Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci
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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Format: | Journal Article biblioteca |
Language: | English |
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Oxford University Press
2022-02-03
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Subjects: | genomes, genetics, animal breeding, sheep, small ruminants, loci, |
Online Access: | https://hdl.handle.net/10568/116684 https://doi.org/10.1093/molbev/msab353 |
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dig-cgspace-10568-1166842023-12-08T19:36:04Z Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci Feng-Hua Lv Yin-Hong Cao Guang-Jian Liu Ling-Yun Luo Ran Lu Ming-Jun Liu Wen-Rong Li Ping Zhou Xin-Hua Wang Min Shen Lei Gao Jing-Quan Yang Hua Yang Yong-Lin Yang Chang-Bin Liu Peng-Cheng Wan Yun-Sheng Zhang Wen-Hui Pi Yan-Ling Ren Zhi-Qiang Shen Feng Wang Yu-Tao Wang Jin-Quan Li Salehian-Dehkordi, H. Eer Hehua Yong-Gang Liu Jian-Fei Chen Jian-Kui Wang Xue-Mei Deng Esmailizadeh, A. Dehghani-Antezana, M. Charati, H. Nosrati, M. Štěpánek, O. Rushdi, H.E. Olsaker, I. Curik, I. Gorkhali, N.A. Paiva, S.R. Caetano, A.R. Ciani, E. Amills, M. Weimann, C. Erhardt, G. Amane, A. Mwacharo, Joram M. Han Jianlin Hanotte, Olivier H. Periasamy, K. Johansson, A.M. Hallsson, J.H. Kantanen, J. Coltman, D.W. Bruford, M.W. Lenstra, J.A. Meng-Hua Li genomes genetics animal breeding sheep small ruminants loci 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. 2022-02-03 2021-12-14T10:11:06Z 2021-12-14T10:11:06Z Journal Article Feng-Hua Lv, Yin-Hong Cao, Guang-Jian Liu, Ling-Yun Luo, Ran Lu, Ming-Jun Liu, Wen-Rong Li, Ping Zhou, Xin-Hua Wang, Min Shen, Lei Gao, Jing-Quan Yang, Hua Yang, Yong-Lin Yang, Chang-Bin Liu, Peng-Cheng Wan, Yun-Sheng Zhang, Wen-Hui Pi, Yan-Ling Ren, Zhi-Qiang Shen, Feng Wang, Yu-Tao Wang, Jin-Quan Li, Hosein Salehian-Dehkordi, Eer Hehua, Yong-Gang Liu, Jian-Fei Chen, Jian-Kui Wang, Xue-Mei Deng, Ali Esmailizadeh, Mostafa Dehghani-Qanatqestani, Hadi Charati, Maryam Nosrati, Ondřej Štěpánek, Hossam E Rushdi, Ingrid Olsaker, Ino Curik, Neena A Gorkhali, Samuel R Paiva, Alexandre R Caetano, Elena Ciani, Marcel Amills, Christina Weimann, Georg Erhardt, Agraw Amane, Joram M Mwacharo, Jian-Lin Han, Olivier Hanotte, Kathiravan Periasamy, Anna M Johansson, Jón H Hallsson, Juha Kantanen, David W Coltman, Michael W Bruford, Johannes A Lenstra, Meng-Hua Li. 2022. Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci. Molecular Biology and Evolution 39(2):msab353. 1537-1719 https://hdl.handle.net/10568/116684 https://doi.org/10.1093/molbev/msab353 en CC-BY-4.0 Open Access Oxford University Press Molecular Biology and Evolution |
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genomes genetics animal breeding sheep small ruminants loci genomes genetics animal breeding sheep small ruminants loci |
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genomes genetics animal breeding sheep small ruminants loci genomes genetics animal breeding sheep small ruminants loci Feng-Hua Lv Yin-Hong Cao Guang-Jian Liu Ling-Yun Luo Ran Lu Ming-Jun Liu Wen-Rong Li Ping Zhou Xin-Hua Wang Min Shen Lei Gao Jing-Quan Yang Hua Yang Yong-Lin Yang Chang-Bin Liu Peng-Cheng Wan Yun-Sheng Zhang Wen-Hui Pi Yan-Ling Ren Zhi-Qiang Shen Feng Wang Yu-Tao Wang Jin-Quan Li Salehian-Dehkordi, H. Eer Hehua Yong-Gang Liu Jian-Fei Chen Jian-Kui Wang Xue-Mei Deng Esmailizadeh, A. Dehghani-Antezana, M. Charati, H. Nosrati, M. Štěpánek, O. Rushdi, H.E. Olsaker, I. Curik, I. Gorkhali, N.A. Paiva, S.R. Caetano, A.R. Ciani, E. Amills, M. Weimann, C. Erhardt, G. Amane, A. Mwacharo, Joram M. Han Jianlin Hanotte, Olivier H. Periasamy, K. Johansson, A.M. Hallsson, J.H. Kantanen, J. Coltman, D.W. Bruford, M.W. Lenstra, J.A. Meng-Hua Li Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci |
description |
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. |
format |
Journal Article |
topic_facet |
genomes genetics animal breeding sheep small ruminants loci |
author |
Feng-Hua Lv Yin-Hong Cao Guang-Jian Liu Ling-Yun Luo Ran Lu Ming-Jun Liu Wen-Rong Li Ping Zhou Xin-Hua Wang Min Shen Lei Gao Jing-Quan Yang Hua Yang Yong-Lin Yang Chang-Bin Liu Peng-Cheng Wan Yun-Sheng Zhang Wen-Hui Pi Yan-Ling Ren Zhi-Qiang Shen Feng Wang Yu-Tao Wang Jin-Quan Li Salehian-Dehkordi, H. Eer Hehua Yong-Gang Liu Jian-Fei Chen Jian-Kui Wang Xue-Mei Deng Esmailizadeh, A. Dehghani-Antezana, M. Charati, H. Nosrati, M. Štěpánek, O. Rushdi, H.E. Olsaker, I. Curik, I. Gorkhali, N.A. Paiva, S.R. Caetano, A.R. Ciani, E. Amills, M. Weimann, C. Erhardt, G. Amane, A. Mwacharo, Joram M. Han Jianlin Hanotte, Olivier H. Periasamy, K. Johansson, A.M. Hallsson, J.H. Kantanen, J. Coltman, D.W. Bruford, M.W. Lenstra, J.A. Meng-Hua Li |
author_facet |
Feng-Hua Lv Yin-Hong Cao Guang-Jian Liu Ling-Yun Luo Ran Lu Ming-Jun Liu Wen-Rong Li Ping Zhou Xin-Hua Wang Min Shen Lei Gao Jing-Quan Yang Hua Yang Yong-Lin Yang Chang-Bin Liu Peng-Cheng Wan Yun-Sheng Zhang Wen-Hui Pi Yan-Ling Ren Zhi-Qiang Shen Feng Wang Yu-Tao Wang Jin-Quan Li Salehian-Dehkordi, H. Eer Hehua Yong-Gang Liu Jian-Fei Chen Jian-Kui Wang Xue-Mei Deng Esmailizadeh, A. Dehghani-Antezana, M. Charati, H. Nosrati, M. Štěpánek, O. Rushdi, H.E. Olsaker, I. Curik, I. Gorkhali, N.A. Paiva, S.R. Caetano, A.R. Ciani, E. Amills, M. Weimann, C. Erhardt, G. Amane, A. Mwacharo, Joram M. Han Jianlin Hanotte, Olivier H. Periasamy, K. Johansson, A.M. Hallsson, J.H. Kantanen, J. Coltman, D.W. Bruford, M.W. Lenstra, J.A. Meng-Hua Li |
author_sort |
Feng-Hua Lv |
title |
Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci |
title_short |
Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci |
title_full |
Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci |
title_fullStr |
Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci |
title_full_unstemmed |
Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci |
title_sort |
whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci |
publisher |
Oxford University Press |
publishDate |
2022-02-03 |
url |
https://hdl.handle.net/10568/116684 https://doi.org/10.1093/molbev/msab353 |
work_keys_str_mv |
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