How Well Does a Multi-Breed Reference Panel Impute an Unrepresented Breed? Low-Coverage Sequencing of Native Kalmyk Cattle Against Holstein and Aberdeen-Angus

Low-coverage (low-pass) whole-genome sequencing (lcWGS) followed by imputation is a cost-effective alternative to array genotyping, but its accuracy depends on how well the target genotypes are represented in the reference panel. We assessed lcWGS imputation quality for three cattle breeds differing in their representation in a multi-breed panel: Holstein, Aberdeen-Angus and the native Russian Kalmyk breed. Imputed genotypes of 86 Kalmyk, 75 Holstein, and 72 Aberdeen-Angus animals were compared with BovineSNP50 array genotypes at 46,715 shared SNPs. Concordance and dosage R² were 99.3% and 0.98 for Holstein and 99.2% and 0.98 for Aberdeen-Angus, and 94.4% and 0.86 for Kalmyk, for which R² exceeded 0.8 at MAF > 5%, an acceptable level for common-variant analyses. PCA and ADMIXTURE placed Kalmyk cattle closest to Central- and East-Asian breeds (Kazakh, Mongolian, Hanwoo) that are poorly represented in the panel. Kalmyk cattle also showed the fastest LD decay (r² ≈ 0.04 vs. ≈ 0.10 in Holstein at 450 kb). Both the absence of the breed from the panel and the fast LD decay are expected to reduce imputation accuracy, and their contributions cannot be separated in a study of three breeds. Imputation nearly doubled the coverage of known functional markers from OMIA and other sources (from 70 to 134 positions), although casein variants absent from the panel were not recovered. Imputed lcWGS data for Kalmyk cattle are suitable for GWAS on common variants and population-structure analysis, whereas rare-variant genotyping requires a breed-specific reference panel.