Analysis of locus estimates of allelic diversity of STR markers in a sample of breeding bulls

• Main Authors: V. M. Kuznetsov, В. М. Кузнецов
• Other Authors: the research was carried out under the support of the Ministry of Science and Higher Education of the Russian Federation within the state assignment of the Federal Agricultural Research Center of the North -East named N. V. Rudnitsky (theme No. 123011900029-6). The author thanks the reviewers for their contribution to the peer review of this work., работа выполнена при поддержке Минобрнауки РФ в рамках Государственного задания ФГБНУ «Федеральный аграрный научный центр Северо-Востока имени Н. В. Рудницкого» (№ гос. регистрации 123011900029-6). Автор благодарит рецензентов за их вклад в экспертную оценку этой работы.
• Format: Article in Journal/Newspaper
• Language: Russian
• Published: FARC North-East 2023
• Subjects: ординация; loci; microsatellites; diversity; differentiation; methods of multidimensional statistics; ordination; локусы; микросателлиты; разнообразие; дифференциация; методы многомерной статистики; Kendall; Rangifer
• Online Access: https://www.agronauka-sv.ru/jour/article/view/1459; https://doi.org/10.30766/2072-9081.2023.24.5.888-906

Genotypes of the 11 DNA microsatellite loci of 84 bulls of seven breeds were used to evaluate 14 indicators of allelic diversity/differentiation. Traditional and multidimensional statistical methods were applied to the data matrices from the original and transformed estimates (11×14). Estimates of heterozygosity had coefficients of variability of 8-14 %, the number of alleles per locus and indicators of differentiation of breeds at the level of 20-26 %, fixation indices – 38-44 %. Statistically significant Kendall correlations (0.8-1.0) between indicators of allelic richness and heterozygosity, fixation indices, and differentiation indicators were established. The variability of the transformed estimates of diversity/differentiation indicators by loci was in the range of 6-32 %. Including by loci Eth3, Tgla122, Eth225, Bm2113 – 6-12 %, loci Inra23, Tgla126, Eth10 – 15-20 %, loci Tgla227, Sps115, Tgla53, Bm1824 – 28-32 %. The nonparametric Mann-Whitney-Wilcoxon test showed statistically significant differences in the medians of the Eth3 locus with the Bm2113 locus, the Tgla126 locus with the Eth3, Inra23, Tgla122, Eth225, Bm2113, Bm1824, Eth10 loci. The principal component analysis (PCA) identified two components with a total information content of 95,2 %. The first one took into account 59.4 % of the total variance, had the highest loads in intra-breed diversity data and was defined as an «alpha component». The second accounted for 35.8 % of the total variance, had the highest loads in inter-breed differentiation data and was defined as a «beta component». 2D-PCA-ordination showed that a characteristic grouping of loci took place for the analyzed breeds (samples), loci and measures of diversity. Loci Tgla227 and Tgla53 formed group A, group B – loci Tgla122, Eth225, Eth10, group C – loci Inra23, Bm2113 and Bm1824. The loci of the conditional group D (Eth3, Tgla126, Sps115) were defined as «untypical». Validation of ordination was confirmed by calculations on reduced data (dimension 11×7) and the method of ...