Abstract
BackgroundThe number of teats in pigs is related to a sow’s ability to rear piglets to weaning age. Several studies have identified genes and genomic regions that affect teat number in swine but few common results were reported. The objective of this study was to identify genetic factors that affect teat number in pigs, evaluate the accuracy of genomic prediction, and evaluate the contribution of significant genes and genomic regions to genomic broad-sense heritability and prediction accuracy using 41,108 autosomal single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing on 2936 Duroc boars.ResultsNarrow-sense heritability and dominance heritability of teat number estimated by genomic restricted maximum likelihood were 0.365 ± 0.030 and 0.035 ± 0.019, respectively. The accuracy of genomic predictions, calculated as the average correlation between the genomic best linear unbiased prediction and phenotype in a tenfold validation study, was 0.437 ± 0.064 for the model with additive and dominance effects and 0.435 ± 0.064 for the model with additive effects only. Genome-wide association studies (GWAS) using three methods of analysis identified 85 significant SNP effects for teat number on chromosomes 1, 6, 7, 10, 11, 12 and 14. The region between 102.9 and 106.0 Mb on chromosome 7, which was reported in several studies, had the most significant SNP effects in or near the PTGR2, FAM161B, LIN52, VRTN, FCF1, AREL1 and LRRC74A genes. This region accounted for 10.0% of the genomic additive heritability and 8.0% of the accuracy of prediction. The second most significant chromosome region not reported by previous GWAS was the region between 77.7 and 79.7 Mb on chromosome 11, where SNPs in the FGF14 gene had the most significant effect and accounted for 5.1% of the genomic additive heritability and 5.2% of the accuracy of prediction. The 85 significant SNPs accounted for 28.5 to 28.8% of the genomic additive heritability and 35.8 to 36.8% of the accuracy of prediction.ConclusionsThe three methods used for the GWAS identified 85 significant SNPs with additive effects on teat number, including SNPs in a previously reported chromosomal region and SNPs in novel chromosomal regions. Most significant SNPs with larger estimated effects also had larger contributions to the total genomic heritability and accuracy of prediction than other SNPs.
Highlights
The number of teats in pigs is related to a sow’s ability to rear piglets to weaning age
The observed accuracy of predicting phenotypic values from the tenfold validation study was 0.437 ± 0.064 for the mixed model with additive and dominance single nucleotide polymorphisms (SNPs) effects (R0tp, Model 1A in Table 2), and was 0.435 ± 0.064 for the mixed model with additive effects only (R0αp, Model 2A in Table 2), which is only 0.46% lower than that from the mixed model with additive and dominance effects. These slight differences in both heritability and accuracy of prediction between the additive model and the model with additive and dominance effects indicates that additive SNP effects were the primary genetic effects that affect teat number and that dominance SNP effects only had a negligible contribution to the prediction accuracy for teat number
Genome-wide association studies (GWAS) results The GWAS that was done with EPISNP2, which accounted for the sib intraclass correlation and was implemented by a generalized least squares (GLS) analysis [11, 12], identified 73 SNPs on chromosomes 1, 6, 7, 10, 11, 12 and 14 with additive effects but no SNP with dominance effects reached genome-wide significance with the Bonferroni multiple testing correction (p < 10−5.91) (Fig. 3a, b; Table 3; Additional file 1: Table S1)
Summary
The number of teats in pigs is related to a sow’s ability to rear piglets to weaning age. A GWAS using 42,654 SNPs on 936 Large White pigs reported 39 QTL with 211 significant SNP effects on teat number [2] Among those SNP effects, the region between 102.0 and 105.2 Mb on chromosome 7 had the most significant effects and the percentage of the genetic variance explained by SNPs in this region ranged from 0.04 to 2.51%. The chromosomal locations of the significant SNPs that were detected in this GWAS differed from all previously reported QTL for teat number that have been compiled in the animal QTL database [1] Another GWAS, using 32,911 SNPs on 1550 Large White pigs, reported 21 QTL with additive effects on chromosomes 6, 7 and 12, one QTL with a dominant effect on chromosome 4, and identified VRTN as the most promising candidate gene for teat number [3]. It is unclear what the impact of the highly significant SNPs is on the accuracy of genomic prediction for teat number
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