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

Xin Li, Ji Yang, Min Shen, Xing-Long Xie, Guang-Jian Liu, Ya-Xi Xu, Feng-Hua Lv, Hua Yang, Yong-Lin Yang, Chang-Bin Liu, Ping Zhou, Peng-Cheng Wan, Yun-Sheng Zhang, Lei Gao, Jing-Quan Yang, Wen-Hui Pi, Yan-Ling Ren, Zhi-Qiang Shen, Feng Wang, Juan Deng, Song-Song Xu, Hosein Salehian-Dehkordi, Eer Hehua, Ali Esmailizadeh, Mostafa Dehghani-Qanatqestani, Ondřej Štěpánek, Christina Weimann, Georg Erhardt, Agraw Amane, Joram M. Mwacharo, Jian-Lin Han, Olivier Hanotte, Johannes A. Lenstra, Juha Kantanen, David W. Coltman, James W. Kijas, Michael W. Bruford, Kathiravan Periasamy, Xin-Hua Wang () and Meng-Hua Li ()
Additional contact information
Xin Li: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS)
Ji Yang: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS)
Min Shen: Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences
Xing-Long Xie: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS)
Guang-Jian Liu: Novogene Bioinformatics Institute
Ya-Xi Xu: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS)
Feng-Hua Lv: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS)
Hua Yang: Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences
Yong-Lin Yang: Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences
Chang-Bin Liu: Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences
Ping Zhou: Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences
Peng-Cheng Wan: Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences
Yun-Sheng Zhang: Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences
Lei Gao: Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences
Jing-Quan Yang: Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences
Wen-Hui Pi: Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences
Yan-Ling Ren: Shandong Binzhou Academy of Animal Science and Veterinary Medicine
Zhi-Qiang Shen: Shandong Binzhou Academy of Animal Science and Veterinary Medicine
Feng Wang: Institute of Sheep and Goat Science, Nanjing Agricultural University
Juan Deng: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS)
Song-Song Xu: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS)
Hosein Salehian-Dehkordi: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS)
Eer Hehua: Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences
Ali Esmailizadeh: Shahid Bahonar University of Kerman
Mostafa Dehghani-Qanatqestani: Shahid Bahonar University of Kerman
Ondřej Štěpánek: Institute of Molecular Genetics of the ASCR, v. v. i.
Christina Weimann: Institute of Animal Breeding and Genetics, Justus Liebig University
Georg Erhardt: Institute of Animal Breeding and Genetics, Justus Liebig University
Agraw Amane: Addis Ababa University
Joram M. Mwacharo: Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA)
Jian-Lin Han: CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS)
Olivier Hanotte: LiveGene Program, International Livestock Research Institute
Johannes A. Lenstra: Faculty of Veterinary Medicine, Utrecht University
Juha Kantanen: Production Systems, Natural Resources Institute Finland (Luke)
David W. Coltman: Department of Biological Sciences, University of Alberta
James W. Kijas: CSIRO Livestock Industries, St Lucia
Michael W. Bruford: School of Biosciences, Cardiff University, Cathays Park
Kathiravan Periasamy: Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency
Xin-Hua Wang: Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences
Meng-Hua Li: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS)

Nature Communications, 2020, vol. 11, issue 1, 1-16

Abstract: Abstract 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.

Date: 2020
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DOI: 10.1038/s41467-020-16485-1

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