Genome-Wide Association Study of Single Nucleotide Polymorphisms with Milk Traits in Red Gorbatov Cattle

Abstract

In order to preserve the gene pool of the Red Gorbatov breed, it is necessary to use a set of genomic analysis tools that allows more efficient planning in obtaining individuals who meet the economic requirements of dairy farming. The aim of the work was to identify candidate genes associated with milk production traits in Red Gorbatov cattle using a genome-wide association analysis. Genotyping was performed using the BovineSNP50 v3 Bead Chip panel and the Bead Studio program, quality control, data filtering, and identification of associations for each single-nucleotide polymorphism with milk productivity indicators was performed by Multiple linear regression analysis using the PLINK 1.90 software package. The process of data visualization was performed using the qqman package in the R programming language. 44 full-genome and 178 suggestive Single Nucleotide Polymorphisms (SNPs) associated with the milk parameters in Red Gorbatov cows have been identified, while the largest number of SNPs with a full genome were located on chromosomes 18 and 20-6 in both cases. On chromosome 18, one SNP (ARS-BFGL-NGS-18019) was common for two traits (protein and β-casein content). On chromosome 20, 2 SNPs (BTB-01636657 and ARS-BFGL-NGS-91235) were common for two traits (protein and β-casein content). Structural annotation of genomic regions within a window of ±0.20 Mb revealed 20 genes with the described functions in terms of gene ontology. The genes ODAM, HS3ST2, SLIT2, ADARB2, TBC1D22A, ZFPM2, ARHGEF28, LRRC8D, OTOG, UNC80, GRIA1, C1QTNF3, CTNND2 are involved in processes related to the chemical composition of milk and milk productivity.