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Research Article | 09 Oct 2026

Genome-wide identification of candidate breed-specific markers and selection signatures in Kalmyk cattle

Zanda Bochkaeva1, Aleksandra Abdelmanova2, Tatiana Deniskova2, Victoria Ubushieva1, Altana Ubushieva1, Nadezhda Chimidova1, Arslang Khakhlinov1, Baatr Bolaev1, Badma Salaev1, and Natalia Zinovieva2 Show more
VETERINARY WORLD | Article No. 13 | pg no. 4498-4528 | Vol. 19, Issue 10 | DOI: 10.14202/vetworld.2026.4498-4528
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ABSTRACT

                      
Background and Aim: Kalmyk cattle (KALMYK) represent an indigenous Russian beef breed with valuable adaptive and productive characteristics under harsh continental steppe conditions. However, previous genomic studies have involved relatively small populations, and candidate markers that distinguish KALMYK from both specialized beef and steppe cattle remain insufficiently characterized. This study aimed to characterize the population structure and genetic diversity of KALMYK and identify candidate breed-specific single-nucleotide polymorphisms (SNPs), genomic regions under putative selection pressure, and associated candidate genes using genome-wide genotyping.
Materials and Methods: Genome-wide genotypes were obtained from 100 purebred KALMYK using the Illumina BovineSNP50 v3 BeadChip and compared with Hereford (n = 27), Kazakh White-Headed (n = 93), Red Steppe (n = 45), and Mongolian (n = 47) cattle. Across platforms, 44,774 common SNPs were retained before quality control. The final dataset comprised 312 animals and 30,839 SNPs, with 27,932 linkage disequilibrium-pruned SNPs used for population structure analyses. Genetic diversity, population structure, differentiating SNPs, runs of homozygosity, F_ST, and cross-population extended haplotype homozygosity were evaluated.
Results: KALMYK showed the closest genetic relationship with Mongolian cattle (F_ST = 0.019). Two comparisons, Kalmyk versus specialized beef breeds and Kalmyk versus steppe cattle, each identified 31 highly differentiated SNPs. After accounting for one shared locus, 61 candidate SNPs were retained. Fifty-one genomic regions across 19 chromosomes contained 202 genes, including a shared region on Bos taurus autosome (BTA)12 harboring RNASEH2B. Other prioritized genes included USP18, C1QTNF6, SSTR3, RAC2, and SYT10. Three islands of homozygosity were detected on BTA5, BTA7, and BTA13. The mean genomic inbreeding coefficient was 0.05 in KALMYK compared with 0.133 in specialized beef breeds.
Conclusion: This study provides a genome-wide framework for characterizing the KALMYK gene pool and proposes 61 candidate SNPs for future breed authentication and genetic monitoring. Because we did not perform phenotypic association or independent validation, these markers remain candidates that require validation in independent purebred and crossbred populations before practical implementation.
                      
Keywords: breed authentication, cattle genomics, genetic diversity, genome-wide genotyping, Kalmyk cattle, selection signatures, single-nucleotide polymorphisms, SNP markers.