Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes.
Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770 K bp). After quality control, 820 SNPs showed at least one sample with ASE. These SNPs were widespread among all autosomal chromosomes, being 32.01% found in 3'UTR and 31.41% in coding regions. We observed a considerable variation of ASE profile among individuals, which highlighted the need for biological replicates in ASE studies. Functional analysis revealed that ASE genes play critical biological functions in the development and maintenance of muscle tissue. Additionally, some of these genes were previously reported as associated with beef production and quality traits in livestock, thus indicating a possible source of bias on genomic predictions for these traits.
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Format: | Artigo de periódico biblioteca |
Language: | Ingles English |
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2020-10-09
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Subjects: | Expressão gênica, Regulação da expressão gênica, Allelic expression, Allele-specific expression, Bos Indicus, Gene expression regulation, |
Online Access: | http://www.alice.cnptia.embrapa.br/alice/handle/doc/1125395 https://doi.org/10.1038/S41598-020-67089-0 |
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dig-alice-doc-11253952020-10-10T09:14:38Z Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes. SOUZA, M. M. de ZERLOTINI NETO, A. ROCHA, M. I. P. BRUSCADIN, J. J. DINIZ, W. J. da S. CARDOSO, T. F. CESAR, A. S. M. AFONSO, J. ANDRADE, B. G. N. MUDADU, M. de A. MOKRY, F. B. TIZIOTO, P. C. OLIVEIRA, P. S. N. de NICIURA, S. C. M. COUTINHO, L. L. REGITANO, L. C. de A. MARCELA MARIA DE SOUZA, UFSCar; ADHEMAR ZERLOTINI NETO, CNPTIA; MARINA IBELLI PEREIRA ROCHA, UFSCar; JENNIFER JESSICA BRUSCADIN, UFSCar; WELLISON JARLES DA SILVA DINIZ, UFSCar; TAINÃ FIGUEIREDO CARDOSO; ALINE SILVA MELLO CESAR, ESALQ/USP; JULIANA AFONSO, UFSCar; BRUNO GABRIEL NASCIMENTO ANDRADE, UFSCar; MAURICIO DE ALVARENGA MUDADU, CNPTIA; FABIANA BARICHELLO MOKRY, UFSCar; POLYANA CRISTINE TIZIOTO, NGS Soluções Genômicas, Piracicaba; PRISCILA SILVA NEUBERN DE OLIVEIRA; SIMONE CRISTINA MEO NICIURA, CPPSE; LUIZ LEHMANN COUTINHO, ESALQ/USP; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE. Expressão gênica Regulação da expressão gênica Allelic expression Allele-specific expression Bos Indicus Gene expression regulation Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770 K bp). After quality control, 820 SNPs showed at least one sample with ASE. These SNPs were widespread among all autosomal chromosomes, being 32.01% found in 3'UTR and 31.41% in coding regions. We observed a considerable variation of ASE profile among individuals, which highlighted the need for biological replicates in ASE studies. Functional analysis revealed that ASE genes play critical biological functions in the development and maintenance of muscle tissue. Additionally, some of these genes were previously reported as associated with beef production and quality traits in livestock, thus indicating a possible source of bias on genomic predictions for these traits. Na publicação: Adhemar Zerlotini. Article number: 10204. 2020-10-10T09:14:31Z 2020-10-10T09:14:31Z 2020-10-09 2020 Artigo de periódico Scientific Reports, v. 10, n. 1, p. 1-11, 2020. http://www.alice.cnptia.embrapa.br/alice/handle/doc/1125395 https://doi.org/10.1038/S41598-020-67089-0 Ingles en openAccess |
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Expressão gênica Regulação da expressão gênica Allelic expression Allele-specific expression Bos Indicus Gene expression regulation Expressão gênica Regulação da expressão gênica Allelic expression Allele-specific expression Bos Indicus Gene expression regulation |
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Expressão gênica Regulação da expressão gênica Allelic expression Allele-specific expression Bos Indicus Gene expression regulation Expressão gênica Regulação da expressão gênica Allelic expression Allele-specific expression Bos Indicus Gene expression regulation SOUZA, M. M. de ZERLOTINI NETO, A. ROCHA, M. I. P. BRUSCADIN, J. J. DINIZ, W. J. da S. CARDOSO, T. F. CESAR, A. S. M. AFONSO, J. ANDRADE, B. G. N. MUDADU, M. de A. MOKRY, F. B. TIZIOTO, P. C. OLIVEIRA, P. S. N. de NICIURA, S. C. M. COUTINHO, L. L. REGITANO, L. C. de A. Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes. |
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Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770 K bp). After quality control, 820 SNPs showed at least one sample with ASE. These SNPs were widespread among all autosomal chromosomes, being 32.01% found in 3'UTR and 31.41% in coding regions. We observed a considerable variation of ASE profile among individuals, which highlighted the need for biological replicates in ASE studies. Functional analysis revealed that ASE genes play critical biological functions in the development and maintenance of muscle tissue. Additionally, some of these genes were previously reported as associated with beef production and quality traits in livestock, thus indicating a possible source of bias on genomic predictions for these traits. |
author2 |
MARCELA MARIA DE SOUZA, UFSCar; ADHEMAR ZERLOTINI NETO, CNPTIA; MARINA IBELLI PEREIRA ROCHA, UFSCar; JENNIFER JESSICA BRUSCADIN, UFSCar; WELLISON JARLES DA SILVA DINIZ, UFSCar; TAINÃ FIGUEIREDO CARDOSO; ALINE SILVA MELLO CESAR, ESALQ/USP; JULIANA AFONSO, UFSCar; BRUNO GABRIEL NASCIMENTO ANDRADE, UFSCar; MAURICIO DE ALVARENGA MUDADU, CNPTIA; FABIANA BARICHELLO MOKRY, UFSCar; POLYANA CRISTINE TIZIOTO, NGS Soluções Genômicas, Piracicaba; PRISCILA SILVA NEUBERN DE OLIVEIRA; SIMONE CRISTINA MEO NICIURA, CPPSE; LUIZ LEHMANN COUTINHO, ESALQ/USP; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE. |
author_facet |
MARCELA MARIA DE SOUZA, UFSCar; ADHEMAR ZERLOTINI NETO, CNPTIA; MARINA IBELLI PEREIRA ROCHA, UFSCar; JENNIFER JESSICA BRUSCADIN, UFSCar; WELLISON JARLES DA SILVA DINIZ, UFSCar; TAINÃ FIGUEIREDO CARDOSO; ALINE SILVA MELLO CESAR, ESALQ/USP; JULIANA AFONSO, UFSCar; BRUNO GABRIEL NASCIMENTO ANDRADE, UFSCar; MAURICIO DE ALVARENGA MUDADU, CNPTIA; FABIANA BARICHELLO MOKRY, UFSCar; POLYANA CRISTINE TIZIOTO, NGS Soluções Genômicas, Piracicaba; PRISCILA SILVA NEUBERN DE OLIVEIRA; SIMONE CRISTINA MEO NICIURA, CPPSE; LUIZ LEHMANN COUTINHO, ESALQ/USP; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE. SOUZA, M. M. de ZERLOTINI NETO, A. ROCHA, M. I. P. BRUSCADIN, J. J. DINIZ, W. J. da S. CARDOSO, T. F. CESAR, A. S. M. AFONSO, J. ANDRADE, B. G. N. MUDADU, M. de A. MOKRY, F. B. TIZIOTO, P. C. OLIVEIRA, P. S. N. de NICIURA, S. C. M. COUTINHO, L. L. REGITANO, L. C. de A. |
format |
Artigo de periódico |
topic_facet |
Expressão gênica Regulação da expressão gênica Allelic expression Allele-specific expression Bos Indicus Gene expression regulation |
author |
SOUZA, M. M. de ZERLOTINI NETO, A. ROCHA, M. I. P. BRUSCADIN, J. J. DINIZ, W. J. da S. CARDOSO, T. F. CESAR, A. S. M. AFONSO, J. ANDRADE, B. G. N. MUDADU, M. de A. MOKRY, F. B. TIZIOTO, P. C. OLIVEIRA, P. S. N. de NICIURA, S. C. M. COUTINHO, L. L. REGITANO, L. C. de A. |
author_sort |
SOUZA, M. M. de |
title |
Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes. |
title_short |
Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes. |
title_full |
Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes. |
title_fullStr |
Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes. |
title_full_unstemmed |
Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes. |
title_sort |
allele-specific expression is widespread in bos indicus muscle and affects meat quality candidate genes. |
publishDate |
2020-10-09 |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1125395 https://doi.org/10.1038/S41598-020-67089-0 |
work_keys_str_mv |
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