Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle

Detalhes bibliográficos
Autor(a) principal: Berton, Mariana Piatto [UNESP]
Data de Publicação: 2022
Outros Autores: de Lemos, Marcos Vinícius Antunes [UNESP], Stafuzza, Nedenia Bonvino, Simielli Fonseca, Larissa Fernanda [UNESP], Silva, Danielly Beraldo dos Santos [UNESP], Peripolli, Elisa [UNESP], Pereira, Angélica S. C., Magalhães, Ana Fabricia Braga [UNESP], Albuquerque, Lucia G. [UNESP], Baldi, Fernando [UNESP]
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1111/age.13242
http://hdl.handle.net/11449/241299
Resumo: This study aimed to integrate analyses of structural variations and differentially expressed genes (DEGs) associated with the beef fatty acid (FA) profile in Nellore cattle. Copy numbers variation (CNV) detection was performed using the penncnv algorithm and CNVRuler software in 3794 genotyped animals through the High-Density Bovine BeadChip. In order to perform the genomic wide association study (GWAS), a total of 963 genotyped animals were selected to obtain the intramuscular lipid concentration and quantify the beef FA profile. A total of 48 animals belonging to the same farm and management lot were extracted from the 963 genotyped and phenotyped animals to carry out the transcriptomic and differentially expressed gene analyses. The GWAS with extreme groups of FA profiles was performed using a logistic model. A total of 43, 42, 66 and 35 significant CNV regions (p < 0.05) for saturated, monounsaturated, polyunsaturated and omega 3 and 6 fatty acids were identified respectively. The paired-end sequencing of 48 samples was performed using the Illumina HiSeq2500 platform. Real-time quantitative PCR was used to validate the DEGs identified by RNA-seq analysis. The results showed several DEGs associated with the FA profile of Longissimus thoracis, such as BSCL2 and SAMD8. Enriched terms as the cellular response to corticosteroid (GO:0071384) and glucocorticoid stimulus (GO:0071385) could be highlighted. The identification of structural variations harboring candidate genes for beef FA must contribute to the elucidation of the genetic basis that determines the beef FA composition of intramuscular fat in Nellore cattle. Our results will contribute to the identification of potential biomarkers for complex phenotypes, such as the FA profile, to improve the reliability of the genomic predictions including pre-selected variants using differentiated weighting in the genomic models.
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spelling Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattleBos indicuscopy numbers variationgenomic selectiongenomic wide association studyRNA-seqThis study aimed to integrate analyses of structural variations and differentially expressed genes (DEGs) associated with the beef fatty acid (FA) profile in Nellore cattle. Copy numbers variation (CNV) detection was performed using the penncnv algorithm and CNVRuler software in 3794 genotyped animals through the High-Density Bovine BeadChip. In order to perform the genomic wide association study (GWAS), a total of 963 genotyped animals were selected to obtain the intramuscular lipid concentration and quantify the beef FA profile. A total of 48 animals belonging to the same farm and management lot were extracted from the 963 genotyped and phenotyped animals to carry out the transcriptomic and differentially expressed gene analyses. The GWAS with extreme groups of FA profiles was performed using a logistic model. A total of 43, 42, 66 and 35 significant CNV regions (p < 0.05) for saturated, monounsaturated, polyunsaturated and omega 3 and 6 fatty acids were identified respectively. The paired-end sequencing of 48 samples was performed using the Illumina HiSeq2500 platform. Real-time quantitative PCR was used to validate the DEGs identified by RNA-seq analysis. The results showed several DEGs associated with the FA profile of Longissimus thoracis, such as BSCL2 and SAMD8. Enriched terms as the cellular response to corticosteroid (GO:0071384) and glucocorticoid stimulus (GO:0071385) could be highlighted. The identification of structural variations harboring candidate genes for beef FA must contribute to the elucidation of the genetic basis that determines the beef FA composition of intramuscular fat in Nellore cattle. Our results will contribute to the identification of potential biomarkers for complex phenotypes, such as the FA profile, to improve the reliability of the genomic predictions including pre-selected variants using differentiated weighting in the genomic models.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Departamento de Zootecnia Universidade Estadual Paulista Faculdade de Ciências Agrárias e VeterináriasCentro de Pesquisa em Bovinos de Corte Instituto de ZootecniaDepartamento de Nutrição e Produção Animal Universidade de São Paulo Faculdade de Medicina Veterinária e ZootecniaDepartamento de Zootecnia Universidade Estadual Paulista Faculdade de Ciências Agrárias e VeterináriasFAPESP: 2009/16118-5FAPESP: 2011/21241-0FAPESP: 2017/06603-0FAPESP: 2017/10493-5FAPESP: 2017/10630-2FAPESP: 2017/27148-9FAPESP: 2018/19216-7FAPESP: 2018/19463-4FAPESP: 2018/20026-8FAPESP: 2018/25247-2FAPESP: 2019/04929-0FAPESP: 2019/10438-0FAPESP: 2019/16732-7Universidade Estadual Paulista (UNESP)Instituto de ZootecniaUniversidade de São Paulo (USP)Berton, Mariana Piatto [UNESP]de Lemos, Marcos Vinícius Antunes [UNESP]Stafuzza, Nedenia BonvinoSimielli Fonseca, Larissa Fernanda [UNESP]Silva, Danielly Beraldo dos Santos [UNESP]Peripolli, Elisa [UNESP]Pereira, Angélica S. C.Magalhães, Ana Fabricia Braga [UNESP]Albuquerque, Lucia G. [UNESP]Baldi, Fernando [UNESP]2023-03-01T20:55:53Z2023-03-01T20:55:53Z2022-10-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article570-582http://dx.doi.org/10.1111/age.13242Animal Genetics, v. 53, n. 5, p. 570-582, 2022.1365-20520268-9146http://hdl.handle.net/11449/24129910.1111/age.132422-s2.0-85133714619Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengAnimal Geneticsinfo:eu-repo/semantics/openAccess2024-06-07T18:39:01Zoai:repositorio.unesp.br:11449/241299Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T13:41:34.353799Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle
title Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle
spellingShingle Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle
Berton, Mariana Piatto [UNESP]
Bos indicus
copy numbers variation
genomic selection
genomic wide association study
RNA-seq
title_short Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle
title_full Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle
title_fullStr Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle
title_full_unstemmed Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle
title_sort Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle
author Berton, Mariana Piatto [UNESP]
author_facet Berton, Mariana Piatto [UNESP]
de Lemos, Marcos Vinícius Antunes [UNESP]
Stafuzza, Nedenia Bonvino
Simielli Fonseca, Larissa Fernanda [UNESP]
Silva, Danielly Beraldo dos Santos [UNESP]
Peripolli, Elisa [UNESP]
Pereira, Angélica S. C.
Magalhães, Ana Fabricia Braga [UNESP]
Albuquerque, Lucia G. [UNESP]
Baldi, Fernando [UNESP]
author_role author
author2 de Lemos, Marcos Vinícius Antunes [UNESP]
Stafuzza, Nedenia Bonvino
Simielli Fonseca, Larissa Fernanda [UNESP]
Silva, Danielly Beraldo dos Santos [UNESP]
Peripolli, Elisa [UNESP]
Pereira, Angélica S. C.
Magalhães, Ana Fabricia Braga [UNESP]
Albuquerque, Lucia G. [UNESP]
Baldi, Fernando [UNESP]
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (UNESP)
Instituto de Zootecnia
Universidade de São Paulo (USP)
dc.contributor.author.fl_str_mv Berton, Mariana Piatto [UNESP]
de Lemos, Marcos Vinícius Antunes [UNESP]
Stafuzza, Nedenia Bonvino
Simielli Fonseca, Larissa Fernanda [UNESP]
Silva, Danielly Beraldo dos Santos [UNESP]
Peripolli, Elisa [UNESP]
Pereira, Angélica S. C.
Magalhães, Ana Fabricia Braga [UNESP]
Albuquerque, Lucia G. [UNESP]
Baldi, Fernando [UNESP]
dc.subject.por.fl_str_mv Bos indicus
copy numbers variation
genomic selection
genomic wide association study
RNA-seq
topic Bos indicus
copy numbers variation
genomic selection
genomic wide association study
RNA-seq
description This study aimed to integrate analyses of structural variations and differentially expressed genes (DEGs) associated with the beef fatty acid (FA) profile in Nellore cattle. Copy numbers variation (CNV) detection was performed using the penncnv algorithm and CNVRuler software in 3794 genotyped animals through the High-Density Bovine BeadChip. In order to perform the genomic wide association study (GWAS), a total of 963 genotyped animals were selected to obtain the intramuscular lipid concentration and quantify the beef FA profile. A total of 48 animals belonging to the same farm and management lot were extracted from the 963 genotyped and phenotyped animals to carry out the transcriptomic and differentially expressed gene analyses. The GWAS with extreme groups of FA profiles was performed using a logistic model. A total of 43, 42, 66 and 35 significant CNV regions (p < 0.05) for saturated, monounsaturated, polyunsaturated and omega 3 and 6 fatty acids were identified respectively. The paired-end sequencing of 48 samples was performed using the Illumina HiSeq2500 platform. Real-time quantitative PCR was used to validate the DEGs identified by RNA-seq analysis. The results showed several DEGs associated with the FA profile of Longissimus thoracis, such as BSCL2 and SAMD8. Enriched terms as the cellular response to corticosteroid (GO:0071384) and glucocorticoid stimulus (GO:0071385) could be highlighted. The identification of structural variations harboring candidate genes for beef FA must contribute to the elucidation of the genetic basis that determines the beef FA composition of intramuscular fat in Nellore cattle. Our results will contribute to the identification of potential biomarkers for complex phenotypes, such as the FA profile, to improve the reliability of the genomic predictions including pre-selected variants using differentiated weighting in the genomic models.
publishDate 2022
dc.date.none.fl_str_mv 2022-10-01
2023-03-01T20:55:53Z
2023-03-01T20:55:53Z
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/10.1111/age.13242
Animal Genetics, v. 53, n. 5, p. 570-582, 2022.
1365-2052
0268-9146
http://hdl.handle.net/11449/241299
10.1111/age.13242
2-s2.0-85133714619
url http://dx.doi.org/10.1111/age.13242
http://hdl.handle.net/11449/241299
identifier_str_mv Animal Genetics, v. 53, n. 5, p. 570-582, 2022.
1365-2052
0268-9146
10.1111/age.13242
2-s2.0-85133714619
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Animal Genetics
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 570-582
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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