Identification of the carriers of the mutant alleles in the cattle in the Central Black Earth region of Russia using NGS sequencing

Background. To carry out high-quality breeding work in the cattle populations, it is necessary to use next generation sequencing (NGS) methods, which allow large samples of the animals to be assessed for a significant number of the single nucleotide substitutions (SNPs) in a short period of time.

Materials and methods. Genotyping of the Holstein black-and-white cattle bred in the Central Black Earth region of Russia (Belgorod region) was carried out using NGS sequencing (multilocus panel TruSeq® Bovine Parentage Kit, Illumina USA).

Results. It was found that most of the animals studied are the inter-line hybrids. Correlation analysis of the "Reflection Sovereign", "Montvik Chieftain" and "Vis Back Ideal" lines showed no correlation dependency (r=0,165, p=0,106). Additionally, 10,4% of the cattle were carriers of the gene related to the Holstein red-and-white coat color. Furthermore, 61,5% of the cattle were carriers of the mutant allele G (_SNPchr8_108833985), which lowers immunity and contributes to the development of moraxellosis. Carriers of several unfavorable mutations were identified, such as Syndactyly (SY) – 8,3%, mutations leading to leukism (MITF gene) – 12,3%, and mutations in the melanocortin receptor gene (MC1R) – 10,4%. Carriers of the semi-lethal mutation (allele T) in the APAF1 gene accounted for 3,0% of the cattle, carriers of the lethal mutation (allele C) in the HH3 gene – 14,6%, carriers of the lethal mutation (allele C) in the HHB (BLAD) gene – 1,0%, carriers of the semi-lethal mutation (allele A) in the SLC35A3 gene – 2,0%. All this indicates errors in the breeding work. Against the backdrop of these unfavorable genetic factors, carriers of mutations with a positive effect on meat and milk productivity were observed, namely carriers of the MSTN gene mutation (allele T) – 50%, carriers of the ABCG2 gene mutation (allele C) – 4.2%, carriers of the DGAT1 gene mutation (allele A) – 28,1%, carrier of the CSN1S1 gene mutation (allele A) – 1,0%.

Conclusion. We believe that adjusting the breeding work regarding these mutations, both with negative and positive effects, will allow farms to create core herds of high-productivity animals, which will contribute to increasing the quantity and quality of dairy products.