Genomic analyses reveal distinct genetic architectures and selective pressures in buffaloes

Abstract

Background The domestic buffalo (Bubalus bubalis) is an essential farm animal in tropical and subtropical regions, whose genomic diversity is yet to be fully discovered. Results In this study, we describe the demographic events and selective pressures of buffalo by analyzing 121 whole genomes (98 newly reported) from 25 swamp and river buffalo breeds. Both uniparental and biparental markers were investigated to provide the final scenario. The ancestors of swamp and river buffalo diverged ∼0.23 million years ago and then experienced independent demographic histories. They were domesticated in different regions, the swamp buffalo at the border between southwest China and southeast Asia, while the river buffalo in south Asia. The domestic stocks migrated to other regions and further differentiated, as testified by (at least) 2 ancestral components identified in each subspecies. Different signals of selective pressures were also detected in these 2 types of buffalo. The swamp buffalo, historically used as a draft animal, shows selection signatures in genes associated with the nervous system, while in river dairy breeds, genes under selection are related to heat stress and immunity. Conclusions Our findings substantially expand the catalogue of genetic variants in buffalo and reveal new insights into the evolutionary history and distinct selective pressures in river and swamp buffalo.

Evolution and domestication of the Bovini species

“…For the domestication of two other highly successful bovines, the river and the swamp buffalo, we refer to Zhang et al (2020a), Sun et al . (2020) and Luo et al . (2020).…”

“…2010) and have been domesticated separately (Sun et al . 2020). Selection targeting the dairy production of the river buffalo and the draught power of the swamp buffalo is likely to have led to divergent domestication traits (Luo et al .…”

Detection of Selection Signatures Underlying Production and Adaptive Traits Based on Whole-Genome Sequencing of Six Donkey Populations

“…Individual Hp values were Z-transformed as: where μHp is the overall average heterozygosity and σHp is the standard deviation for all windows in each subpopulation. To detect putative selected loci in this study, we first calculated the pooled heterozygosity (Hp) and its Z-transformations, ZHp , in sliding 50 KB windows along the scaffolds [ 20 , 21 ]. Putatively selected loci were defined as genetic regions in overlapping windows with extremely low ZHp values (<−7) and extremely high di values (top 1%).…”

Mitogenome Diversity and Maternal Origins of Guangxi Buffalo Breeds

“…The swamp buffalo is traditionally raised as a draught animal for rice cultivation, and is mainly bred in extensive rural areas in Northeast India, Southeast Asia and South China. Previous studies have reported that the two types of buffalo descended from different wild Asian water buffalo in separate geographical regions [4,5]. The river buffalo was domesticated in the western region of the Indian subcontinent, and then spread to the west.…”