SNP discovery and association study for growth, fatness and meat quality traits in Iberian crossbred pigs

• Published in: Scientific reports Vol. 12; no. 1; p. 16361
• Main Authors: Óvilo, C., Trakooljul, N., Núñez, Y., Hadlich, F., Murani, E., Ayuso, M., García-Contreras, C., Vázquez-Gómez, M., Rey, A. I., Garcia, F., García-Casco, J. M., López-Bote, C., Isabel, B., González-Bulnes, A., Wimmers, K., Muñoz, M.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 30-09-2022; Nature Publishing Group; Nature Portfolio
• Subjects: 631/208; 631/208/1348; 631/208/205; 631/208/212; 631/208/480; 631/208/514; 631/208/721; 631/208/726; Adipose tissue; Biomarkers; Body weight; Divergence; Fatty acid composition; Gene frequency; Genomes; Growth patterns; Humanities and Social Sciences; Marker-assisted selection; Meat; Meat products; Meat quality; multidisciplinary; Phenotypes; Science; Science (multidisciplinary); Single-nucleotide polymorphism; Swine; Whole genome sequencing
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-022-20817-0

Iberian pigs and its crosses are produced to obtain high-quality meat products. The objective of this work was to evaluate a wide panel of DNA markers, selected by biological and functional criteria, for association with traits related to muscle growth, fatness, meat quality and metabolism. We used 18 crossbred Iberian pigs with divergent postnatal growth patterns for whole genome sequencing and SNP discovery, with over 13 million variants being detected. We selected 1023 missense SNPs located on annotated genes and showing different allele frequencies between pigs with makerdly different growth patterns. We complemented this panel with 192 candidate SNPs obtained from literature mining and from muscle RNAseq data. The selected markers were genotyped in 480 Iberian × Duroc pigs from a commercial population, in which phenotypes were obtained, and an association study was performed for the 1005 successfully genotyped SNPs showing segregation. The results confirmed the effects of several known SNPs in candidate genes (such as
LEPR
,
ACACA, FTO, LIPE
or
SCD
on fatness, growth and fatty acid composition) and also disclosed interesting effects of new SNPs in less known genes such as
LRIG3
,
DENND1B
,
SOWAHB, EPHX1
or
NFE2L2
affecting body weight, average daily gain and adiposity at different ages, or
KRT10
,
NLE1
,
KCNH2
or
AHNAK
affecting fatness and FA composition. The results provide a valuable basis for future implementation of marker-assisted selection strategies in swine and contribute to a better understanding of the genetic architecture of relevant traits.