Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus

Abstract Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern...

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Autores principales:	Jennifer Jessica Bruscadin, Marcela Maria de Souza, Karina Santos de Oliveira, Marina Ibelli Pereira Rocha, Juliana Afonso, Tainã Figueiredo Cardoso, Adhemar Zerlotini, Luiz Lehmann Coutinho, Simone Cristina Méo Niciura, Luciana Correia de Almeida Regitano
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e3faf1f40f044ff0b11769337d7eeeb5
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spelling	oai:doaj.org-article:e3faf1f40f044ff0b11769337d7eeeb52021-12-02T14:25:16ZMuscle allele-specific expression QTLs may affect meat quality traits in Bos indicus10.1038/s41598-021-86782-22045-2322https://doaj.org/article/e3faf1f40f044ff0b11769337d7eeeb52021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86782-2https://doaj.org/toc/2045-2322Abstract Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes.Jennifer Jessica BruscadinMarcela Maria de SouzaKarina Santos de OliveiraMarina Ibelli Pereira RochaJuliana AfonsoTainã Figueiredo CardosoAdhemar ZerlotiniLuiz Lehmann CoutinhoSimone Cristina Méo NiciuraLuciana Correia de Almeida RegitanoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jennifer Jessica Bruscadin Marcela Maria de Souza Karina Santos de Oliveira Marina Ibelli Pereira Rocha Juliana Afonso Tainã Figueiredo Cardoso Adhemar Zerlotini Luiz Lehmann Coutinho Simone Cristina Méo Niciura Luciana Correia de Almeida Regitano Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus
description	Abstract Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes.
format	article
author	Jennifer Jessica Bruscadin Marcela Maria de Souza Karina Santos de Oliveira Marina Ibelli Pereira Rocha Juliana Afonso Tainã Figueiredo Cardoso Adhemar Zerlotini Luiz Lehmann Coutinho Simone Cristina Méo Niciura Luciana Correia de Almeida Regitano
author_facet	Jennifer Jessica Bruscadin Marcela Maria de Souza Karina Santos de Oliveira Marina Ibelli Pereira Rocha Juliana Afonso Tainã Figueiredo Cardoso Adhemar Zerlotini Luiz Lehmann Coutinho Simone Cristina Méo Niciura Luciana Correia de Almeida Regitano
author_sort	Jennifer Jessica Bruscadin
title	Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus
title_short	Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus
title_full	Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus
title_fullStr	Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus
title_full_unstemmed	Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus
title_sort	muscle allele-specific expression qtls may affect meat quality traits in bos indicus
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/e3faf1f40f044ff0b11769337d7eeeb5
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Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus

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