Functional analysis of candidate genes for meat quality traits and muscle transcriptomics in pigs
- Autores: Lourdes Criado Mesas
- Directores de la Tesis: Josep María Folch Albareda (dir. tes.)
- Lectura: En la Universitat Autònoma de Barcelona ( España ) en 2020
- Idioma: español
- Tribunal Calificador de la Tesis: Armando Sánchez Bonastre (presid.), Rayner Gonzalez Prendes (secret.), Cristina Óvilo Martín (voc.)
- Programa de doctorado: Programa de Doctorado en Producción Animal por la Universidad Autónoma de Barcelona
- Materias:
- Enlaces
- Tesis en acceso abierto en: TESEO
- Resumen
Nowadays, global meat consumption is rising, being pork one of the most consumed meats. The improvement of meat quality is subjected to consumer preferences for healthier and tastier meat products. Fatty acid composition and intramuscular fat are important factors determining meat quality traits, although a complex network of processes and pathways are involved. In the present thesis we aimed to elucidate the molecular mechanisms affecting fatty acid composition in pigs.
We studied the expression of candidate genes affecting intramuscular fat deposition and fatty acid composition traits, selected in previous studies of our group. The mRNA expression level of 45 genes was measured by RT-qPCR in a total of 355 pigs belonging to three different backcrosses based on Iberian boards. The eGWAS identified two cis-eQTL regions for IGF2 and ACSM5 genes, and ten trans-eQTL effects. The eGWAS performed in each backcross individually revealed different eQTL regions as well as six trans-eQTL hotspots, two per backcross, suggesting that breed-specific genetic variants are regulating the expression of these candidate genes.
Furthermore, we aimed to study the association between the IGF2:g.3072G>A polymorphism and the IGF2 gene expression, and its effect on fatty acid composition in backfat adipose tissue in 355 pigs belonging to the three backcrosses. The eGWAS identified a cis-eQTL region associated with the IGF2 gene expression in adipose tissue, being the IGF2:g.3072G>A polymorphism the most significantly associated SNP. In addition, the IGF2 gene expression in both muscle and adipose tissue was explained by an imprinting model. Finally, animals carrying the A allele showed a higher PUFA and lower MUFA percentages in adipose tissue.
To better understand the regulation and role of miR-33a and miR-33b in porcine lipid metabolism, we studied the expression of these miRNAs in liver, adipose tissue and muscle, and their association with fatty acid composition. A total of 42 pigs were analysed and different expression patterns among tissues were observed for both miRNAs, suggesting that expression regulatory mechanisms are tissue dependent. In adipose tissue and muscle, a high correlation between miR-33a and miR-33b expression was observed, indicating a similar regulation. Conversely, a low correlation between the two miRNAs in liver suggests a different regulation and function, and the miR-33b may be involved in fatty acid β-oxidation. Lastly, significant correlations among the expression of miR-33a and miR-33b in liver and adipose tissue and the adipose tissue fatty acid composition reinforced the involvement of these miRNAs in the regulation of lipid metabolism.
Finally, a preliminary study on muscle transcriptome of 132 pigs by RNA-Seq was performed with the aim to identify potential muscle gene-expression regulators. The eGWAS identified a total of 324 eQTLs, of which 247 were classified as cis-eQTL and 77 as trans-eQTLs. The two most significant associations were found for HGFAC and HUS1 genes. The main processes identified for the expression of 291 genes with significant eQTLs were metabolic pathways and the top three canonical pathways were Granzyme B signalling, glutathione-mediated detoxification and NRF2-mediated Oxidative Stress Response. At last, HNF4A, KLF3, E2F4, mir-483 and RORC were proposed as the main transcription factors, nuclear receptors or miRNAs involved in the muscle gene expression regulation.
