Identification of QTLs in dairy cattle by wide-genome associative analysis

Over the past 10 years, as a result of full genomic sequencing of cattle, a chip technology based on single nucleotide polymorphism (SNP) in the animal genome was created. With the help of a genome - wide comparative analysis of Holstein cattle of the Leningrad Region have been identified genes that can be responsible for potential QTLs. All animals were genotyped by the BovineSNP50 v.2 chip. The criteria for editing SNPs were as follows: The minor alleles frequency of SNPs was < 1%. The genotyping error of SNPs is not more than 5%. Reliability of SNPs genotypes deviation from Hardy-Weinberg equilibrium was (P <0.001). ANIMAL MODEL was used for breeding values evaluation. In carrying out the associative analysis, the Plink 1.9 and EMMAX programs were applied. Associative analysis was carried out on 280 bulls and 500 cows including traits of milk yield and milk fat yield, which were evaluated with ANIMAL MODEL. Five SNPs overcome the confidence threshold of 10^-8 for milk yield (DYD of the bulls) and 12 SNP for milk fat yield (YD of the cows and DYD of the bulls). In bulls, the genes 6-β-N-acetylgucosamintransferase and RASA1 are identified as the most likely candidates for QTL responsible for milk yield and the gene RASA1 for milk fat yield. It may be the result of a negative correlation between milk yield and milk fat yield. In cows, the localization of the ZNF704 gene coincides with QTL in the Animal Genome database affecting of the milk fat yield. Associative analysis of BV with SNP markers confirmed the expected lower reliability of cows' breeding value evaluation in comparison with bulls ones in case of milk yield, but not for milk fat yield. The obtained data indicate that QTLs affecting the of milk fat yield were detected both in bulls and in cows, and in different chromosomes or in different regions of chromosome 7. The data obtained should be considered as preliminary, since the sample of animals did not exceed 280 bulls and 500 cows.

QTL, SNPs, WGAS, Animal Model, EMMAX, YD, DYD, QTL, SNPs, WGAS, Animal Model, EMMAX, YD, DYD, milk fat, milk yield, milk cattle

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