Genome-wide analysis across Indian camel populations reveals genetic distinctiveness of the Kharai camel breed.

Authors

Amisha, Ved Prakash, Basanti Jyotsana, Ashish Yadav, Karan Mahar, Shubham Kumar Singh, Rani Alex, G R Gowane

Published in

BMC genomics. Jul 06, 2026. Epub Jul 06, 2026.

Abstract

In India, indigenous camel populations have evolved under diverse ecological conditions, leading to the emergence of several distinct breeds with specialised adaptive traits. Understanding the genomic architecture and population structure of such camel populations is essential for their conservation and sustainable utilisation. In the present study, whole-genome sequencing data were generated and analysed for Indian dromedary camels representing nine recognised breeds, along with Indian Bactrian (double-humped) and Arabian Peninsula dromedaries with the primary objective to investigate population structure and to assess the genetic distinctiveness of the geographically isolated Kharai camel, a unique breed adapted to coastal and saline environments.
The sequencing depth ranged from 11.3× to 25.4× for Indian dromedaries, with high mapping efficiency to the reference genome (mCamDro1). Population structure analyses consistently revealed limited genetic differentiation among most Indian dromedary populations, reflecting shared ancestry and historical gene flow. However, the Kharai camel exhibited clear genetic distinctiveness across multiple analytical approaches. Principal component analysis separated Kharai from other dromedaries, and admixture analysis at K = 2 demonstrated near-complete clustering of Kharai individuals to a distinct ancestral component. Pairwise genetic distances (F_ST) further supported moderate differentiation in Kharai (0.07-0.10), compared with the low differentiation observed among other populations. Neighbour-Net and phylogenetic tree analyses corroborated these findings, showing breed-specific clustering with clear separation of Kharai. Genome-wide diversity analysis revealed a predominance of low-frequency alleles (57.7% of SNPs with MAF 0.05-0.10), indicating population subdivision and localised demographic histories. Moderate genetic diversity was observed (Hₒ = 0.303 ± 0.001; Hₑ = 0.319 ± 0.0001), with evidence of a mild heterozygote deficit likely attributable to the Wahlund effect. Linkage disequilibrium (LD) analysis showed strong short-range LD (r² = 0.783 at 0-10 kb) with gradual decay up to 10 Mb, suggesting a moderate historical effective population size. LD-based reconstruction indicated a decline in effective population size from > 2,500 ancestral individuals to approximately 167 individuals in recent generations, highlighting demographic contraction.
These findings demonstrate substantial genetic homogeneity among Indian dromedary populations while highlighting the distinct genomic identity of the Kharai camel breed. The results underscore the evolutionary uniqueness of this breed and emphasise the need for targeted conservation and management strategies to preserve its genetic resources.

PMID:
42402553
Bibliographic data and abstract were imported from PubMed on 06 Jul 2026.

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