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Integrated Genome-Wide Analysis of MicroRNA Expression Quantitative Trait Loci in Pig Longissimus Dorsi Muscle

Determining mechanisms regulating complex traits in pigs is essential to improve the production efficiency of this globally important protein source. MicroRNAs (miRNAs) are a class of non-coding RNAs known to post-transcriptionally regulate gene expression affecting numerous phenotypes, including th...

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Autores principales: Daza, Kaitlyn R., Velez-Irizarry, Deborah, Casiró, Sebastian, Steibel, Juan P., Raney, Nancy E., Bates, Ronald O., Ernst, Catherine W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8042294/
https://www.ncbi.nlm.nih.gov/pubmed/33859669
http://dx.doi.org/10.3389/fgene.2021.644091
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author Daza, Kaitlyn R.
Velez-Irizarry, Deborah
Casiró, Sebastian
Steibel, Juan P.
Raney, Nancy E.
Bates, Ronald O.
Ernst, Catherine W.
author_facet Daza, Kaitlyn R.
Velez-Irizarry, Deborah
Casiró, Sebastian
Steibel, Juan P.
Raney, Nancy E.
Bates, Ronald O.
Ernst, Catherine W.
author_sort Daza, Kaitlyn R.
collection PubMed
description Determining mechanisms regulating complex traits in pigs is essential to improve the production efficiency of this globally important protein source. MicroRNAs (miRNAs) are a class of non-coding RNAs known to post-transcriptionally regulate gene expression affecting numerous phenotypes, including those important to the pig industry. To facilitate a more comprehensive understanding of the regulatory mechanisms controlling growth, carcass composition, and meat quality phenotypes in pigs, we integrated miRNA and gene expression data from longissimus dorsi muscle samples with genotypic and phenotypic data from the same animals. We identified 23 miRNA expression Quantitative Trait Loci (miR-eQTL) at the genome-wide level and examined their potential effects on these important production phenotypes through miRNA target prediction, correlation, and colocalization analyses. One miR-eQTL miRNA, miR-874, has target genes that colocalize with phenotypic QTL for 12 production traits across the genome including backfat thickness, dressing percentage, muscle pH at 24 h post-mortem, and cook yield. The results of our study reveal genomic regions underlying variation in miRNA expression and identify miRNAs and genes for future validation of their regulatory effects on traits of economic importance to the global pig industry.
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spelling pubmed-80422942021-04-14 Integrated Genome-Wide Analysis of MicroRNA Expression Quantitative Trait Loci in Pig Longissimus Dorsi Muscle Daza, Kaitlyn R. Velez-Irizarry, Deborah Casiró, Sebastian Steibel, Juan P. Raney, Nancy E. Bates, Ronald O. Ernst, Catherine W. Front Genet Genetics Determining mechanisms regulating complex traits in pigs is essential to improve the production efficiency of this globally important protein source. MicroRNAs (miRNAs) are a class of non-coding RNAs known to post-transcriptionally regulate gene expression affecting numerous phenotypes, including those important to the pig industry. To facilitate a more comprehensive understanding of the regulatory mechanisms controlling growth, carcass composition, and meat quality phenotypes in pigs, we integrated miRNA and gene expression data from longissimus dorsi muscle samples with genotypic and phenotypic data from the same animals. We identified 23 miRNA expression Quantitative Trait Loci (miR-eQTL) at the genome-wide level and examined their potential effects on these important production phenotypes through miRNA target prediction, correlation, and colocalization analyses. One miR-eQTL miRNA, miR-874, has target genes that colocalize with phenotypic QTL for 12 production traits across the genome including backfat thickness, dressing percentage, muscle pH at 24 h post-mortem, and cook yield. The results of our study reveal genomic regions underlying variation in miRNA expression and identify miRNAs and genes for future validation of their regulatory effects on traits of economic importance to the global pig industry. Frontiers Media S.A. 2021-03-30 /pmc/articles/PMC8042294/ /pubmed/33859669 http://dx.doi.org/10.3389/fgene.2021.644091 Text en Copyright © 2021 Daza, Velez-Irizarry, Casiró, Steibel, Raney, Bates and Ernst. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Daza, Kaitlyn R.
Velez-Irizarry, Deborah
Casiró, Sebastian
Steibel, Juan P.
Raney, Nancy E.
Bates, Ronald O.
Ernst, Catherine W.
Integrated Genome-Wide Analysis of MicroRNA Expression Quantitative Trait Loci in Pig Longissimus Dorsi Muscle
title Integrated Genome-Wide Analysis of MicroRNA Expression Quantitative Trait Loci in Pig Longissimus Dorsi Muscle
title_full Integrated Genome-Wide Analysis of MicroRNA Expression Quantitative Trait Loci in Pig Longissimus Dorsi Muscle
title_fullStr Integrated Genome-Wide Analysis of MicroRNA Expression Quantitative Trait Loci in Pig Longissimus Dorsi Muscle
title_full_unstemmed Integrated Genome-Wide Analysis of MicroRNA Expression Quantitative Trait Loci in Pig Longissimus Dorsi Muscle
title_short Integrated Genome-Wide Analysis of MicroRNA Expression Quantitative Trait Loci in Pig Longissimus Dorsi Muscle
title_sort integrated genome-wide analysis of microrna expression quantitative trait loci in pig longissimus dorsi muscle
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8042294/
https://www.ncbi.nlm.nih.gov/pubmed/33859669
http://dx.doi.org/10.3389/fgene.2021.644091
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