Genome-wide association analyses for growth, carcass composition, and meat quality traits of Iberian pigs fattened in free open air

This study aimed to identify genomic regions and candidate genes associated with body composition and meat quality traits in Iberian pigs fattened in Montanera. A genome-wide association study (GWAS) was conducted on 528 pigs for 29 phenotypic traits using genomic data from the GGP Porcine HD Array. After quality control, 526 animals and 35,894 single nucleotide polymorphisms (SNPs) were retained for the association analysis. Despite the limitations of the genotyping chip used, which lacked coverage for Iberian-specific variants, the GWAS performed with genome-wide complex trait analysis (GCTA) software identified 165 SNPs significantly associated with 11 traits. Among these, 145 SNPs were clustered into 25 quantitative trait loci (QTL) regions. Five QTLs were identified for ham yield, containing genes such as KCNIP4, ZNF438, and PID1. Eight QTLs were associated with loin yield, with genes like PREX2, RSPO1, and PDE4B. One QTL was associated with shear force, and 16 QTLs were related to fatty acid composition. Genes linked to these traits included ELOVL6, associated with myristic and palmitic acids, and ADCY9 and ROBO1, associated with linoleic acid. Overall, these results provide novel genomic insights and markers that could enhance selection strategies in Iberian pig breeding programs, while highlighting the need for improved genomic tools tailored to local breeds.