Modulació de la producció porcina y fenotips moleculars mitjançant factors nutricionals y genètics
- Autores: Emilio Mármol Sánchez
- Directores de la Tesis: M. Amills (dir. tes.)
- Lectura: En la Universitat Autònoma de Barcelona ( España ) en 2020
- Idioma: español
- ISBN: 9788449098697
- Tribunal Calificador de la Tesis: Ramona Natacha Pena Subirá (presid.), Roger Ros Freixedes (secret.), Denis Milan (voc.)
- Programa de doctorado: Programa de Doctorado en Producción Animal por la Universidad Autónoma de Barcelona
- Materias:
- Enlaces
- Tesis en acceso abierto en: TDX
- Resumen
The genetic modulators of porcine fatness and meat quality traits, as well as their mechanisms of action, are still poorly understood. First, we investigated the variability of candidate genes located within QTL regions associated with meat quality traits and intramuscular fat content and composition. Polymorphic sites located at candidate genes were identified based on RNA-seq data and whole-genome sequencing of five Duroc boars. Significant association between ATP1A2 genotype and electric conductivity (CE) in the longissimus dorsi (LD) muscle, as well as in a chromosome-wide analysis, were revealed. Our results suggest that the ATP1A2 gene might be involved in the regulation of the CE of the skeletal muscle. Moreover, we employed whole-genome sequencing data from the five Duroc boars to identify putative stop gained mutations segregating in a Duroc population (Lipgen). Seven pigs homozygous for a potentially lethal nonsense recessive mutation in the ASS1 gene were detected. After sequencing such region at the genomic and transcriptomic levels, the presence of an additional polymorphism located immediately before the nonsense mutation that disrupts the stop codon was revealed, forming a dinucleotide polymorphism that causes a benign amino acid substitution in the ASS1 sequence.
Furthermore, we used previous RNA-seq differential expression data to investigate the association of candidate genes with meat quality traits. Two polymorphisms located in the CRY2 and MIGA2 genes showed significant associations with stearic acid content in LD and with LDL serum concentration, respectively. These SNPs were also associated with the mRNA levels of the corresponding genes. Joint chromosome-wide association analyses showed that these polymorphisms are not the ones showing the most significant associations. We also studied polymorphisms residing in microRNA genes. A total of 120 whole-genome sequences from European and Asian wild boars and domestic pigs were used for variant calling analyses, and polymorphisms within miRNA loci were investigated. Variability within miRNA loci was strongly reduced in the seed region compared with the rest of the miRNA sequence and other regions in the genome. Fifteen SNPs mapping to miRNA genes were genotyped in the Lipgen population. Our results revealed, among others, one variant located in the apical loop of ssc-miR-326 as significantly associated with the expression of some of its targets. This SNP might contribute to a structural rearrangement of the miRNA hairpin pairing, thus modifying the efficiency of the miRNA maturation.
Subsequently, we aimed to improve the yet poorly annotated porcine miRNAome by developing a bioinformatic pipeline for the discovery and annotation of miRNA genes. The small RNA fraction of 48 Duroc gilts was sequenced and used to detect novel and known expressed miRNAs. Small RNA-seq transcripts and annotated human mature miRNAs were mapped to the porcine genome. Reconstruction of candidate hairpin sequences was performed by applying a motif search correction approach. A series of sequence and thermodynamic features were obtained from each sequence and a Machine-Learning graph-based transductive algorithm was employed for predicting novel and annotated miRNA sequences. A total of 47 unreported putative porcine miRNAs were detected with this approach. The expression of three of the unreported miRNAs was assessed by using RT-qPCR analyses and their expression in an independent Göttingen minipig population was confirmed.
Finally, we employed the muscle small RNA-seq data set to determine differentially expressed (DE) miRNAs between fasting and fed pigs. Gene regulatory networks for miRNA-mRNA interactions highlighted co-expression modules containing lipid-related genes. The potential influence of several DE miRNAs in regulating the expression of mRNA genes with key roles in glucose metabolism and energy homeostasis was evidenced.
