A genome-wide association analysis for carcass traits in a commercial Duroc pig population

We performed a genome-wide association study to map the genetic determinants of carcass traits in 350 Duroc pigs typed with the Porcine SNP60 BeadChip. Association analyses were carried out using the gemma software. The proportion of phenotypic variance explained by the SNPs ranged between negligible to moderate (urn:x-wiley:02689146:media:age12545:age12545-math-0001= 0.01–0.30) depending on the trait under consideration. At the genome-wide level, we detected one significant association between backfat thickness between the 3rd and 4th ribs and six SNPs mapping to SSC12 (37–40 Mb). We also identified several chromosome-wide significant associations for ham weight (SSC11: 51–53 Mb, three SNPs; 67–68 Mb, two SNPs), carcass weight (SSC11: 66–68 Mb, two SNPs), backfat thickness between the 3rd and 4th ribs (SSC12: 21 Mb, one SNP; 33–40 Mb, 17 SNPs; 51–58 Mb, two SNPs), backfat thickness in the last rib (SSC12: 37 Mb, one SNP; 40–41 Mb, nine SNPs) and lean meat content (SSC13: 34 Mb, three SNPs and SSC16: 45.1 Mb, one SNP; 62–63 Mb, 10 SNPs; 71–75 Mb, nine SNPs). The ham weight trait-associated region on SSC11 contains two genes (UCHL3 and LMO7) related to muscle development. In addition, the ACACA gene, which encodes an enzyme for the catalysis of fatty acid synthesis, maps to the SSC12 (37–41 Mb) region harbouring trait-associated regions for backfat thickness traits. Sequencing of these candidate genes may help to uncover the causal mutations responsible for the associations found in the present study.This research was partially funded by projects AGL2010-22208-C02-01 and AGL2010-22208-C02-02 awarded by the Spanish Ministry of Economy and Competitiveness and grant 2014 SGR 1528 from the Agency for Management of University and Research Grants of the Generalitat de Catalunya. Tainã F Cardoso was funded with a fellowship from the CAPES Foundation-Coordination of Improvement of Higher Education, Ministry of Education of the Federal Government of Brazil. Rayner Gonzalez-Prendes was funded with a FPU Ph.D. grant from the Spanish Ministry of Education (FPU12/00860). We also acknowledge the support of the Spanish Ministry of Economy and Competitiveness for the Center of Excellence Severo Ochoa 2016–2019 (SEV-2015-0533) grant awarded to the Center for Research in Agricultural Genomics. Thanks also to the CERCA Programme of the Generalitat de Catalunya.Peer reviewe