Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci
Lv, Feng-Hua; Cao, Yin-Hong; Liu, Guang-Jian; Luo, Ling-Yun; Lu, Ran; Liu, Ming-Jun; Li, Wen-Rong; Zhou, Ping; Wang, Xin-Hua; Shen, Min; Gao, Lei; Yang, Jing-Quan; Yang, Hua; Yang, Yong-Lin; Liu, Chang-Bin; Wan, Peng-Cheng; Zhang, Yun-Sheng; Pi, Wen-Hui; Ren, Yan-Ling; Shen, Zhi-Qiang; Wang, Feng; Wang, Yu-Tao; Li, Jin-Quan; Salehian-Dehkordi, Hosein; Hehua, Eer; Liu, Yong-Gang; Chen, Jian-Fei; Wang, Jian-Kui; Deng, Xue-Mei; Esmailizadeh, Ali; Dehghani-Qanatqestani, Mostafa; Charati, Hadi; Nosrati, Maryam; Štěpánek, Ondřej; Rushdi, Hossam E; Olsaker, Ingrid; Curik, Ino; Gorkhali, Neena A; Paiva, Samuel R; Caetano, Alexandre R; Ciani, Elena; Amills, Marcel; Weimann, Christina; Erhardt, Georg; Amane, Agraw; Mwacharo, Joram M; Han, Jian-Lin; Hanotte, Olivier; Periasamy, Kathiravan; Johansson, Anna M; Hallsson, Jón H; Kantanen, Juha; Coltman, David W; Bruford, Michael W; Lenstra, Johannes A; Li, Meng-Hua (2022)
Lv, Feng-Hua
Cao, Yin-Hong
Liu, Guang-Jian
Luo, Ling-Yun
Lu, Ran
Liu, Ming-Jun
Li, Wen-Rong
Zhou, Ping
Wang, Xin-Hua
Shen, Min
Gao, Lei
Yang, Jing-Quan
Yang, Hua
Yang, Yong-Lin
Liu, Chang-Bin
Wan, Peng-Cheng
Zhang, Yun-Sheng
Pi, Wen-Hui
Ren, Yan-Ling
Shen, Zhi-Qiang
Wang, Feng
Wang, Yu-Tao
Li, Jin-Quan
Salehian-Dehkordi, Hosein
Hehua, Eer
Liu, Yong-Gang
Chen, Jian-Fei
Wang, Jian-Kui
Deng, Xue-Mei
Esmailizadeh, Ali
Dehghani-Qanatqestani, Mostafa
Charati, Hadi
Nosrati, Maryam
Štěpánek, Ondřej
Rushdi, Hossam E
Olsaker, Ingrid
Curik, Ino
Gorkhali, Neena A
Paiva, Samuel R
Caetano, Alexandre R
Ciani, Elena
Amills, Marcel
Weimann, Christina
Erhardt, Georg
Amane, Agraw
Mwacharo, Joram M
Han, Jian-Lin
Hanotte, Olivier
Periasamy, Kathiravan
Johansson, Anna M
Hallsson, Jón H
Kantanen, Juha
Coltman, David W
Bruford, Michael W
Lenstra, Johannes A
Li, Meng-Hua
Julkaisusarja
Molecular Biology and Evolution
Volyymi
39
Numero
2
Sivut
1-15
Oxford University Press (OUP)
2022
Julkaisun pysyvä osoite on
http://urn.fi/URN:NBN:fi-fe2022021418846
http://urn.fi/URN:NBN:fi-fe2022021418846
Tiivistelmä
Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3′-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.
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