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. 2024 Dec 4:e2407615.
doi: 10.1002/advs.202407615. Online ahead of print.

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

Jingfang Si  1 , Dongmei Dai  1 , Neena Amatya Gorkhali  2 , Mingshan Wang  3 , Sheng Wang  3 , Saroj Sapkota  2 , Ram Chandra Kadel  4 , Amir Sadaula  5 , Aashish Dhakal  1 , Md Omar Faruque  6 , Abdullah Ibne Omar  1 , Eka Meutia Sari  7 , Hidayat Ashari  7 , Muhammad Ihsan Andi Dagong  8 , Marnoch Yindee  9 , Hossam E Rushdi  10 , Hussein Elregalaty  11 , Ahmed Amin  10 , Mohamed A Radwan  10 , Lan Doan Pham  12 , W M M P Hulugalla  13 , G L L Pradeepa Silva  13 , Wei Zheng  14 , Shahid Mansoor  15   16 , Muhammad Basil Ali  15 , Farhad Vahidi  17 , Sahar Ahmed Al-Bayatti  18 , Alfredo Pauciullo  19 , Johannes A Lenstra  20 , J Stuart F Barker  21 , Lingzhao Fang  22 , Dong-Dong Wu  3 , Jianlin Han  23 , Yi Zhang  1
Affiliations

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

Jingfang Si et al. Adv Sci (Weinh). .

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.

Keywords: CSN2; MC1R; buffalo; population genomics; selection; single‐cell RNA‐seq.

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