Understanding divergent domestication traits from the whole-genome sequencing of swamp- and river-buffalo populations

Author:

Luo Xier1,Zhou Yu1,Zhang Bing2,Zhang Yi3ORCID,Wang Xiaobo14,Feng Tong14ORCID,Li Zhipeng1,Cui Kuiqing1,Wang Zhiqiang1,Luo Chan1,Li Hui1,Deng Yanfei1,Lu Fenghua1ORCID,Han Jianlin56,Miao Yongwang7,Mao Huaming7,Yi Xiaoyan4,Ai Cheng4,Wu Shigang4,Li Alun4,Wu Zhichao4,Zhuo Zijun4,Da Giang Do18,Mitra Bikash9,Vahidi Mohammad Farhad10,Mansoor Shahid11,Al-Bayatti Sahar Ahmed12,Sari Eka Meutia13,Gorkhali Neena Amatya14,Prastowo Sigit15,Shafique Laiba1,Ye Guoyou16,Qian Qian4ORCID,Chen Baoshan1,Shi Deshun1,Ruan Jue4,Liu Qingyou1

Affiliation:

1. State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China

2. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China

3. National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100083, China

4. Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China

5. CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China

6. International Livestock Research Institute, Nairobi 00100, Kenya

7. Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China

8. Bacgiang Agriculture and Forestry University, Bacgiang 230000, Vietnam

9. Cellular Immunology Lab, Department of Zoology, University of North Bengal, Siligun 734013, India

10. Animal Biotechnology Department, Agricultural Biotechnology Research Institute of Iran-North Region, Agricultural Research, Education and Extension Organization, Rasht 999067, Iran

11. National Institute for Biotechnology and Genetic Engineering, Faisalabad 999010, Pakistan

12. Animal Genetic Sources Department, Directorate of Animal Resources, Ministry of Agriculture, Baghdad 19207, Iraq

13. Department of Animal Science, Faculty of Agriculture, Syiah Kuala University, Darussalam-Banda Aceh 23111, Indonesia

14. Animal Breeding Division, National Animal Science Research Institute, Nepal Agriculture Research Council, Khumaltar 999098, Nepal

15. Animal Science Department Universitas Sebelas Maret, Surakarta 999006, Indonesia

16. International Rice Research Institute, Manila 999005, Philippines

Abstract

Abstract Domesticated buffaloes have been integral to rice-paddy agro-ecosystems for millennia, yet relatively little is known about the buffalo genomics. Here, we sequenced and assembled reference genomes for both swamp and river buffaloes and we re-sequenced 230 individuals (132 swamp buffaloes and 98 river buffaloes) sampled from across Asia and Europe. Beyond the many actionable insights that our study revealed about the domestication, basic physiology and breeding of buffalo, we made the striking discovery that the divergent domestication traits between swamp and river buffaloes can be explained with recent selections of genes on social behavior, digestion metabolism, strengths and milk production.

Funder

National Natural Science Foundation of China

Guangxi Natural Science Foundation

Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources

Guangxi Department of Science and Technology

Publisher

Oxford University Press (OUP)

Subject

Multidisciplinary

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