Complete Genomic Landscape Reveals Hidden Evolutionary History and Selection Signature in Asian Water Buffaloes (<i>Bubalus bubalis</i>)

To identify the genetic determinants of domestication and productivity of Asian water buffaloes (Bubalus bubalis), 470 genomes of domesticated river and swamp buffaloes along with their putative ancestors, the wild water buffaloes (Bubalus arnee) are sequenced and integrated. The swamp buffaloes inherit the morphology of the wild buffaloes. In contrast, most river buffaloes are unique in their morphology, but their genomes cluster with the wild buffaloes. The levels of genomic diversity in Italian river and Indonesian swamp buffaloes decrease at opposite extremes of their distribution range. Purifying selection prevented the accumulation of harmful loss-of-function variants in the Indonesian buffaloes. Genes that evolved rapidly (e.g., GKAP1) following differential selections in the river and swamp buffaloes are involved in their reproduction. Genes related to milk production (e.g., CSN2) and coat color (e.g., MC1R) underwent strong selections in the dairy river buffaloes via soft and hard selective sweeps, respectively. The selective sweeps and single-cell RNA-seq data revealed the luminal cells as the key cell type in response to artificial selection for milk production of the dairy buffaloes. These findings show how artificial selection has been driving the evolutionary divergence and genetic differentiation in morphology and productivity of Asian water buffaloes.

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Publication Details

Journal
Advanced Science
Published
2024-12-04
DOI
https://doi.org/10.1002/advs.202407615
Citations
8
Primary Topic
Genetic and phenotypic traits in livestock
Type
article
Field-Weighted Citation Impact
4.40

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article

Complete Genomic Landscape Reveals Hidden Evolutionary History and Selection Signature in Asian Water Buffaloes (Bubalus bubalis)

Lingzhao Fang, Raju Kadel, Johannes A. Lenstra, Neena Amatya Gorkhali et al.
8 citations
Advanced Science
Genetic and phenotypic traits in livestock
4.40
article

Complete Genomic Landscape Reveals Hidden Evolutionary History and Selection Signature in Asian Water Buffaloes (Bubalus bubalis)

Lingzhao Fang, Raju Kadel, Johannes A. Lenstra, Neena Amatya Gorkhali, Aashish Dhakal, Dongmei Dai, Amir Sadaula, Eka Meutia Sari, Alfredo Pauciullo, Farhad Vahidi, Wei Zheng, Sahar Ahmed Al‐Bayatti, Yi Zhang, W. M. M. P. Hulugalla, Muhammad Basil Ali, Marnoch Yindee, Dong‐Dong Wu, Omar Faruque, Hossam E. Rushdi, Gamamada Liyanage Lalanie Pradeepa Silva, Shahid Mansoor, J. S. F. Barker, Abdullah Ibne Omar, Muhammad Ihsan Andi Dagong, Hidayat Ashari, H. El-Regalaty, Lan Doan Pham, M. A. Radwan, Saroj Sapkota, Ahmed Amin, Mingshan Wang, Jingfang Si, Han Jianlin, Sheng Wang
article en
8 citations

Abstract

To identify the genetic determinants of domestication and productivity of Asian water buffaloes (Bubalus bubalis), 470 genomes of domesticated river and swamp buffaloes along with their putative ancestors, the wild water buffaloes (Bubalus arnee) are sequenced and integrated. The swamp buffaloes inherit the morphology of the wild buffaloes. In contrast, most river buffaloes are unique in their morphology, but their genomes cluster with the wild buffaloes. The levels of genomic diversity in Italian river and Indonesian swamp buffaloes decrease at opposite extremes of their distribution range. Purifying selection prevented the accumulation of harmful loss-of-function variants in the Indonesian buffaloes. Genes that evolved rapidly (e.g., GKAP1) following differential selections in the river and swamp buffaloes are involved in their reproduction. Genes related to milk production (e.g., CSN2) and coat color (e.g., MC1R) underwent strong selections in the dairy river buffaloes via soft and hard selective sweeps, respectively. The selective sweeps and single-cell RNA-seq data revealed the luminal cells as the key cell type in response to artificial selection for milk production of the dairy buffaloes. These findings show how artificial selection has been driving the evolutionary divergence and genetic differentiation in morphology and productivity of Asian water buffaloes.

Advanced ScienceVol. 12(4)
University of Peradeniya (LK), National Institute for Biotechnology and Genetic Engineering (PK), Cairo University (EG), Kunming Institute of Zoology (CN), Universitas Syiah Kuala (ID), Utrecht University (NL), University of Karachi (PK), Chinese Academy of Sciences (CN), Aarhus University (DK), Bangladesh Agricultural University (BD), Government of Nepal (NP), National Institute of Animal Sciences (VN), Guangxi Buffalo Research Institute (CN), International Center for Chemical and Biological Sciences (PK), Ministry of Higher Education and Scientific Research (IQ), Chinese Academy of Agricultural Sciences (CN), Nepal Agricultural Research Council (NP), Agricultural Biotechnology Research Institute of Iran (IR), Ministry of Agriculture and Rural Affairs (CN), Agricultural Research Center (EG), China Agricultural University (CN), University of Turin (IT), University of New England (AU), National Trust for Nature Conservation (NP), Walailak University (TH), Hasanuddin University (ID)
National Natural Science Foundation of China, China Agricultural University, National Key Research and Development Program of China
Clean water and sanitation
Openalex Percentile: Top 5%
Genetic and phenotypic traits in livestock
4.40
DOIOpen Access PDFOpenAlex
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