Genome-wide association study for ethological traits of purebred Landrace and Yorkshire populations

Abstract

Some behaviors of pigs that are not expressed in the wild state or are observed in a small minority of individuals after groups of pigs are mixed have been reported to indicate poor welfare. A GWAS analysis was performed by measuring the frequency and duration of the four ethological traits and using the mlma command provided by the genome-wide complex trait analysis (GCTA). The positional candidate genes on significantly identified single nucleotide polymorphism (SNP) markers were identified by using the dbSNP provided by the National Center for Biotechnology Information (NCBI). When the GWAS analysis was applied the 43,565 (of the purebred Landrace population) and 41,700 (of the purebred Yorkshire population) SNP markers, 1, 2, and 1 significant SNP markers were identified for the traits of feeding frequency (LOC110262254), locomotion time (LOC110260361), and locomotion frequency (LOC110260361) of the purebred Landrace population, respectively. Meanwhile, 1 and 7 significant SNP markers were identified for the traits of drinking time (LOC110260090) and feeding frequency (MAP3K19; LOC110257013; ACMSD; TMEM163; RAB3GAP1) of the purebred Yorkshire population, respectively. The results of this study may suggest that the GWAS analysis of the ethological traits of purebred Landrace and Yorkshire populations could be used to perform a GWAS analysis on non-economic traits, and the results can thus be provided as basic data for GWAS analyses of other non-economic traits in the future.