Genome-Wide Association Study of Litter Size in Pigs using both Compressed Mixed Linear and Bayes Models

GWAS (Genome-wide association study) strategy has been extensively utilized for identification of economical trait loci in livestock animals. Using Illumina’s PorcineSNP60 BeadChip, a GWA study of 820 commercial pigs with reproductive traits recorded was performed. Principle Component Analysis showed that there was no significant population stratification. Two different statistical models including Compressed Mixed Linear Model (GAPIT program package) and Bayes CPi Model (GenSel software) were used to implement GWAS on total number born (TNB) and number born alive (NBA) for the first and second parity, respectively. To compare the most significant 50 SNPs from each method, a total of 31 coincided SNPs for TNB in the first parity were identified, and there were 20 coincided SNPs for NBA in the first parity from the results of both methods. For the second parity, the number of coincided SNPs for TNB and NBA are 28 and 27， respectively. From the significant associated SNPs, a downstream gene named MELK of M1GA0001337 that located at 248.5Mb on SSC1 has not been previously reported in the pig. Another downstream gene named MAP3K1 of ALGA0090341 that located at 33.4Mb on SSC16 has been proved important during early mouse embryonic development period.