10.1371/journal.pone.0145162
Miriam Ayuso
Miriam
Ayuso
Almudena Fernández
Almudena
Fernández
Yolanda Núñez
Yolanda
Núñez
Rita Benítez
Rita
Benítez
Beatriz Isabel
Beatriz
Isabel
Carmen Barragán
Carmen
Barragán
Ana Isabel Fernández
Ana
Isabel Fernández
Ana Isabel Rey
Ana
Isabel Rey
Juan F. Medrano
Juan
F. Medrano
Ángela Cánovas
Ángela
Cánovas
Antonio González-Bulnes
Antonio
González-Bulnes
Clemente López-Bote
Clemente
López-Bote
Cristina Ovilo
Cristina
Ovilo
Comparative Analysis of Muscle Transcriptome between Pig Genotypes Identifies Genes and Regulatory Mechanisms Associated to Growth, Fatness and Metabolism
Public Library of Science
2016
IBxDU pigs
fgf
10 IBxDU pigs
2d
mef
muscle tissues development
plasma cholesterol content
foxo
Biceps femoris intramuscular
phenotypic differences
dlk
ubc
transcription factors
muscle growth
production traits
Regulatory Mechanisms Associated
function
meat quality
meat quality differences
Pig Genotypes Identifies Genes
egr
biceps femoris muscle
gene expression differences
TRIM 63 genes
myod
cebpa
Metabolism Iberian ham production
PPARGC 1B
2016-01-05 14:52:53
Dataset
https://plos.figshare.com/articles/dataset/_Comparative_Analysis_of_Muscle_Transcriptome_between_Pig_Genotypes_Identifies_Genes_and_Regulatory_Mechanisms_Associated_to_Growth_Fatness_and_Metabolism_/1629114
<div><p>Iberian ham production includes both purebred (IB) and Duroc-crossbred (IBxDU) Iberian pigs, which show important differences in meat quality and production traits, such as muscle growth and fatness. This experiment was conducted to investigate gene expression differences, transcriptional regulation and genetic polymorphisms that could be associated with the observed phenotypic differences between IB and IBxDU pigs. Nine IB and 10 IBxDU pigs were slaughtered at birth. Morphometric measures and blood samples were obtained and samples from <i>Biceps femoris</i> muscle were employed for compositional and transcriptome analysis by RNA-Seq technology. Phenotypic differences were evident at this early age, including greater body size and weight in IBxDU and greater <i>Biceps femoris</i> intramuscular fat and plasma cholesterol content in IB newborns. We detected 149 differentially expressed genes between IB and IBxDU neonates (<i>p</i> < 0.01 and Fold-Change > 1. 5). Several were related to adipose and muscle tissues development (<i>DLK1</i>, <i>FGF21</i> or <i>UBC</i>). The functional interpretation of the transcriptomic differences revealed enrichment of functions and pathways related to lipid metabolism in IB and to cellular and muscle growth in IBxDU pigs. Protein catabolism, cholesterol biosynthesis and immune system were functions enriched in both genotypes. We identified transcription factors potentially affecting the observed gene expression differences. Some of them have known functions on adipogenesis (<i>CEBPA</i>, <i>EGRs</i>), lipid metabolism (<i>PPARGC1B</i>) and myogenesis (<i>FOXOs</i>, <i>MEF2D</i>, <i>MYOD1</i>), which suggest a key role in the meat quality differences existing between IB and IBxDU hams. We also identified several polymorphisms showing differential segregation between IB and IBxDU pigs. Among them, non-synonymous variants were detected in several transcription factors as <i>PPARGC1B</i> and <i>TRIM63</i> genes, which could be associated to altered gene function. Taken together, these results provide information about candidate genes, metabolic pathways and genetic polymorphisms potentially involved in phenotypic differences between IB and IBxDU pigs associated to meat quality and production traits.</p></div>