Genome-wide association study and accuracy of genomic prediction for teat number in Duroc pigs using genotyping-by-sequencing.
Genome-wide association study and accuracy of genomic prediction for teat number in Duroc pigs using genotyping-by-sequencing.
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DOI：
10.1186/s12711-017-0311-8
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发表时间：
2017-03-29
期刊：
影响因子：
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通讯作者：
Hu X
中科院分区：
文献类型：
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作者：
Tan C;Wu Z;Ren J;Huang Z;Liu D;He X;Prakapenka D;Zhang R;Li N;Da Y;Hu X
猪的泌乳数与母猪哺育仔猪至断奶期的能力有关。一些研究已经确定了影响猪产奶量的基因和基因组区域，但很少有共同的结果被报道。本研究旨在利用2936头杜洛克公猪基因分型的41108个常染色体单核苷酸多态性（snp），确定影响猪产奶量的遗传因素，评估基因组预测的准确性，并评估重要基因和基因组区域对基因组广义遗传力和预测准确性的贡献。基因组限制最大似然法估计的毛重数狭义遗传力和显性遗传力分别为0.365±0.030和0.035±0.019。在10倍验证研究中，以基因组最佳线性无偏预测与表型的平均相关性计算的基因组预测精度为：加性效应和显性效应模型为0.437±0.064，仅加性效应模型为0.435±0.064。使用三种分析方法的全基因组关联研究（GWAS）鉴定出85个显著SNP对1、6、7、10、11、12和14号染色体上的tetenumber有影响。在7号染色体上102.9 ~ 106.0 Mb之间的区域，在PTGR2、FAM161B、LIN52、VRTN、FCF1、AREL1和LRRC74A基因内或附近的SNP效应最为显著，有多项研究报道。该区域占基因组加性遗传力的10.0%，预测准确率的8.0%。第二大显著性染色体区域是第11号染色体上77.7 ~ 79.7 Mb之间的区域，其中FGF14基因的snp影响最显著，占基因组加性遗传力的5.1%和预测准确性的5.2%。85个显著snp占基因组加性遗传力的28.5% ~ 28.8%，预测准确率的35.8% ~ 36.8%。用于GWAS的三种方法鉴定了85个显著的snp，这些snp对染色体数量具有加性效应，包括先前报道的染色体区域的snp和新染色体区域的snp。与其他snp相比，具有较大估计效应的大多数显著snp对总基因组遗传力和预测准确性的贡献也更大。本文的在线版本（doi:10.1186/s12711-017-0311-8）包含补充材料，仅供授权用户使用。
The 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. Narrow-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. The 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. The online version of this article (doi:10.1186/s12711-017-0311-8) contains supplementary material, which is available to authorized users.