Detection of changes in allelic frequencies due to selection on complex traits in the genomes of pigs from four genetic lines using generation proxy selection mapping

Most economically relevant traits in pig breeding programs are controlled by numerous causal variants spread across the genome and undergo selection pressure to improve the genetic merit of commercial pigs.  As a result, small changes in allele frequency over relatively short time scales are induced at these loci.  Identification of genomic loci that exhibit directional changes in allele frequency due to artificial selection identifies areas of the genome that can aid in genetic improvement of populations of pigs.  Thus, the objective of this research was to use Generation Proxy Selection Mapping (GPSM) of the dependent variable birth date to detect quantitative trait locis in the genomes of 3 genetic lines of pigs and crossbred pigs that have experienced changes in allelic frequency as a result of artificial selection.  Pigs in the current study were born between July 2010 and September 2020 and were owned by The Maschhoff’s, LLC.  Duroc, Landrace, Yorkshire, and Crossbred [Duroc × (Landrace × Yorkshire)] pigs were genotyped with the GGP Porcine 50K (Neogen, Corp., Lansing, Michigan, USA) SNP assay.  Quality control procedures were applied by removing SNPs and pigs that had a call rate of less than 0.90 and SNPs that had a minor allele frequency less than 0.01.  After quality control, 16,633, 18,834, 17,764, and 8,447 pigs and 38,377, 45,316, 45,196, and 46,529 SNPs remained for Duroc, Landrace, Yorkshire, and Crossbred pigs, respectively.  A genomic relationship matrix was estimated and fit in univariate linear mixed models as a part of a genome-wide association analysis of birth date for each genetic line using the software GCTA (v1.93.2).  P-values were converted to FDR (False Discovery Rate) corrected Q-values and a significance threshold of Q < 0.10 was used.  Across the genomes, 98, 134, 121, and 49 SNPs were identified (Q < .10) as having responded to artificial directional selection in Duroc, Landrace, Yorkshire, and Crossbred genetic lines, respectively.  Results of this study suggest that artificial selection in pig breeding programs has a directional effect on allelic frequencies across the genomes pigs, and that GPSM methodology can be utilized to detect these effects over relatively short time frames.

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