Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, Denmark.
SEGES Danish Pig Research Centre, Copenhagen, Denmark.
J Anim Sci. 2020 Jul 1;98(7). doi: 10.1093/jas/skaa229.
Whole-genome sequencing of 217 animals from three Danish commercial pig breeds (Duroc, Landrace [LL], and Yorkshire [YY]) was performed. Twenty-six million single-nucleotide polymorphisms (SNPs) and 8 million insertions or deletions (indels) were uncovered. Among the SNPs, 493,099 variants were located in coding sequences, and 29,430 were predicted to have a high functional impact such as gain or loss of stop codon. Using the whole-genome sequence dataset as the reference, the imputation accuracy for pigs genotyped with high-density SNP chips was examined. The overall average imputation accuracy for all biallelic variants (SNP and indel) was 0.69, while it was 0.83 for variants with minor allele frequency > 0.1. This study provides whole-genome reference data to impute SNP chip-genotyped animals for further studies to fine map quantitative trait loci as well as improving the prediction accuracy in genomic selection. Signatures of selection were identified both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during breed development or subsequent divergent selection. However, the fixation indices did not indicate a strong divergence among these three breeds. In LL and YY, the integrated haplotype score identified genomic regions under recent selection. These regions contained genes for olfactory receptors and oxidoreductases. Olfactory receptor genes that might have played a major role in the domestication were previously reported to have been under selection in several species including cattle and swine.
对来自丹麦三个商业猪品种（杜洛克、长白[LL]和约克夏[YY]）的 217 只动物进行了全基因组测序。发现了 2600 万个单核苷酸多态性（SNP）和 800 万个插入或缺失（indel）。在这些 SNP 中，有 493099 个变异位于编码序列中，有 29430 个被预测具有高功能影响，如终止密码子的获得或丢失。使用全基因组序列数据集作为参考，检查了用高密度 SNP 芯片基因型的猪的估计准确性。所有二态变体（SNP 和 indel）的总体平均估计准确性为 0.69，而次要等位基因频率>0.1 的变体的准确性为 0.83。这项研究提供了全基因组参考数据，以对 SNP 芯片基因型的动物进行估计，以便进一步研究精细定位数量性状基因座，并提高基因组选择中的预测准确性。通过固定和分化分析鉴定了选择的特征，以揭示可能在品种发展或随后的分歧选择中发挥重要作用的选择 sweep。然而，固定指数并没有表明这三个品种之间存在强烈的分歧。在 LL 和 YY 中，综合单倍型得分确定了近期选择下的基因组区域。这些区域包含嗅觉受体和氧化还原酶的基因。嗅觉受体基因可能在驯化中发挥了主要作用，以前在包括牛和猪在内的几个物种中被报道受到选择。
