title: A genome-wide association study of production traits in a commercial population of Large White pigs: evidence of haplotypes affecting meat quality.
abstract: BACKGROUND
  Numerous quantitative trait loci (QTL) have been detected in pigs over the past 20 years using microsatellite markers. However, due to the low density of these markers, the accuracy of QTL location has generally been poor. Since 2009, the dense genome coverage provided by the Illumina PorcineSNP60 BeadChip has made it possible to more accurately map QTL using genome-wide association studies (GWAS). Our objective was to perform high-density GWAS in order to identify genomic regions and corresponding haplotypes associated with production traits in a French Large White population of pigs.
  
  
  METHODS
  Animals (385 Large White pigs from 106 sires) were genotyped using the PorcineSNP60 BeadChip and evaluated for 19 traits related to feed intake, growth, carcass composition and meat quality. Of the 64,432 SNPs on the chip, 44,412 were used for GWAS with an animal mixed model that included a regression coefficient for the tested SNPs and a genomic kinship matrix. SNP haplotype effects in QTL regions were then tested for association with phenotypes following phase reconstruction based on the Sscrofa10.2 pig genome assembly.
  
  
  RESULTS
  Twenty-three QTL regions were identified on autosomes and their effects ranged from 0.25 to 0.75 phenotypic standard deviation units for feed intake and feed efficiency (four QTL), carcass (12 QTL) and meat quality traits (seven QTL). The 10 most significant QTL regions had effects on carcass (chromosomes 7, 10, 16, 17 and 18) and meat quality traits (two regions on chromosome 1 and one region on chromosomes 8, 9 and 13). Thirteen of the 23 QTL regions had not been previously described. A haplotype block of 183 kb on chromosome 1 (six SNPs) was identified and displayed three distinct haplotypes with significant (0.0001 < P < 0.03) associations with all evaluated meat quality traits.
  
  
  CONCLUSIONS
  GWAS analyses with the PorcineSNP60 BeadChip enabled the detection of 23 QTL regions that affect feed consumption, carcass and meat quality traits in a LW population, of which 13 were novel QTL. The proportionally larger number of QTL found for meat quality traits suggests a specific opportunity for improving these traits in the pig by genomic selection.
authors: INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78350 Jouy-en-Josas, France. marie-pierre.sanchez@jouy.inra.fr.
authors: Marie-Pierre
authors: MP
authors: Sanchez
authors: Thierry
authors: T
authors: Tribout
authors: Nathalie
authors: N
authors: Iannuccelli
authors: Marcel
authors: M
authors: Bouffaud
authors: Bertrand
authors: B
authors: Servin
authors: Amabel
authors: A
authors: Tenghe
authors: Patrice
authors: P
authors: Dehais
authors: Nelly
authors: N
authors: Muller
authors: Maria Pilar
authors: MP
authors: Del Schneider
authors: Marie-José
authors: MJ
authors: Mercat
authors: Claire
authors: C
authors: Rogel-Gaillard
authors: Denis
authors: D
authors: Milan
authors: Jean-Pierre
authors: JP
authors: Bidanel
authors: Hélène
authors: H
authors: Gilbert
mesh_terms: D000818:Animals; D001823:Body Composition; D016678:Genome; D055106:Genome-Wide Association Study; D005838:Genotype; D006239:Haplotypes; D008297:Male; D008460:Meat / Q000032:analysis*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D034421:Sus scrofa / Q000235:genetics* / Q000254:growth & development / Q000502:physiology