Identification of Genomic Regions Associated With Sow Lactation Performance in Yorkshire Pigs

Abstract Text: Lactation is an energy demanding process for sows. The objective of this study was to identify genomic regions in sows related to lactation and litter growth through a genome wide association study(GWAS). Data from 868 litters from 531 Yorkshire sows that were genotyped using the Illumina porcine 60k Bead chip were utilized. The sows were weighed and scanned for back fat and loin depth before farrowing and at weaning and piglets were weighed at birth, weaning and death. The GWAS focused on total weaning weight (TWW), litter weight gain (LWG), sow weight loss (WL), back fat loss (BFL), and loin loss (LL). Estimates of heritability were moderate (0.24) for WL but low for all other traits (0.11-0.14). The GWAS was implemented separately for parity1 (N= 414) and parity2 (N=340) trait phenotypes using the BayesB method in the GENSEL software. A one Mb region on chromosome 2, which exhibited strong linkage disequilibrium, explained 59% of the genetic variance for TWW and 48% for LWG for parity 2 phenotypes but less than 0.1% of genetic variation for parity 1 records. The same region explained the highest proportion of variance for BFL for parity 2 records (0.33%) but less than 0.2% of genetic variance for LL and WL in both parities. The favorable allele of the most significant SNP in this region had a frequency of 0.6 and the genotypes were in Hardy Weinberg equilibrium. To further evaluate the effects of this SNP, it was included as a fixed class effect in an animal model analysis of parity 1, 2, and 3 records, as an interaction with parity. Genotype effects for parities 2 and 3 were significant for LWG, TWW, LL (p<0.001) and BFL (p=0.01 and 0.09) but were not significant for parity 1 (p>0.32). For TWW, estimates of allele substitution effects were 0.6, 5.6 and 1.7 kg for parities 1, 2, and 3 respectively, and 0.4, 5.3 and 2.6 kg for LWG. Positional candidate genes for this region are associated with monosaccharide metabolic processes. It can be concluded that this region on SCC2 had a significant impact on litter growth traits for Yorkshire sows in parity 2 and later. These results can aid in marker assisted selection but need further validation in other samples and breeds. Funding from Genome Alberta, Alberta Livestock and Meat Agency, Genesus Inc. and State of Iowa and Hatch funds is appreciated.

Keywords:

Sow Lactation GWAS