Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups
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/10.3390/ani13030359 http://hdl.handle.net/11449/249645 |
Resumo: | The identification and selection of genetically superior animals for residual feed intake (RFI) could enhance productivity and minimize environmental impacts. The aim of this study was to use RNA-seq data to identify the differentially expressed genes (DEGs), known non-coding RNAs (ncRNAs), specific biomarkers and enriched biological processes associated with RFI of the liver in Nellore cattle in two genetic groups. In genetic group 1 (G1), 24 extreme RFI animals (12 low RFI (LRFI) versus 12 high RFI (HRFI)) were selected from a population of 60 Nellore bulls. The RNA-seq of the samples from their liver tissues was performed using an Illumina HiSeq 2000. In genetic group 2 (G2), 20 samples of liver tissue of Nellore bulls divergent for RFI (LRFI, n = 10 versus HRFI, n = 10) were selected from 83 animals. The raw data of the G2 were chosen from the ENA repository. A total of 1811 DEGs were found for the G1 and 2054 for the G2 (p-value ≤ 0.05). We detected 88 common genes in both genetic groups, of which 33 were involved in the immune response and in blocking oxidative stress. In addition, seven (B2M, ADSS, SNX2, TUBA4A, ARHGAP18, MECR, and ABCF3) possible gene biomarkers were identified through a receiver operating characteristic analysis (ROC) considering an AUC > 0.70. The B2M gene was overexpressed in the LRFI group. This gene regulates the lipid metabolism protein turnover and inhibits cell death. We also found non-coding RNAs in both groups. MIR25 was up-regulated and SNORD16 was down-regulated in the LRFI for G1. For G2, up-regulated RNase_MRP and SCARNA10 were found. We highlight MIR25 as being able to act by blocking cytotoxicity and oxidative stress and RMRP as a blocker of mitochondrial damage. The biological pathways associated with RFI of the liver in Nellore cattle in the two genetic groups were for energy metabolism, protein turnover, redox homeostasis and the immune response. The common transcripts, biomarkers and metabolic pathways found in the two genetic groups make this unprecedented work even more relevant, since the results are valid for different herds raised in different ways. The results reinforce the biological importance of these known processes but also reveal new insights into the complexity of the liver tissue transcriptome of Nellore cattle. |
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Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groupsbiomarkersbovinefeed efficiencyliver tissuenon-coding RNAsRNA-SeqThe identification and selection of genetically superior animals for residual feed intake (RFI) could enhance productivity and minimize environmental impacts. The aim of this study was to use RNA-seq data to identify the differentially expressed genes (DEGs), known non-coding RNAs (ncRNAs), specific biomarkers and enriched biological processes associated with RFI of the liver in Nellore cattle in two genetic groups. In genetic group 1 (G1), 24 extreme RFI animals (12 low RFI (LRFI) versus 12 high RFI (HRFI)) were selected from a population of 60 Nellore bulls. The RNA-seq of the samples from their liver tissues was performed using an Illumina HiSeq 2000. In genetic group 2 (G2), 20 samples of liver tissue of Nellore bulls divergent for RFI (LRFI, n = 10 versus HRFI, n = 10) were selected from 83 animals. The raw data of the G2 were chosen from the ENA repository. A total of 1811 DEGs were found for the G1 and 2054 for the G2 (p-value ≤ 0.05). We detected 88 common genes in both genetic groups, of which 33 were involved in the immune response and in blocking oxidative stress. In addition, seven (B2M, ADSS, SNX2, TUBA4A, ARHGAP18, MECR, and ABCF3) possible gene biomarkers were identified through a receiver operating characteristic analysis (ROC) considering an AUC > 0.70. The B2M gene was overexpressed in the LRFI group. This gene regulates the lipid metabolism protein turnover and inhibits cell death. We also found non-coding RNAs in both groups. MIR25 was up-regulated and SNORD16 was down-regulated in the LRFI for G1. For G2, up-regulated RNase_MRP and SCARNA10 were found. We highlight MIR25 as being able to act by blocking cytotoxicity and oxidative stress and RMRP as a blocker of mitochondrial damage. The biological pathways associated with RFI of the liver in Nellore cattle in the two genetic groups were for energy metabolism, protein turnover, redox homeostasis and the immune response. The common transcripts, biomarkers and metabolic pathways found in the two genetic groups make this unprecedented work even more relevant, since the results are valid for different herds raised in different ways. The results reinforce the biological importance of these known processes but also reveal new insights into the complexity of the liver tissue transcriptome of Nellore cattle.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)School of Agricultural and Veterinary Sciences Sao Paulo State University (UNESP)Igenomix S.L.Department of Physiology Faculty of Medicine and Odontology University of ValenciaNational Council for Scientific and Technological Development (CNPq), Distrito FederalInstitute of Animal ScienceSchool of Agricultural and Veterinary Sciences Sao Paulo State University (UNESP)Universidade Estadual Paulista (UNESP)Igenomix S.L.University of ValenciaNational Council for Scientific and Technological Development (CNPq)Institute of Animal ScienceSerna-García, Marta [UNESP]Fonseca, Larissa Fernanda Simielli [UNESP]Panadero Romero, Joaquin JavierCarretero Asuncion, Juliandos Santos Silva, Danielly Beraldo [UNESP]Salatta, Bruna Maria [UNESP]Frezarim, Gabriela Bonfá [UNESP]Mercadante, Maria Eugênia ZerlottiBonilha, Sarah Figueiredo MartinsFerro, Jesus Aparecido [UNESP]De Albuquerque, Lucia Galvão [UNESP]2023-07-29T16:05:23Z2023-07-29T16:05:23Z2023-02-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.3390/ani13030359Animals, v. 13, n. 3, 2023.2076-2615http://hdl.handle.net/11449/24964510.3390/ani130303592-s2.0-85147802954Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengAnimalsinfo:eu-repo/semantics/openAccess2024-06-07T18:40:39Zoai:repositorio.unesp.br:11449/249645Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T15:50:10.648758Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups |
title |
Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups |
spellingShingle |
Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups Serna-García, Marta [UNESP] biomarkers bovine feed efficiency liver tissue non-coding RNAs RNA-Seq |
title_short |
Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups |
title_full |
Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups |
title_fullStr |
Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups |
title_full_unstemmed |
Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups |
title_sort |
Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups |
author |
Serna-García, Marta [UNESP] |
author_facet |
Serna-García, Marta [UNESP] Fonseca, Larissa Fernanda Simielli [UNESP] Panadero Romero, Joaquin Javier Carretero Asuncion, Julian dos Santos Silva, Danielly Beraldo [UNESP] Salatta, Bruna Maria [UNESP] Frezarim, Gabriela Bonfá [UNESP] Mercadante, Maria Eugênia Zerlotti Bonilha, Sarah Figueiredo Martins Ferro, Jesus Aparecido [UNESP] De Albuquerque, Lucia Galvão [UNESP] |
author_role |
author |
author2 |
Fonseca, Larissa Fernanda Simielli [UNESP] Panadero Romero, Joaquin Javier Carretero Asuncion, Julian dos Santos Silva, Danielly Beraldo [UNESP] Salatta, Bruna Maria [UNESP] Frezarim, Gabriela Bonfá [UNESP] Mercadante, Maria Eugênia Zerlotti Bonilha, Sarah Figueiredo Martins Ferro, Jesus Aparecido [UNESP] De Albuquerque, Lucia Galvão [UNESP] |
author2_role |
author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (UNESP) Igenomix S.L. University of Valencia National Council for Scientific and Technological Development (CNPq) Institute of Animal Science |
dc.contributor.author.fl_str_mv |
Serna-García, Marta [UNESP] Fonseca, Larissa Fernanda Simielli [UNESP] Panadero Romero, Joaquin Javier Carretero Asuncion, Julian dos Santos Silva, Danielly Beraldo [UNESP] Salatta, Bruna Maria [UNESP] Frezarim, Gabriela Bonfá [UNESP] Mercadante, Maria Eugênia Zerlotti Bonilha, Sarah Figueiredo Martins Ferro, Jesus Aparecido [UNESP] De Albuquerque, Lucia Galvão [UNESP] |
dc.subject.por.fl_str_mv |
biomarkers bovine feed efficiency liver tissue non-coding RNAs RNA-Seq |
topic |
biomarkers bovine feed efficiency liver tissue non-coding RNAs RNA-Seq |
description |
The identification and selection of genetically superior animals for residual feed intake (RFI) could enhance productivity and minimize environmental impacts. The aim of this study was to use RNA-seq data to identify the differentially expressed genes (DEGs), known non-coding RNAs (ncRNAs), specific biomarkers and enriched biological processes associated with RFI of the liver in Nellore cattle in two genetic groups. In genetic group 1 (G1), 24 extreme RFI animals (12 low RFI (LRFI) versus 12 high RFI (HRFI)) were selected from a population of 60 Nellore bulls. The RNA-seq of the samples from their liver tissues was performed using an Illumina HiSeq 2000. In genetic group 2 (G2), 20 samples of liver tissue of Nellore bulls divergent for RFI (LRFI, n = 10 versus HRFI, n = 10) were selected from 83 animals. The raw data of the G2 were chosen from the ENA repository. A total of 1811 DEGs were found for the G1 and 2054 for the G2 (p-value ≤ 0.05). We detected 88 common genes in both genetic groups, of which 33 were involved in the immune response and in blocking oxidative stress. In addition, seven (B2M, ADSS, SNX2, TUBA4A, ARHGAP18, MECR, and ABCF3) possible gene biomarkers were identified through a receiver operating characteristic analysis (ROC) considering an AUC > 0.70. The B2M gene was overexpressed in the LRFI group. This gene regulates the lipid metabolism protein turnover and inhibits cell death. We also found non-coding RNAs in both groups. MIR25 was up-regulated and SNORD16 was down-regulated in the LRFI for G1. For G2, up-regulated RNase_MRP and SCARNA10 were found. We highlight MIR25 as being able to act by blocking cytotoxicity and oxidative stress and RMRP as a blocker of mitochondrial damage. The biological pathways associated with RFI of the liver in Nellore cattle in the two genetic groups were for energy metabolism, protein turnover, redox homeostasis and the immune response. The common transcripts, biomarkers and metabolic pathways found in the two genetic groups make this unprecedented work even more relevant, since the results are valid for different herds raised in different ways. The results reinforce the biological importance of these known processes but also reveal new insights into the complexity of the liver tissue transcriptome of Nellore cattle. |
publishDate |
2023 |
dc.date.none.fl_str_mv |
2023-07-29T16:05:23Z 2023-07-29T16:05:23Z 2023-02-01 |
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/10.3390/ani13030359 Animals, v. 13, n. 3, 2023. 2076-2615 http://hdl.handle.net/11449/249645 10.3390/ani13030359 2-s2.0-85147802954 |
url |
http://dx.doi.org/10.3390/ani13030359 http://hdl.handle.net/11449/249645 |
identifier_str_mv |
Animals, v. 13, n. 3, 2023. 2076-2615 10.3390/ani13030359 2-s2.0-85147802954 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Animals |
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_ |
1808128570627719168 |