Genome-wide association analysis of meat quality and gene expression phenotypes in Duroc pigs

• Autores: Rayner Gonzalez Prendes
• Directores de la Tesis: M. Amills (dir. tes.)
• Lectura: En la Universitat Autònoma de Barcelona ( España ) en 2017
• Idioma: inglés
• Tribunal Calificador de la Tesis: Joan Estany Illa (presid.), José María Folch i Albareda (secret.), Jordi Estellé Fabrellas (voc.)
• Programa de doctorado: Programa Oficial de Doctorado en Producción Animal
• Materias:
  • Ciencias de la vida
    • Biología animal (zoología)
      • Genética animal
• Enlaces
  • Tesis en acceso abierto en:  DDD  TDX 
• Resumen

  • Summary The main objective of this thesis was to identify genomic regions associated with technological and lipid composition meat quality traits. In this way, we carried out a GWAS for 57 phenotypes measured in the gluteus medius (GM) and longissimus dorsi (LD) muscles of pigs from a commercial Duroc line. In general, SNPs included in the PorcineSNP60 BeadChip only explained a limited amount of the phenotypic variance of the meat quality traits recorded in our population (0-51%). Moreover, we detected 40 and 101 genome- and chromosome-wide significant associations respectively. The majority of these associations were muscle-specific, maybe because the GM and LD muscles have different profiles of mRNA expression. Several of these regions were associated with more than one trait, suggesting the existence of pleiotropic effects. Specifically relevant was the genomic region located on SSC14 (120-124 Mb) which was associated with stearic, linoleic, unsaturated, and saturated fatty acids in both LD and GM muscles. We also investigated if QTL regions contain expression QTL (eQTL) influencing the mRNA levels of loci transcribed in the GM muscle. The number of eQTL co-localizing with QTL for meat technological traits (5 cis-eQTLs) was lower than that of QTL for intramuscular fat (IMF) composition traits (20 cis-eQTL). Besides, we detected SNPs mapping to IMF QTL with trans-regulatory effects on gene expression (116 trans-eQTL).

    We were also interested in analysing the genetic regulation of lipid genes. With this goal, we have performed an eQTL scan for 63 loci that are known to have a key role in lipid metabolism. Our results revealed 13 cis- and 18 trans-eQTL modulating the expression of 19 loci with a broad variety of biochemical functions. Moreover, we did not detect a clear predominance of either cis- or trans- effects on gene expression and none of the 31 eQTLs mapped to QTLs for lipid traits. This finding suggests that detected eQTLs have effects on gene expression but not on fatness phenotypes.

    We have also investigated the existence of eQTL regulating gene expression in the GM muscle and liver, two tissues with a key role in the regulation of energy homeostasis. In this way, we have mapped 436 cis- and 450 trans-eQTLs in the GM muscle, while for hepatic genes the number of cis- and trans-eQTLs was more unbalanced i.e. 504 cis- vs 3,228 trans-eQTLs. The positional concordance between eQTLs maps generated in both tissues was weak, suggesting that the determinism of gene expression is mostly tissue-specific. In addition, we have used SNP data to identify 104 copy number variant regions, 47% of which co-localize with structural variants reported in previous studies. Approximately 39% of these CNVR co-localized with cis-eQTL signals, whilst the co-localization of CNVR and trans-eQTL was somewhat higher (≈60%). The consistency of these co-localizations in the liver and muscle was weak.