Genome-wide association study of swine farrowing traits. Part II: Bayesian analysis of marker data

Reproductive efficiency has a great impact on the economic success of pork (sus scrofa) production. Number born alive (NBA) and average piglet birth weight (ABW) contribute greatly to reproductive efficiency. To better understand the underlying genetics of birth traits, a genome-wide association study (GWAS) was undertaken. Samples of DNA were collected and tested using the Illumina PorcineSNP60 BeadChip from 1,152 first parity gilts. Traits included total number born (TNB), NBA, number born dead (NBD), number stillborn (NSB), number of mummies (MUM), total litter birth weight (LBW), and ABW. A total of 41,151 SNP were tested using a Bayesian approach. Beginning with the first 5 SNP on SSC1 and ending with the last 5 SNP on the SSCX, SNP were assigned to groups of 5 consecutive SNP by chromosome-position order and analyzed again using a Bayesian approach. From that analysis, 5-SNP groups were selected having no overlap with another 5-SNP groups and no overlap across chromosomes. These selected 5-SNP non-overlapping groups were defined as QTL. Of the available 8,814 QTL, 124 were found to be statistically significant (P < 0.01). Multiple testing was considered using the probability of false positives. Eleven QTL were found for TNB, 3 on SSC1, 3 on SSC4, 1 on SSC13, 1 on SSC14, 2 on SSC15, and 1 on SSC17. Statistical testing for NBA identified 14 QTL, 4 on SSC1, 1 on SSC4, 1 on SSC6, 1 on SSC10, 1on SSC13, 3 on SSC15, and 3 on SSC17. A single NBD QTL was found on SSC11. No QTL were identified for NSB or MUM. Thirty-three QTL were found for LBW, 3 on SSC1, 1 on SSC2, 1 on SSC3, 5 on SSC4, 2 on SSC5, 5 on SSC6, 3 on SSC7, 2 on SSC9, 1 on SSC10, 2 on SSC14, 6 on SSC15, and 2 on SSC17. A total of 65 QTL were found for ABW, 9 on SSC1, 3 on SSC2, 9 on SSC5, 5 on SSC6, 1 on SSC7, 2 on SSC8, 2 on SSC9, 3 on SSC10, 1 on SSC11, 3 on SSC12, 2 on SSC13, 8 on SSC14, 8 on SSC15, 1 on SSC17, and 8 on SSC18. Several candidate genes have been identified that overlap QTL locations among TNB, NBA, NBD, and ABW. These QTL when combined with information on genes found in the same regions should provide useful information that could be used for marker assisted selection, marker assisted management, or genomic selection applications in commercial pig populations.