2 results on '"Wen-Hui Pi"'
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2. Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression, and agronomically important loci
- Author
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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, Nowick, Katja, National Natural Science Foundation of China, National Key Research and Development Program (China), Chinese Academy of Sciences, FENG-HUA LV, China Agricultural University, China, YIN-HONG CAO, Chinese Academy of Sciences (CAS), China, GUANG-JIAN LIU, Novogene Bioinformatics Institute, China, LING-YUN LUO, China Agricultural University, China, RAN LU, China Agricultural University, China, MING-JUN LIU, Xinjiang Academy of Animal Science, China, WEN-RONG LI, Xinjiang Academy of Animal Science, China, PING ZHOU, Xinjiang Academy of Agricultural and Reclamation Sciences, China, XIN-HUA WANG, Xinjiang Academy of Agricultural and Reclamation Sciences, China, MIN SHEN, Xinjiang Academy of Agricultural and Reclamation Sciences, China, LEI GAO, Xinjiang Academy of Agricultural and Reclamation Sciences, China, JING-QUAN YANG, Xinjiang Academy of Agricultural and Reclamation Sciences, China, HUA YANG, Xinjiang Academy of Agricultural and Reclamation Sciences, China, YONG-LIN YANG, Xinjiang Academy of Agricultural and Reclamation Sciences, China, CHANG-BIN LIU, Xinjiang Academy of Agricultural and Reclamation Sciences, China, PENG-CHENG WAN, Xinjiang Academy of Agricultural and Reclamation Sciences, China, YUN-SHENG ZHANG, Xinjiang Academy of Agricultural and Reclamation Sciences, China, WEN-HUI PI, Xinjiang Academy of Agricultural and Reclamation Sciences, China, YAN-LING REN, Shandong Binzhou Academy of Animal Science and Veterinary Medicine, China, ZHI-QIANG SHEN, Shandong Binzhou Academy of Animal Science and Veterinary Medicine, China, FENG WANG, Nanjing Agricultural University, China, YU-TAO WANG, Kashi University, China, JIN-QUAN LI, Inner Mongolia Agricultural University, China, HOSEIN SALEHIAN-DEHKORDI, Chinese Academy of Sciences (CAS), China, EER HEHUA, Ningxia Academy of Agriculture and Forestry Sciences, China, YONG-GANG LIU, Yunnan Agricultural University, China, JIAN-FEI CHEN, China Agricultural University, China, JIAN-KUI WANG, China Agricultural University, China, XUE-MEI DENG, China Agricultural University, China, ALI ESMAILIZADEH, Shahid Bahonar University of Kerman, Iran, MOSTAFA DEHGHANI-QANATQESTANI, Shahid Bahonar University of Kerman, Iran, HADI CHARATI, Shahid Bahonar University of Kerman, Iran, MARYAM NOSRATI, Payame Noor University, Iran, ONDREJ STEPANEK, State Veterinary Institute Jihlava, Czech Republic, HOSSAM E. RUSHDI, Cairo University, Egypt, INGRID OLSAKER, Norwegian University of Life Sciences, Norway, INO CURIK, University of Zagreb, Croatia, NEENA A. GORKHALI, Nepal Agriculture Research Council (NARC), Nepal, SAMUEL REZENDE PAIVA, Cenargen, ALEXANDRE RODRIGUES CAETANO, Cenargen, ELENA CIANI, Universita degli Studi di Bari Aldo 24 Moro, Italy, MARCEL AMILLS, Campus de la Universitat Autonoma de Barcelona, Spain, CHRISTINA WEIMANN, Justus-Liebig-University Giessen, Germany, GEORG ERHARDT, Justus-Liebig-University Giessen, Germany, AGRAW AMANE, Addis Ababa University, Ethiopia, JORAM M. MWACHARO, International Centre for Agricultural Research in the Dry Areas (ICARDA), Ethiopia, JIAN-LIN HAN, Chinese Academy of Agricultural Sciences (CAAS), China, OLIVIER HANOTTE, International Livestock Research Institute, Ethiopia, KATHIRAVAN PERIASAMY, International Atomic Energy Agency (IAEA), Austria, ANNA M. JOHANSSON, Swedish University of Agricultural Sciences, Sweden, JON H. HALLSSON, Agricultural University of Iceland, Iceland, JUHA KANTANEN, Natural Resources Institute Finland (Luke), Finland, DAVID W. COLTMAN, University of Alberta, Edmonton, Canada, MICHAEL W. BRUFORD, Cardiff University, United Kingdom, JOHANNES A. LENSTRA, Utrecht University, The Netherlands, and MENG-HUA LI, China Agricultural University, China.
- Subjects
Asia ,Genome ,Sheep ,Whole-genome sequences ,Genetic Variation ,Genetic selection ,Sequence Analysis, DNA ,Iran ,Polymorphism, Single Nucleotide ,Genetic diversity ,whole-genome sequences ,genetic diversity ,adaptive introgression ,genetic selection ,agronomic traits ,migration ,Europe ,Adaptive introgression ,Genetics ,Animals ,Agronomic traits ,Molecular Biology ,Sheep, Domestic ,Ecology, Evolution, Behavior and Systematics ,Migration - Abstract
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., This study was financially supported by grants from the National Natural Science Foundation of China (Nos. 32061133010, 31825024, 31661143014, and 31972527), the National Key Research and Development Program-Key Projects of International Innovation Cooperation between Governments (2017YFE0117900), the External Cooperation Program of Chinese Academy of Sciences (152111KYSB20150010), and the Second Tibetan Plateau Scientific Expedition and Research Program (STEP) (No. 2019QZKK0501), and the Special Funds of the State Key Laboratory of Sheep Genetic Improvement and Healthy Production (Nos. 2018CA001, and 2019CA009, 2020CA001).
- Published
- 2022
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