A genome-wide association study of production traits in a commercial population of Large White pigs: evidence of haplotypes affecting meat quality

Abstract

BackgroundNumerous 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.MethodsAnimals (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.ResultsTwenty-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.ConclusionsGWAS 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.

Joint QTL mapping and gene expression analysis identify positional candidate genes influencing pork quality traits

“…For instance, when we compared our a*, b* and pH 24 data with those described in six additional GWAS studies4629303132 we only found one positional coincidence between the SSC10 (70.6 Mb) genomic region associated with LD a* in the Lipgen population (Table 3) and the SSC10 (72.8 Mb) region identified by Ma et al 4. as associated with the same trait in the semimembranosus muscle of White Duroc × Erhualian F 2 pigs.…”

“…Only about 20% of the regions identified as significantly associated with any of these phenotypes were shared between two studies or more, indicating that the majority of associations are population-specific. These shared regions were: (a*) SSC4 (80–85 Mb)630, SSC6 (17–22 Mb)430, SSC7 (31–32 Mb)431, SSC12 (58–63 Mb)3031, SSC15 (133–136 Mb)303132; (b*) SSC15 (129–133 Mb)3032; and (pH 24 ), SSC3 (15–19 Mb)3031, SSC15 (133–136 Mb)2932. This latter region on SSC15 (133–136 Mb) appeared to be associated with a*, b*, pH 24 , shear force and cook loss in many independent studies29303132 but not in ours.…”

“…The genetic determinism of electrical conductivity, acidity and color, which have been often used as predictors of meat quality, has been explored by performing genome-wide association studies (GWAS) in F 2 populations234 as well as in purebred pigs56. An important limitation of using F 2 intercrosses in GWAS studies is that they are not representative of the purebred populations that constitute the selection nuclei of breeding companies.…”

Recent advances in omic technologies for meat quality management

“…For example, three studies were conducted in France, the Netherlands and Norway for the detection of QTL for androstenone and skatole level in four commercial pig populations (Duijvesteijn et al, 2010;Grindflek et al, 2011;Le Mignon et al, 2010). Another study conducted in the Large White breed in France revealed more QTL for MQ traits than for fattening or carcass quality traits (Sanchez et al, 2014). A recent QTL mapping study in chicken identified many candidate regions in the control of the carcass and meat of a slow-growing population .…”

Genome-Wide Association of Myoglobin Concentrations in Pork Loins

“…Numerous studies have been conducted to identify genomic regions associated with pork color and pH in commercial pigs (Nonneman et al, 2013;Sanchez et al, 2014;Bernal Rubio et al, 2015;Liu et al, 2015). A summary of Quantitative Trait Loci (QTL) discovered in pigs can be found at PigQTLdb (https://www.animalgenome.org/ cgi-bin/QTLdb/SS/browse).…”