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.
Highlights
Numerous quantitative trait loci (QTL) have been detected in pigs over the past 20 years using microsatellite markers
The objective of this work was to perform a high-density genome-wide association study with the PorcineSNP60 BeadChip in the French Large White (LW) breed in order to map the genomic regions that are associated with growth efficiency, carcass and meat quality traits, and to identify haplotypes that may be suitable for inclusion in selection strategies
Genome-wide association studies After checking that no structure was present in our population by applying multidimensional scaling available in the GenABEL R package [24], genome-wide association studies (GWAS) analyses were performed for the 19 traits
Summary
Numerous quantitative trait loci (QTL) have been detected in pigs over the past 20 years using microsatellite markers. 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). Over the past 20 years, several whole-genome scans using mainly microsatellite markers have revealed quantitative trait loci (QTL) for a large number of traits in pigs. Since the PorcineSNP60 BeadChip has become available, several GWAS have been performed in commercial pig populations and have revealed significant associations for economically important traits such as boar taint [7], reproductive characteristics [8], body composition [9], pathogen susceptibility [10], hematological traits [11], feed efficiency [12,13], and meat quality [14]. To date results on dense GWAS are not available for other major traits in commercial pig populations such as growth rate
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
