Chen Minhui, Su Guosheng, Fu Jinluan, Wang Aiguo, Liu Jian-Feng, Lund Mogens S, Guldbrandtsen Bernt
Department of Molecular Biology and Genetics, Centre for Quantitative Genetics and Genomics Aarhus University Tjele Denmark.
Department of Animal Genetics, Breeding and Reproduction China Agricultural University Beijing China.
Evol Appl. 2018 Dec 13;12(2):292-300. doi: 10.1111/eva.12716. eCollection 2019 Feb.
The distribution of Asian ancestry in the genome of Danish Duroc pigs was investigated using whole-genome sequencing data from European wild boars, Danish Duroc, Chinese Meishan and Bamaxiang pigs. Asian haplotypes deriving from Meishan and Bamaxiang occur widely across the genome. Signatures of selection on Asian haplotypes are common in the genome, but few of these haplotypes have been fixed. By defining 50-kb windows with more than 50% Chinese ancestry, which did not exhibit extreme genetic differentiation between Meishan and Bamaxiang as candidate regions, the enrichment of quantitative trait loci in candidate regions supports that Asian haplotypes under selection play an important role in contributing genetic variation underlying production, reproduction, meat and carcass, and exterior traits. Gene annotation of regions with the highest proportion of Chinese ancestry revealed genes of biological interest, such as . Further haplotype clustering analysis suggested that a haplotype of Chinese origin around the gene was introduced to Europe and then underwent a selective sweep in European pigs. Besides, functional genes in candidate regions, such as and , associated with fertility, and , associated with meat quality, were identified. Our results demonstrate the contribution of Asian haplotypes to the genomes of European pigs. Findings herein facilitate further genomic studies such as genomewide association study and genomic prediction by providing ancestry information of variants.
利用欧洲野猪、丹麦杜洛克猪、中国梅山猪和巴马香猪的全基因组测序数据，研究了丹麦杜洛克猪基因组中亚洲血统的分布情况。源自梅山猪和巴马香猪的亚洲单倍型在整个基因组中广泛存在。基因组中对亚洲单倍型的选择特征很常见，但这些单倍型中很少有被固定下来的。通过定义中国血统超过50%且梅山猪和巴马香猪之间未表现出极端遗传分化的50千碱基窗口作为候选区域，候选区域中数量性状位点的富集支持了正在接受选择的亚洲单倍型在贡献生产、繁殖、肉和胴体以及外貌性状潜在遗传变异方面发挥着重要作用。对中国血统比例最高区域的基因注释揭示了具有生物学意义的基因，如 。进一步的单倍型聚类分析表明， 基因周围的一个中国起源单倍型被引入欧洲，然后在欧洲猪中经历了一次选择性清除。此外，还鉴定了候选区域中与繁殖力相关的功能基因，如 和 ，以及与肉质相关的 。我们的研究结果证明了亚洲单倍型对欧洲猪基因组的贡献。本文的研究结果通过提供变异的祖先信息，有助于进一步的基因组研究，如全基因组关联研究和基因组预测。
