Genetic Dissection of Production Traits in Commercial Pigs: Comparative Effects of Terminal Sire Lines and Genome‐Wide Associations

The genetic antagonism between lean meat yield and meat quality dictates the need for precise selection in pigs. This study evaluated the impact of terminal sire lines (Duroc [D], Pietrain [P], and their F1 cross [PD]) on production traits and performed a genome-wide association study (GWAS) in a 1295 commercial population. Results revealed a clear genetic trade-off: D-sired progeny showed superior intramuscular fat (IMF) and meat color (p < 0.05), while P-sired progeny excelled in loin muscle area and leanness. PD-sired pigs generally showed intermediate performance and did not outperform the purebred terminal-sire groups for the major traits evaluated. GWAS replicated major known QTLs, including the VRTN locus for rib count (SSC7:97575068_A_G, p = 2.30e-39) and the BMP2 locus for carcass length (SSC17:15820953_G_A, p = 1.59e-09). Rib count was positively correlated with adjusted carcass straight length (r = 0.393, p = 5.80e-31), and combined genotype analysis of the VRTN and BMP2 loci revealed a joint effect on axial skeleton traits. Novel QTLs were discovered for drip loss (SSC13, SSC14) and myofiber perimeter (SSC1), with TUSC1 identified as a candidate gene. Our findings demonstrate that the PD cross does not mitigate the leanness-quality trade-off and highlight the VRTN and BMP2 loci, together with novel trait-associated markers, as potential targets for crossbred breeding programs.