Population genetic structure of the Ukrainian black-pied dairy breed with the genome BoLA-DRB3

Abstract

The second exon of the BoLA-DRB3 gene has the highest level of polymorphism among all studied loci of the major histocompatibility complex (MHC) in cattle, which allows it to be used for studying population-genetic structure and assessing the level of biodiversity of populations or comparing the biodiversity of particular herds. According to the results of typing the blood samples of 293 cows using the method of PCR-RLFP, we determined allele frequencies of the BoLA-DRB3 gene for the Ukrainian black-pied dairy breed. The study was conducted on three herds in Khmelnytskyi Oblast: LLC “Kozatska Dolyna 2006” (herd A, n = 122), agrofirm “Perlyna Podillya” (herd B, n = 82) and branch “Ridnyy kray” (herd C, n = 89). In total, 37 alleles were found: herd A 31, herd B 25 and herd C 28. In total, in the three subpopulations seven alleles were found with frequency of over 5%, the total share of which equaled 55.8%. The most widely distributed allele was BoLA-DRB3.2*24, which composed 22.2% of the allele pool of the breed. We determined a high level of observed (0.89 to 0.95) and expected (0.93 to 0.94) heterozygosity. In herds A and B, there was determined domination of homozygotes. Deviation from HWE, calculated using the value of Wright`s individual fixation index, equaled FIS(A) = 0.016 (χ2 = 0.03; P > 0.05) and FIS(B) = 0.044 (χ2 = 0.076; P > 0.05). In herd C, we found excess of heterozygotes FIS(C) = -0.017 (χ2 = 0.026; P > 0.05). Rather low values were determined for the subpopulation fixation index: FST(A) = 0.009 (χ2 = 65.9; P < 0.01), FST(B) = 0.012 (χ2 = 47.2; P < 0.05) and FST(C) = 0.003 (χ2 = 14.4; P > 0.05), which were significantly different from the mean value for cattle (FST = 0.078), indicating insignificant reduction of heterozygosity and divergence between the subpopulations by the BoLA-DRB3 gene. To assess genetic diversity, we calculated parameters of effective allele number (Ae) and Shannon’s information index (I). In spite of the different numbers of alleles found in the selections, it was suggested that for assessing their diversity, an efficiency index will be used which shows the share of effective alleles among all alleles found in a subpopulation (Ae/Nа). The calculated values of the parameters equaled: herd A Ae = 14.9, Ae/Nа = 0.48, I = 3.05; herd B Ae = 14.5, Ae/Nа = 0.58, I = 2.87; herd C Ae = 16.4, Ae/Nа = 0.59, I = 3.01. Frequencies of BoLA-DRB3 alleles were used for calculating genetic similarity and standard genetic distances according to Nei. Cows of herds B and C were found to be more genetically affinitive by the BoLA-DRB3 gene. Standard genetic distance between them was the lowest D = 0.13, which coincides with the geographic locations and historical development of these populations. The results of the study prove that the studied herds have a high level of polymorphism. Frequency characteristics, values of expected heterozygosity, effective allele number, efficiency index and Shannon’s information index compared to the similar parameters for Holstein, black-pied and some other local breeds of cattle indicate the high genetic diversity of the studied subpopulations of the Ukrainian black-pied dairy breed.