Genomic Analysis of the Interaction Between Energy Intake and SNP Genotypes on Age at Puberty

Age at puberty is moderately heritable and an early indicator of sow reproductive longevity. Environmental factors, such as energy balance, influence these traits. Crossbred gilts (n = 1,232) were fed a standard or energy restricted diet from 123 to 240 days of age, phenotyped for reproductive and growth traits, and genotyped with 56,424 SNPs. Interactions between energy intake and SNPs were analyzed using genome-wide association based on a BayesB model, and diet-dependent effects of genotypes on age at puberty were identified. Early age at puberty and restricted energy intake before breeding increased the probability that sows would generate parities two and three (P < 0.05). Diet-dependent SNPs were responsible for 0.29% of the phenotypic variation in age at puberty compared to 28.5% explained by the whole SNP panel. The eight top diet-dependent SNP effects were identified on SSC6, 7, 8, 11, 14, and 16. Subsequent single-SNP analyses of these markers showed no additive effects (P > 0.05), but SNP x energy intake interaction (P < 0.001) on age at puberty was observed. These SNPs were associated with a specific diet or the direction of the effects were opposite in the two dietary treatments. For example, the effect of the SNP located on SSC7 was observed only in the energy-restricted diet (P < 0.0001), with the AA genotype associated with earlier age at puberty compared to AC and CC genotypes (P < 0.005). This study provides the first evidence of diet-dependent effects of SNP genotypes on age at puberty in gilts.