title: Comparative Analysis of Muscle Transcriptome between Pig Genotypes Identifies Genes and Regulatory Mechanisms Associated to Growth, Fatness and Metabolism.
abstract: 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 Biceps femoris 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 Biceps femoris intramuscular fat and plasma cholesterol content in IB newborns. We detected 149 differentially expressed genes between IB and IBxDU neonates (p < 0.01 and Fold-Change > 1. 5). Several were related to adipose and muscle tissues development (DLK1, FGF21 or UBC). 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 (CEBPA, EGRs), lipid metabolism (PPARGC1B) and myogenesis (FOXOs, MEF2D, MYOD1), 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 PPARGC1B and TRIM63 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.
authors.affiliation: Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain.
authors.forename: Miriam
authors.initials: M
authors.lastname: Ayuso
authors.affiliation: Departamento de Mejora Genética Animal, INIA, Madrid, Spain.
authors.forename: Almudena
authors.initials: A
authors.lastname: Fernández
authors.affiliation: Departamento de Mejora Genética Animal, INIA, Madrid, Spain.
authors.forename: Yolanda
authors.initials: Y
authors.lastname: Núñez
authors.affiliation: Departamento de Mejora Genética Animal, INIA, Madrid, Spain.
authors.forename: Rita
authors.initials: R
authors.lastname: Benítez
authors.affiliation: Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain.
authors.forename: Beatriz
authors.initials: B
authors.lastname: Isabel
authors.affiliation: Departamento de Mejora Genética Animal, INIA, Madrid, Spain.
authors.forename: Carmen
authors.initials: C
authors.lastname: Barragán
authors.affiliation: Departamento de Mejora Genética Animal, INIA, Madrid, Spain.
authors.forename: Ana Isabel
authors.initials: AI
authors.lastname: Fernández
authors.affiliation: Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain.
authors.forename: Ana Isabel
authors.initials: AI
authors.lastname: Rey
authors.affiliation: Department of Animal Science, University of California Davis, Davis, California, United States of America.
authors.forename: Juan F
authors.initials: JF
authors.lastname: Medrano
authors.affiliation: Department of Animal Science, University of California Davis, Davis, California, United States of America.
authors.forename: Ángela
authors.initials: Á
authors.lastname: Cánovas
authors.affiliation: Comparative Physiology Lab SGIT-INIA, Madrid, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: González-Bulnes
authors.affiliation: Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain.
authors.forename: Clemente
authors.initials: C
authors.lastname: López-Bote
authors.affiliation: Departamento de Mejora Genética Animal, INIA, Madrid, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Ovilo
mesh_terms: D050154:Adiposity / Q000502:physiology*; D000818:Animals; D005838:Genotype; D009124:Muscle Proteins / Q000096:biosynthesis / Q000235:genetics; D018482:Muscle, Skeletal / Q000254:growth & development / Q000378:metabolism; D013045:Species Specificity; D013552:Swine / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D059467:Transcriptome / Q000502:physiology*
chemical_list: D009124:Muscle Proteins