Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits

• Published in: Nature communications Vol. 11; no. 1; pp. 2815 - 16
• Main Authors: Li, Xin, Yang, Ji, Shen, Min, Xie, Xing-Long, Liu, Guang-Jian, Xu, Ya-Xi, Lv, Feng-Hua, Yang, Hua, Yang, Yong-Lin, Liu, Chang-Bin, Zhou, Ping, Wan, Peng-Cheng, Zhang, Yun-Sheng, Gao, Lei, Yang, Jing-Quan, Pi, Wen-Hui, Ren, Yan-Ling, Shen, Zhi-Qiang, Wang, Feng, Deng, Juan, Xu, Song-Song, Salehian-Dehkordi, Hosein, Hehua, Eer, Esmailizadeh, Ali, Dehghani-Qanatqestani, Mostafa, Štěpánek, Ondřej, Weimann, Christina, Erhardt, Georg, Amane, Agraw, Mwacharo, Joram M., Han, Jian-Lin, Hanotte, Olivier, Lenstra, Johannes A., Kantanen, Juha, Coltman, David W., Kijas, James W., Bruford, Michael W., Periasamy, Kathiravan, Wang, Xin-Hua, Li, Meng-Hua
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 04.06.2020; Nature Publishing Group; Nature Portfolio
• Subjects: 38/1; 38/23; 38/39; 38/43; 38/77; 38/88; 38/91; 631/208/514; 631/208/8; 82/80; Agronomy; Alleles; Animal husbandry; Animal Husbandry - methods; Animals; Animals, Wild - genetics; Breeding; Demography; Domestic animals; Domestication; Female; Gene expression; Gene Frequency; Genes; Genetic diversity; Genetic resources; Genetic Variation; Genetics; Genomes; Genomics; Genotype; High-Throughput Nucleotide Sequencing; Humanities and Social Sciences; Linkage Disequilibrium; Livestock; Morphology; multidisciplinary; Mutation; Ovis aries; Ovis orientalis; Phenotype; Phenotypic variations; Platelet-Derived Growth Factor - metabolism; Polymerase chain reaction; Polymorphism, Single Nucleotide; Science; Science (multidisciplinary); Selection, Genetic; Sequence Analysis, DNA; Sheep; Sheep, Domestic - genetics; Species Specificity; Whole Genome Sequencing
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-16485-1

Understanding the genetic changes underlying phenotypic variation in sheep ( Ovis aries ) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor ( O. orientalis ), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals. Genetic resources for livestock are valuable for understanding their demography and past selection, and may inform future breeding programs and agricultural improvement. Here, the authors present deep resequencing of 248 wild and domestic sheep, with associated data and analysis.