Genomic Diversity and Population Structure of Red Steppe Cattle Based on High-Density SNP Genotyping
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In this study, we genotyped 40 Red Steppe cattle using the Illumina BovineSNP50 BeadChip (∼53,000 SNPs) to provide a comprehensive, high-resolution genomic characterization of the breed. Key population metrics including observed heterozygosity (Ho), runs of homozygosity (ROH), and genomic inbreeding coefficients (F_ROH) were calculated. Population structure was analyzed using ADMIXTURE and principal component analysis (PCA), revealing three ancestral components (K = 3) and internal stratification. A composite index (Ho − F_ROH) was used to rank individuals based on genetic merit and inbreeding load. These results offer foundational data for genome-informed breeding strategies and conservation management in Red Steppe cattle.
Objective.
To provide the first comprehensive genomic characterization of Red Steppe cattle by assessing their genetic diversity, inbreeding levels, and population structure using high-density single-nucleotide polymorphism (SNP) genotyping.
Methods.
Forty Red Steppe cattle were genotyped using the Illumina BovineSNP50 BeadChip (∼53,000 SNPs). Quality control filtering retained 52,781 autosomal SNPs for analysis. We calculated observed heterozygosity (Ho), runs of homozygosity (ROH), and the corresponding genomic inbreeding coefficient (F_ROH). Population structure was examined with model-based clustering (ADMIXTURE) and principal component analysis (PCA). We also applied a composite metric (Ho–F_ROH) to identify individuals combining high diversity with low inbreeding.
Results.
The Red Steppe breed demonstrated moderate genetic diversity (mean Ho = 0.307 ± 0.014) and heterogeneous inbreeding (mean F_ROH = 0.076 ± 0.022; range 0.030– 0.130). ADMIXTURE analysis consistently identified three ancestral components (K = 3), revealing subtle stratification within the herd. PCA results were concordant, highlighting the same internal substructure. Notably, several peripheral PCA outliers with distinct admixture profiles were observed, potentially representing reservoirs of unique genetic variation. Using the composite metric, we pinpointed specific low-inbreeding, high-heterozygosity animals as candidates for breeding programs.
Conclusion.
Our findings demonstrate the utility of integrating SNP-based diversity metrics and population structure analyses for evidence-based conservation of regionally adapted cattle. This genomic assessment provides critical baseline data on Red Steppe cattle and supports genomically informed selection strategies to preserve genetic resilience and mitigate inbreeding in the breed.
