Comparative analyses of copy number variations between swamp buffaloes and river buffaloes

Abstract

As an important source of genomic variation, copy number variation (CNV) contributes to environmental adaptation in worldwide buffaloes. Despite this importance, CNV divergence between swamp buffaloes and river buffaloes has not been studied previously. Here, we report 21 152 CNV regions (CNVRs) in 141 buffaloes of 20 breeds detected through multiple CNV calling strategies. Only 248 CNVRs were shared between river buffalo and swamp buffalo, reflecting great variation of CNVRs between the two subspecies. Population structure analysis based on CNVs successfully separated the two buffalo subspecies. We further assessed CNV divergence by calculating FST for genome‐wide CNVs. Totally, we identified 110 significantly divergent CNV segments and 44 putatively selected genes between river buffaloes and swamp buffaloes. In particular, LALBA, a key gene controlling milk production in cattle, presented a highly differentiated CNV in the promoter region, which makes it a strong functional candidate gene for differences between swamp buffaloes and river buffaloes in traits related to milk production. Our study provides useful information of CNVs in buffaloes, which may help explain the genetic differences between the two subspecies.

Read-depth based approach on whole genome resequencing data reveals important insights into the copy number variation (CNV) map of major global buffalo breeds

“…1 (b). The finding was concurrent with previous NGS studies reported in cattle [ 33 ] and buffaloes [ 30 ]. Moreover, the deletion events were abundantly reported from aCGH arrays due to ascertainment bias, pinpointing that deletions are effectively captured by them as compared to the other analytical methods [ 37 ].…”

“…The maximum number of CNVs was observed in Murrah (2627) while Surti scored the minimum number (2092). Yang et al [ 30 ] found 21,152 CNV regions in a whole genome dataset of 20 buffalo breeds comprising 141 buffaloes using LUMPY and CNVnator. Strillacci et al [ 31 ] elucidated the CNV profile of Iranian river buffaloes using 90K genotyping array data and reported lesser number of structural variants (9550 CNVs, representing 1.97% of the buffalo genome) with a loss-gain ratio of more than one.…”

“…It is noteworthy that the genome coverage from other CNV studies in cattle (6%) and yak (5.7–6%) also falls within the same range [ 48 – 50 ]. Recently, Yang et al [ 30 ] identified 21,152 CNVRs, representing 1.99% of the bubaline autosome length using multiple algorithms. Additionally, a couple of studies have discussed the chromosomal distribution of CNVRs including sex chromosomes, X and Y [ 51 ].…”

The prevalence of copy number increase at multiallelic CNVs associated with cave colonization in Mexican tetra (Astyanax mexicanus)

“…We observe strong stratification of CNVs between populations, in line with numerous studies in various species (Sudmant et al 2015; Pezer et al 2015; Xu et al 2016; Dorant et al 2020; Zhu et al 2020; Jang et al 2021; Solé et al 2019; Yang et al 2023). The profile of CNVs based on presence-absence patterns follows the previously established phylogenetic relationship between new and old lineage A. mexicanus populations based on SNPs (Herman et al 2018).…”

The prevalence of copy number increase at multiallelic copy number variants associated with cave colonization

“…2015;Xu et al, 2016;Yang et al, 2023;Zhu et al, 2020). The profile of CNVs based on presence-absence patterns follows the previously established phylogenetic relationship between new and old-lineage A. mexicanus populations based on SNPs(Herman et al, 2018).…”