota (local endangered population from the semiarid area of Brazil) to show outliers loci in genome regions subject to selection. After applying data quality control, 45,600 SNPs were included in this investigation. Principal component analysis (PCAdapt) and FDIST2 analysis signalized 14 genomic regions more affected by selection in the Brazilian dry zone environment. The genome study signalized regions that are close to the sequences of genes related to growth and embryonic skeletal development (FGF12, AMPD2, OSTN). In addition, flagged regions close to the genes UTSB2 and SLC5A2 contribute to research on functional adaptation with low water needs and poor nutritive diet to survive. Both genes encode proteins that act on osmotic pathways and avoid cell flooding on stress cell responses. Further studies on the genetic role and involvement of these outliers? genomic regions, building a robust conceptual high-resolution map of natural selection drives, help to achieve hardiness candidate genes linked to the evolutionary history of Capra hircus in the semiarid area of Brazil. |
id |
EMBR_7991ea9a7941ee2b6c45387c1d83e9e8 |
---|---|
oai_identifier_str |
oai:www.alice.cnptia.embrapa.br:doc/1157489 |
network_acronym_str |
EMBR |
network_name_str |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
repository_id_str |
2154 |
spelling |
Capra hircus outliers markers in Brazil: searching for genomic regions under the action of natural selection.Candidate genesHardinessOutliersNon-neutral lociTropical adaptationSeleção naturalCaprinoCapra HircusSeleçãoGenomaGenomeNatural selectionIdentifying genome regions subject to selection in local breeds of Brazil is an opportunity to elucidate the C. hircus genome plasticity, flowing the colonization history of the country. Using SNP Bead Chip Illumina 50K genotyping of Brazilian Anglo-Nubian (standardized breed) and Marota (local endangered population from the semiarid area of Brazil) to show outliers loci in genome regions subject to selection. After applying data quality control, 45,600 SNPs were included in this investigation. Principal component analysis (PCAdapt) and FDIST2 analysis signalized 14 genomic regions more affected by selection in the Brazilian dry zone environment. The genome study signalized regions that are close to the sequences of genes related to growth and embryonic skeletal development (FGF12, AMPD2, OSTN). In addition, flagged regions close to the genes UTSB2 and SLC5A2 contribute to research on functional adaptation with low water needs and poor nutritive diet to survive. Both genes encode proteins that act on osmotic pathways and avoid cell flooding on stress cell responses. Further studies on the genetic role and involvement of these outliers? genomic regions, building a robust conceptual high-resolution map of natural selection drives, help to achieve hardiness candidate genes linked to the evolutionary history of Capra hircus in the semiarid area of Brazil.FRANCISCO DE A. DINIZ SOBRINHO, UNIVERSIDADE FEDERAL DO PIAUÍ, Teresina-PI; JEANE DE O. MOURA, INSTITUTO FEDERAL DO PIAUÍ, Teresina-PI; MIKLOS M. BAJAY, UNIVERSIDADE DO ESTADO DE SANTA CATARINA, Laguna-SC; LEONARDO CASTELO BRANCO, UNIVERSIDADE FEDERAL RURAL DA AMAZÔNIA, Belém-PA; ROOSEVELT D. S. BEZERRA, INSTITUTO FEDERAL DO PIAUÍ, Teresina-PI; ADRIANA MELLO DE ARAUJO, CPAP.DINIZ SOBRINHO, F. de A.MOURA, J. de O.BAJAY, M. M.CASTELO BRANCO, L.BEZERRA, R. D. S.ARAÚJO, A. M. de2023-10-25T14:52:19Z2023-10-25T14:52:19Z2023-10-252023info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleGenetics and Molecular Biology, v. 46, n. 3, e20230084, 2023.1678-4685http://www.alice.cnptia.embrapa.br/alice/handle/doc/1157489https://doi.org/10.1590/1678-4685-GMB-2023-0084enginfo: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:EMBRAPA2023-10-25T14:52:19Zoai:www.alice.cnptia.embrapa.br:doc/1157489Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542023-10-25T14:52:19falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542023-10-25T14:52:19Repositório 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 |
Capra hircus outliers markers in Brazil: searching for genomic regions under the action of natural selection. |
title |
Capra hircus outliers markers in Brazil: searching for genomic regions under the action of natural selection. |
spellingShingle |
Capra hircus outliers markers in Brazil: searching for genomic regions under the action of natural selection. DINIZ SOBRINHO, F. de A. Candidate genes Hardiness Outliers Non-neutral loci Tropical adaptation Seleção natural Caprino Capra Hircus Seleção Genoma Genome Natural selection |
title_short |
Capra hircus outliers markers in Brazil: searching for genomic regions under the action of natural selection. |
title_full |
Capra hircus outliers markers in Brazil: searching for genomic regions under the action of natural selection. |
title_fullStr |
Capra hircus outliers markers in Brazil: searching for genomic regions under the action of natural selection. |
title_full_unstemmed |
Capra hircus outliers markers in Brazil: searching for genomic regions under the action of natural selection. |
title_sort |
Capra hircus outliers markers in Brazil: searching for genomic regions under the action of natural selection. |
author |
DINIZ SOBRINHO, F. de A. |
author_facet |
DINIZ SOBRINHO, F. de A. MOURA, J. de O. BAJAY, M. M. CASTELO BRANCO, L. BEZERRA, R. D. S. ARAÚJO, A. M. de |
author_role |
author |
author2 |
MOURA, J. de O. BAJAY, M. M. CASTELO BRANCO, L. BEZERRA, R. D. S. ARAÚJO, A. M. de |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
FRANCISCO DE A. DINIZ SOBRINHO, UNIVERSIDADE FEDERAL DO PIAUÍ, Teresina-PI; JEANE DE O. MOURA, INSTITUTO FEDERAL DO PIAUÍ, Teresina-PI; MIKLOS M. BAJAY, UNIVERSIDADE DO ESTADO DE SANTA CATARINA, Laguna-SC; LEONARDO CASTELO BRANCO, UNIVERSIDADE FEDERAL RURAL DA AMAZÔNIA, Belém-PA; ROOSEVELT D. S. BEZERRA, INSTITUTO FEDERAL DO PIAUÍ, Teresina-PI; ADRIANA MELLO DE ARAUJO, CPAP. |
dc.contributor.author.fl_str_mv |
DINIZ SOBRINHO, F. de A. MOURA, J. de O. BAJAY, M. M. CASTELO BRANCO, L. BEZERRA, R. D. S. ARAÚJO, A. M. de |
dc.subject.por.fl_str_mv |
Candidate genes Hardiness Outliers Non-neutral loci Tropical adaptation Seleção natural Caprino Capra Hircus Seleção Genoma Genome Natural selection |
topic |
Candidate genes Hardiness Outliers Non-neutral loci Tropical adaptation Seleção natural Caprino Capra Hircus Seleção Genoma Genome Natural selection |
description |
Identifying genome regions subject to selection in local breeds of Brazil is an opportunity to elucidate the C. hircus genome plasticity, flowing the colonization history of the country. Using SNP Bead Chip Illumina 50K genotyping of Brazilian Anglo-Nubian (standardized breed) and Marota (local endangered population from the semiarid area of Brazil) to show outliers loci in genome regions subject to selection. After applying data quality control, 45,600 SNPs were included in this investigation. Principal component analysis (PCAdapt) and FDIST2 analysis signalized 14 genomic regions more affected by selection in the Brazilian dry zone environment. The genome study signalized regions that are close to the sequences of genes related to growth and embryonic skeletal development (FGF12, AMPD2, OSTN). In addition, flagged regions close to the genes UTSB2 and SLC5A2 contribute to research on functional adaptation with low water needs and poor nutritive diet to survive. Both genes encode proteins that act on osmotic pathways and avoid cell flooding on stress cell responses. Further studies on the genetic role and involvement of these outliers? genomic regions, building a robust conceptual high-resolution map of natural selection drives, help to achieve hardiness candidate genes linked to the evolutionary history of Capra hircus in the semiarid area of Brazil. |
publishDate |
2023 |
dc.date.none.fl_str_mv |
2023-10-25T14:52:19Z 2023-10-25T14:52:19Z 2023-10-25 2023 |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
Genetics and Molecular Biology, v. 46, n. 3, e20230084, 2023. 1678-4685 http://www.alice.cnptia.embrapa.br/alice/handle/doc/1157489 https://doi.org/10.1590/1678-4685-GMB-2023-0084 |
identifier_str_mv |
Genetics and Molecular Biology, v. 46, n. 3, e20230084, 2023. 1678-4685 |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1157489 https://doi.org/10.1590/1678-4685-GMB-2023-0084 |
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.source.none.fl_str_mv |
reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA |
instname_str |
Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
instacron_str |
EMBRAPA |
institution |
EMBRAPA |
reponame_str |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
collection |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
repository.name.fl_str_mv |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
repository.mail.fl_str_mv |
cg-riaa@embrapa.br |
_version_ |
1794503551240634368 |