Genome-wide association study of birth weight and pre-weaning body weight of crossbred pigs

Abstract

In piggery, birth weight and body weight remains most vital economic trait as they directly influence on the production performance of the farm. Implementing the genomic selection would pay way for rapid genetic gain along with increased accuracy than conventional breeding. Prior to genomic selection, genome wide association study (GWAS) has to be conducted in order to find informative SNPs associated with the traits of interest in a given population. Under this study 96 crossbred pigs were genotyped using double digest genotype by sequencing (GBS) technique using Hiseq platform. Raw FASTQ data were processed using dDOCENT Pipeline on Reference based method and variants were called using Free Bayes (version 1.1.0-3). Using Plink (v1.09b), variants having MAF>0.01, HWE<0.001 and genotyping rate >80% were filtered out and 20,467 SNPs were retained after quality control, for ascertaining GWAS in 96 pigs. Before conducting association studies, the data were adjusted for significant nongenetic factors affecting the traits of interest. GWAS was performed using Plink software (v1.9b) identified 9, 11, 12, 23, 28, 24, 30, 33 and 42 SNPs significantly (adjusted P<0.001) associated with birth weight, body weight at weekly interval from 1st week to 8th week, respectively. A large proportion of significant (adjusted P<0.001) SNPs were located on SSC10, SSC6, SSC13, SSC8 and SSC1. One genome wide significant SNP and four genome wide suggestive SNPs were identified. Two common SNPs affecting all body weight at different weeks were located on SSC5:40197442 and SSC13:140562 base pair position. This study helps to identify the genome wide scattered significant SNPs associated with traits of interest which could be used for genomic selection, but further validation studies of these loci in larger population are recommended.