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>