The polymorphism information content of the STR loci in the samples of breeding bulls of three breeds

Genotyping data for 11 microsatellite loci (STR) of the Jersey (JER, n = 10), Red Scandinavian (RED, n = 29) and Holstein (HOL, n = 45) breeds were used to calculate polymorphism information content (𝑷𝑰𝑪). For the JER-sample, the estimates of 𝑷𝑰𝑪 loci were in the range of [0.222; 0.680], for the RED-sample – [0.448; 0.802], for the HOL-sample – [0.466; 0.825]; averages were 0.470, 0.650 and 0.682, respectively. The differences between the average of the JER-sample and the average of the RED- and HOL-samples were statistically significant (p_value < 0.005). Highly informative loci (𝑷𝑰𝑪> 0.6) in the JER-, RED- and HOL-samples were 36.4, 63.6 and 72.7 %, respectively. In the 2D projection of the analysis of the correspondence of bull samples with four 𝑷𝑰𝑪 categories, the first dimension explained 94.5 % of the extracted inversion, the second – 4.5 %. The ordination revealed the proximity of the RED- and HOL-samples and their contrast with the JER-sample. There was also a proximity of 2 (𝑷𝑰𝑪 = 0.4-0.6) and 3 (𝑷𝑰𝑪 = 0.61-0.8) categories, their contrast with category 4 (𝑷𝑰𝑪> 0.8) and a stronger contrast with category 1 (𝑷𝑰𝑪< 0.4). To identify animals with an error of 0.0001, five loci with high 𝑷𝑰𝑪 scores were sufficient in the JER-sample, four in the RED-sample, and three in the HOL-sample. When verifying the origin, when the genotypes of both parents are known, the 99.9 % probability exclusion was achieved in the HOL-sample at 8 loci, in the RED-sample at 10, and in the JER-sample more than 11 loci were required. In the case where the genotype of one parent is known, all 11 loci in the JER-, RED- and HOL-samples could provide probability exclusion of 88.2, 98.3, and 99.1 %, respectively. The indicators of individual heterozygosity of the same bulls, calculated from highly and low-informative loci, were statistically independent (𝒓^𝟐 = 0.07). Estimates of fixation indices (𝑮_𝑺𝑻, 𝑮′_{𝑺𝑻(𝑵)}), their modifications (𝑮′_{𝑺𝑻(𝑯)}, 𝑮′′_𝑺𝑻 ) and interbreed differentiation (𝑫_𝒆𝒔𝒕, 𝑫′ ) the RED- and HOL-samples were: for 11 loci – 0.056 and 0.105, 0.331 and 0.366, 0.292 and 0.343, respectively; for five low–information loci (𝑷𝑰𝑪_𝒎𝒊𝒏) - 0.07 and 0.13, 0.292 and 0.338, 0.238 and 0.269; for five high-information loci (𝑷𝑰𝑪_𝒎𝒂𝒙) – 0.034 and 0.066, 0.319 and 0.342, 0.295 and 0.355. When planning large-scale population-genetic studies, the choice of highly informative DNA markers will at least not reduce the accuracy of genetic assessments and tests, but will cut back the cost of genotyping and analysis of fewer loci.

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