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Analysis of the Southern Meat cattle breed genetic differentiation based on microsatellite loci
Genetic variability and relationships among two lineage of the Southern meat cattle breed from the State Enterprise Experimental Farm “Askaniyske” NAAS Ukraine (Kherson region) were investigated. A total of 192 individuals were analyzed. Of those, 100 individuals represented “Santa Gertrudis” subpopulation and 92 ones represented “Zebu” subpopulation.
A panel of 12 bovine-specific microsatellite markers (TGLA227, BM2113, TGLA53, ETH10, SPS115, TGLA122, INRA23, TGLA126, BM1818, ETH3, ETH225 and BM1824) recommended of the ISAG for cattle genetic diversity studies was selected for genetic characterization and revealing the extent of genetic diversity in the Southern Meat cattle breed. PCR products were detected by АВI 3130xl (Applied Biosystems, USA), subsequently processed via GeneMapper ID v. 3.2 software.
All laboratory tests were conducted in the laboratory of Molecular Genetics, Animal Center of Biotechnology and Molecular Diagnostics, All-Russian Research Institute for Animal Husbandry named after academy member L.K. Ernst (Russian Federation).
Genetic diversity within the Southern Meat cattle breed was analyzed by using three measures of genetic diversity namely allelic richness and private allele richness (AR and ARp), Wright’s coefficient Fst and AMOVA’s coefficient Фst.
We estimated allelic richness (AR) and private allele richness (ARp) with correction for sample size through rarefaction by using the software HP-Rare (Kalinowski, 2005).
The fixation indices or Wright’s F-statistics have been calculated as indicators of the genetic differentiation among subpopulations. Fis and Fit stand for the correlations between two uniting gametes drawn at random from a subpopulation and from the total population, respectively, whereas Fst is the correlation between two gametes randomly drawn from each subpopulation. The parameters F (Fit), Θ (Fst), and f (Fis), following the formulae of Weir and Cockerham (1984), were calculated by using the FSTAT program (Goudet, 1995).
Analyses of molecular variance (AMOVA) to determine the partition of genetic diversity (Фst) was performed among “Santa Gertrudis” subpopulation and “Zebu” subpopulation with the program GenAIEx ( Peakall, Smouse, 2012).
A frequency-based population Аssignment-test (Paetkau et al., 1995) was carried out and the leave-one-out procedure was used GenAIEx software (Peakall, Smouse, 2012).
Results of this study revealed that the allelic richness (AR) ranged from 11.68 (TGLA53; “Santa Gertrudis” subpopulation) to 4.00 (TGLA126; “Zebu” subpopulation) and the private allele richness (AR) ranged from 4.29 (TGLA227; “Zebu” subpopulation) to 0.00 (TGLA122; “Santa Gertrudis” subpopulation). There were no significant differences in allelic richness and private allele richness in “Santa Gertrudis” subpopulation compared with “Zebu” subpopulation (AR = 8.22 ± 0.51 vs 8.56 ± 0.72 alleles per locus; ARp = 1.25 ± 0.25 vs 1.59 ± 0.34 alleles per locus) (the Wilcoxon signed-rank test: p > 0.05).
We observed significant differences in the distribution of the allele frequencies across “Santa Gertrudis” and “Zebu” subpopulations (with one locus exception – TGLA126). Maybe it is because the number of individuals in a study is too small for an effect subpopulation difference for this locus to be investigated.
Avarage values of Fit and Fis were mostly positive and significantly different from zero for most loci studied (for ETH3, TGLA53 and ETH225 loci with high values). A general significant (p < 0.05) deficit of heterozygotes of 21.0% on average (Fis = 0.210 ± 0.075; 95% CI: 0.083-0.358) existed over all loci. The deficit of heterozygotes in the population as a whole (the Southern Meat cattle breed) was equal to 16.6% (Fit = 0.166 ± 0.082; 95% CI: 0.029-0.326; p < 0.05). According to the results of analysis, significant level of inbreeding takes place in the Southern Meat cattle breed, on which positive and significant Fit and Fis indicators point out.
Subpopulations differentiation estimates showed that Fst varied from -0.020 (TGLA126) to 0.138 (BM1824) with an average of 0.053 ± 0.013 at 12 loci and from 0.030 to 0.077 for 95% CI.
Analysis of Molecular Variance (AMOVA) revealed that 8.9% of the total genetic variation was due to differences between subpopulations “Santa Gertrudis” and “Zebu” within the Southern Meat cattle breed, while the remaining 81.1% corresponded to differences within individuals. The results of AMOVA illustrated statistically significant differences between the Southern Meat breed subpopulation (p<0.001). Thus, features of animal origin have an impact on their genetic structure.
The Assignment-test gave 86% of correct individual assignments to the two subpopulations. Twelve “Santa Gertrudis” subpopulation individuals clustered together with “Zebu” subpopulation ones and fourteen “Zebu” subpopulation individuals clustered together with “Santa Gertrudis” subpopulation ones.
Key words: microsatellite loci, polymorphism, genetic differentiation, the Southern Meat cattle breed.
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