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Abstract
Duroc pigs are famous for their high growth rate, feed conversion efficiency, and lean meat percentage. Given that they have been subjected to artificial selection and breeding in multiple countries, various lines with obvious differences in production performance have formed. In this study, we genotyped 3,770 American Duroc (AD) pigs and 2,098 Canadian Duroc (CD) pigs using the GeneSeek Porcine SNP50 Beadchip to dissect the genetic differences and potential selection genes of growth traits in these two Duroc pig lines. Population structure detection showed that there were significant genetic differences between the two Duroc pig lines. Hence, we performed FST and cross-population extended haplotype homozygosity (XP-EHH) analyses between the two lines. As a result, we identified 38 annotated genes that were significantly enriched in the gland development pathway in the AD line, and 61 annotated genes that were significantly enriched in the immune-related pathway in the CD line. For three growth traits including backfat thickness (BFT), loin muscle depth (LMD), and loin muscle area (LMA), we then performed selection signature detection at 5 and 10% levels within the line and identified different selected regions and a series of candidate genes that are involved in lipid metabolism and skeletal muscle development or repair, such as IRX3, EBF2, WNT10B, TLR2, PITX3, and SGCD. The differences in selected regions and genes between the two lines may be the cause of the differences in growth traits. Our study suggests significant genetic differences between the AD and CD lines, which provide a theoretical basis for selecting different Duroc lines as sires for different needs.
Highlights
Lean pigs have been selected and bred in various countries for a long time and have formed distinctive lines, such as English Large White and French Large White
According to the estimated breeding values (EBV) ranking of backfat thickness (BFT), loin muscle depth (LMD), and loin muscle area (LMA) in the American Duroc (AD) and Canadian Duroc (CD) lines, the individuals with the top 5% EBV were selected for a group and the bottom 5% of which were selected for the other group, defined as the 5% level
Our previous study performed principal component analysis (PCA) between these two Duroc pig populations [3], and the results showed that PC1 divided the AD and CD lines into two obvious groups, and PC2 showed that there was stratification phenomenon in the AD line as well
Summary
Lean pigs have been selected and bred in various countries for a long time and have formed distinctive lines, such as English Large White and French Large White. Zhuang et al conducted genome-wide association studies (GWAS) for loin muscle area (LMA) and LMD in American and Canadian Duroc pigs and identified 75 significantly associated SNPs, of which a 283-kb region on chromosome 7 was a pleiotropic quantitative trait loci (QTL) that affected both traits Among these 75 SNPs, the ALGA0040260 marker was the key SNP for the QTL and explained 1.77 and 2.48% of the phenotypic variance in LMA and LMD, respectively [3]. For the same line, we performed selection signature detection through dividing extreme phenotypic groups according to the estimated breeding values (EBV) ranking of BFT, LMD, and LMA, and have identified the selected regions and genes in different lines to reveal the potential genetic mechanisms that caused the differences in growth traits
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