Journal of Biotechnology and its Applications
Open AccessWeighted Single-Step Genome-Wide Association Study of Milk Production Traits in the Russian Black-and-White cattle.
Authors: Khatib Abdulrahman, Prokhortchouk B Egor, Sharko S Fedor, Mazur Alexander, Zarkawi Moataz
Abstract
Weighted single-step genome-wide association study (WssGWAS) has proven effective for exploring genomic regions associated with quantitative traits in dairy cattle. In this study, we conducted WssGWAS to identify candidate genes linked to three of the most frequently assessed milk production traits: daily milk yield (MY), milk fat percentage (FP) and milk protein percentage (PP). The phenotypic and pedigree dataset used in this study was obtained from the national genetic evaluation program in Russia for Black-and-White dairy cattle. Genotypic information for 644 animals (427 bulls and 217 cows) was used to estimate the effects of 52,445 SNPs using WssGWAS. SNPs with call rate < 0.90 and those with minor allele frequency < 0.05 were excluded from the analysis. The results were reported as the proportion of total genetic variance explained by 20 adjacent SNP windows. Only windows that accounted for the largest share of variance (>0.5%) were chosen for additional candidate gene analysis. We identified 12 genomic windows on chromosomes 7, 8 and 12 associated with MY, one genomic window on chromosomes 4 associated with PP and six non-overlapping genomic windows on chromosomes 10 and 14 associated with FP. These windows collectively explained 6.33%, 0.51 % and 6.22% of the total genetic variance for MY, FP and PP, respectively. Different genes were identified within these regions and are believed to be associated with the studied traits. These genes play a role in numerous biological processes, such as metabolism, growth, the preservation of genomic stability, and the control of gene expression.
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