66 A genome-wide association study for gestation length in swine

Abstract

Abstract The objective of the current study was to conduct a genome-wide association on gestation length (GL) in different parities in swine. Sows (n = 831) belonging to the University of Nebraska – Lincoln resource population (Landrace X Nebraska Index Line) were utilized. GL was defined as the number of days between the final insemination and farrowing. Four traits, GL at parity 1, 2, 3 and 4 (GL1, GL2, GL3 and GL4, respectively) were investigated. Animals which were induced 24h prior to a farrowing event were removed from the analysis. Sows were genotyped with the Illumina SNP60 BeadArray. A Bayes C model with π=0.995 was implemented with fixed effects of contemporary group, development pen, diet, linear and quadratic terms for age at puberty (GL1; P < 0.01), and linear and quadratic terms for farrowing age (GL2; P < 0.01). Results are posterior means of 55,000 samples.Single marker association analysis (SMA) was performed in R utilizing a linear model on SNP from 1-Mb windows (n = 10) which explained the largest proportion of genetic variation in GL1. Top 10 (0.5% of all windows) 1-Mb windows accounted for a limited proportion of genetic variance, 7.75, 4.66, 3.45 and 2.05% in GL1, GL2, GL3 and GL4, respectively. Posterior mean heritability estimates (posterior SD) for GL1, GL2, GL3 and GL4 were 0.33 (0.06), 0.34 (0.07), 0.32 (0.08) and 0.20 (0.08), respectively. The top SNP (ASGA0017859, SSC4, 7.8 Mb) located in one of the two top common genomic regions associated with GL1, GL2 and GL3 displayed a difference of 1.1d in GL1 between alternate homozygotes (P < 0.01). The top SNP from nine of the ten regions were significant (P < 0.05) in the SMA. Two of these regions were in common with GL2 and GL3 where SNP with potential functional effects were found in ZFAT, MAML2 and CCDC82. Results suggest GL is a largely polygenic trait.