Identification of copy number variations in the genome of Dairy Gir cattle
Autor(a) principal: | |
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Data de Publicação: | 2023 |
Outros Autores: | , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1371/journal.pone.0284085 http://hdl.handle.net/11449/245623 |
Resumo: | Studying structural variants that can control complex traits is relevant for dairy cattle production, especially for animals that are tolerant to breeding conditions in the tropics, such as the Dairy Gir cattle. This study identified and characterized high confidence copy number variation regions (CNVR) in the Gir breed genome. A total of 38 animals were whole-genome sequenced, and 566 individuals were genotyped with a high-density SNP panel, among which 36 animals had both sequencing and SNP genotyping data available. Two sets of high confidence CNVR were established: one based on common CNV identified in the studied population (CNVR_POP), and another with CNV identified in sires with both sequence and SNP genotyping data available (CNVR_ANI). We found 10 CNVR_POP and 45 CNVR_ANI, which covered 1.05 Mb and 4.4 Mb of the bovine genome, respectively. Merging these CNV sets for functional analysis resulted in 48 unique high confidence CNVR. The overlapping genes were previously related to embryonic mortality, environmental adaptation, evolutionary process, immune response, longevity, mammary gland, resistance to gastrointestinal parasites, and stimuli recognition, among others. Our results contribute to a better understanding of the Gir breed genome. Moreover, the CNV identified in this study can potentially affect genes related to complex traits, such as production, health, and reproduction. |
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Identification of copy number variations in the genome of Dairy Gir cattleStudying structural variants that can control complex traits is relevant for dairy cattle production, especially for animals that are tolerant to breeding conditions in the tropics, such as the Dairy Gir cattle. This study identified and characterized high confidence copy number variation regions (CNVR) in the Gir breed genome. A total of 38 animals were whole-genome sequenced, and 566 individuals were genotyped with a high-density SNP panel, among which 36 animals had both sequencing and SNP genotyping data available. Two sets of high confidence CNVR were established: one based on common CNV identified in the studied population (CNVR_POP), and another with CNV identified in sires with both sequence and SNP genotyping data available (CNVR_ANI). We found 10 CNVR_POP and 45 CNVR_ANI, which covered 1.05 Mb and 4.4 Mb of the bovine genome, respectively. Merging these CNV sets for functional analysis resulted in 48 unique high confidence CNVR. The overlapping genes were previously related to embryonic mortality, environmental adaptation, evolutionary process, immune response, longevity, mammary gland, resistance to gastrointestinal parasites, and stimuli recognition, among others. Our results contribute to a better understanding of the Gir breed genome. Moreover, the CNV identified in this study can potentially affect genes related to complex traits, such as production, health, and reproduction.Coordenação de Aperfeiçoamento de Pessoa de Nível Superior (CAPES)National Council for Scientific and Technological DevelopmentEmbrapa (Brazil)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Univ Estadual Paulista, Dept Engn & Ciencias Exatas, Jaboticabal, SP, BrazilUniv Guelph, Ctr Genet Improvement Livestock, Dept Anim Biosci, Guelph, ON, CanadaMichigan State Univ, Dept Anim Sci, E Lansing, MI USAUniv Fed Goias, Dept Zootecnia, Goiania, GO, BrazilEmbrapa Gado Leite, Juiz De Fora, MG, BrazilUniv Estadual Paulista, Dept Engn & Ciencias Exatas, Jaboticabal, SP, BrazilCAPES: 001National Council for Scientific and Technological Development: CNPq 431629/2016-1Embrapa (Brazil): SEG 02.13.05.011.00.00CNPq: 310199/20158CNPq: PPM00606/16Public Library ScienceUniversidade Estadual Paulista (UNESP)Univ GuelphMichigan State UnivUniversidade Federal de Goiás (UFG)Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Braga, Larissa G. [UNESP]Chud, Tatiane C. S.Watanabe, Rafael N. [UNESP]Savegnago, Rodrigo P.Sena, Thomaz M. [UNESP]Carmo, Adriana S. doMachado, Marco A.Panetto, Joao Claudio do C.Silva, Marcos Vinicius G. B. daMunari, Danisio P. [UNESP]2023-07-29T12:00:19Z2023-07-29T12:00:19Z2023-04-10info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article19http://dx.doi.org/10.1371/journal.pone.0284085Plos One. San Francisco: Public Library Science, v. 18, n. 4, 19 p., 2023.1932-6203http://hdl.handle.net/11449/24562310.1371/journal.pone.0284085WOS:000973087800024Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengPlos Oneinfo:eu-repo/semantics/openAccess2024-06-06T13:42:22Zoai:repositorio.unesp.br:11449/245623Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T15:34:55.919739Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Identification of copy number variations in the genome of Dairy Gir cattle |
title |
Identification of copy number variations in the genome of Dairy Gir cattle |
spellingShingle |
Identification of copy number variations in the genome of Dairy Gir cattle Braga, Larissa G. [UNESP] |
title_short |
Identification of copy number variations in the genome of Dairy Gir cattle |
title_full |
Identification of copy number variations in the genome of Dairy Gir cattle |
title_fullStr |
Identification of copy number variations in the genome of Dairy Gir cattle |
title_full_unstemmed |
Identification of copy number variations in the genome of Dairy Gir cattle |
title_sort |
Identification of copy number variations in the genome of Dairy Gir cattle |
author |
Braga, Larissa G. [UNESP] |
author_facet |
Braga, Larissa G. [UNESP] Chud, Tatiane C. S. Watanabe, Rafael N. [UNESP] Savegnago, Rodrigo P. Sena, Thomaz M. [UNESP] Carmo, Adriana S. do Machado, Marco A. Panetto, Joao Claudio do C. Silva, Marcos Vinicius G. B. da Munari, Danisio P. [UNESP] |
author_role |
author |
author2 |
Chud, Tatiane C. S. Watanabe, Rafael N. [UNESP] Savegnago, Rodrigo P. Sena, Thomaz M. [UNESP] Carmo, Adriana S. do Machado, Marco A. Panetto, Joao Claudio do C. Silva, Marcos Vinicius G. B. da Munari, Danisio P. [UNESP] |
author2_role |
author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (UNESP) Univ Guelph Michigan State Univ Universidade Federal de Goiás (UFG) Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) |
dc.contributor.author.fl_str_mv |
Braga, Larissa G. [UNESP] Chud, Tatiane C. S. Watanabe, Rafael N. [UNESP] Savegnago, Rodrigo P. Sena, Thomaz M. [UNESP] Carmo, Adriana S. do Machado, Marco A. Panetto, Joao Claudio do C. Silva, Marcos Vinicius G. B. da Munari, Danisio P. [UNESP] |
description |
Studying structural variants that can control complex traits is relevant for dairy cattle production, especially for animals that are tolerant to breeding conditions in the tropics, such as the Dairy Gir cattle. This study identified and characterized high confidence copy number variation regions (CNVR) in the Gir breed genome. A total of 38 animals were whole-genome sequenced, and 566 individuals were genotyped with a high-density SNP panel, among which 36 animals had both sequencing and SNP genotyping data available. Two sets of high confidence CNVR were established: one based on common CNV identified in the studied population (CNVR_POP), and another with CNV identified in sires with both sequence and SNP genotyping data available (CNVR_ANI). We found 10 CNVR_POP and 45 CNVR_ANI, which covered 1.05 Mb and 4.4 Mb of the bovine genome, respectively. Merging these CNV sets for functional analysis resulted in 48 unique high confidence CNVR. The overlapping genes were previously related to embryonic mortality, environmental adaptation, evolutionary process, immune response, longevity, mammary gland, resistance to gastrointestinal parasites, and stimuli recognition, among others. Our results contribute to a better understanding of the Gir breed genome. Moreover, the CNV identified in this study can potentially affect genes related to complex traits, such as production, health, and reproduction. |
publishDate |
2023 |
dc.date.none.fl_str_mv |
2023-07-29T12:00:19Z 2023-07-29T12:00:19Z 2023-04-10 |
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/10.1371/journal.pone.0284085 Plos One. San Francisco: Public Library Science, v. 18, n. 4, 19 p., 2023. 1932-6203 http://hdl.handle.net/11449/245623 10.1371/journal.pone.0284085 WOS:000973087800024 |
url |
http://dx.doi.org/10.1371/journal.pone.0284085 http://hdl.handle.net/11449/245623 |
identifier_str_mv |
Plos One. San Francisco: Public Library Science, v. 18, n. 4, 19 p., 2023. 1932-6203 10.1371/journal.pone.0284085 WOS:000973087800024 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Plos One |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
19 |
dc.publisher.none.fl_str_mv |
Public Library Science |
publisher.none.fl_str_mv |
Public Library Science |
dc.source.none.fl_str_mv |
Web of Science 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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1808128536328798208 |