Genetic Polymorphism of Microsatellite Loci and Their Association with Reproductive Traits in Ukrainian Meat Breed Pigs

Genetic diversity of the Central European wild boar (Sus scrofa scrofa) population and domestic pig (Sus scrofa domesticus) breeds based on a microsatellite DNA locus

The results of studies of the genetic structure of the Central European wild boar (Sus scrofa scrofa) population and four breeds of domestic pigs (Duroc, Yorkshire, Large White and Landrace) bred in the Central Black Earth region of Russia are presented in this work. Based on 12 microsatellite loci, a significant ( p <0.05) decrease in the level of genetic variability in bred breeds was shown. The expected heterozygosity and Shannon index were as follows: in the wild boar, Ho = 0.763 ± 0.026, I = 1.717 ± 0.091; in the Duroc breed, Ho = 0.569 ± 0.068, I = 1.191 ± 0.157; in the Landrace, Ho = 0.618 ± 0.062, I = 1.201 ± 0.147; in the Large White, Ho = 0.680 ± 0.029, I = 1.362 ± 0.074; and in the Yorkshire, Ho = 0.642 ± 0.065, I = 1.287 ± 0.156. The results of checking genotypic Hardy–Weinberg equilibrium based on the G-test of maximum likelihood demonstrated that the overwhelming majority of loci in the wild boar population were in the state of said equilibrium. By contrast, in pig breed populations, some loci demonstrated a significant deviation from the indicated equilibrium. In addition, the Yorkshire, Large White, and Landrace populations had loci, for which the hypothesis of neutrality was reliably rejected based on the results of the Ewens–Watterson test. The revealed private alleles, characteristic of the wild boar and breeds, can later be used to identify them. The ordination of the centroids of different herds in the space of the first two principal coordinates based on the matrix of pairwise estimates of Nei’s genetic distances showed that the most distant populations are the Duroc and Boar breeds, and the most genetically close are the Yorkshire and Landrace breeds. The closest to the wild boar population was the Large White breed. The assessment of the effective size, carried out using the method based on the linkage disequilibrium and the molecular coancestry method, showed that in all studied groups, including the wild boar population, the effective size was less than 100 individuals. The low effective size of the wild boar population (Ne = 21.8, Neb = 4.0) is probably caused by the death and shooting of animals due to Pestis africana suum.

Intra- and interbreed genetic heterogeneity and divergence in four commercial pig breeds based on microsatellite markers

In recent years, there has been an increasing amount of attention paid to the genetic health of domesticated animals and its relationship with the level of inbreeding and genetic diversity. At the same time, insufficient attention is still paid to the study of intrabreed genetic diversity and intrabreed stratification. The main goal of our work was to analyze the intra- and interbreed genetic diversity of commercial pig breeds on the basis of DNA microsatellite (MS-DNA) polymorphism. In total, the work used data for 3,308 pigs, which represented 11 herds. The animals belonged to four commercial pig breeds – Duroc (DR), Yorkshire (YR), Landrace (LN) and Large White (LW). 12 microsatellite loci recommended by ISAG-FAO and arranged in one multiplex panel (S0101, S0155, S0228, S0355, S0386, SW24, SW240, SW72, SW857, SW911, SW936, SW951) were used as DNA markers. When analyzing the intra- and interbreed variability of 11 herds, we found that all studied breeds significantly differed in terms of the proportion of both rare and the most common alleles. At the same time, the noted differences were determined, first of all, by the variability between individual herds within their breed. The location of herd centroids is random and is not consistent with their breed affiliation at all. When individuals belonging to the same breed are combined, the centroids of pig breeds in the space of first two axes from a Principal Coordinate Analysis form two clusters. The first one contains the only red pig breed (DR) used in the analysis, while the second one contains white pig breeds. In six pig herds the Ne estimates were below 50 inds., in two herds they were in the range of 50–100 inds., and finally in three herds the Ne estimates exceeded 100 inds. The analysis of the genetic variability of pigs of four commercial breeds showed that the high level of interbreed differences is caused, first of all, by the high variability among pig herds within each studied breed. Such intrabreed stratification can be formed due to the manifestation of many causes: different genetic basis of the founders of intrabreed genealogical groups, geographical isolation, different directions of selection within individual herds, exchange of animals between separate herds, the use of inbreeding in the practice of selection together with isolation, etc. Important consequences of intrabreed stratification are an increase in the level of interherd diversity (which is not lower than the level of interbreed diversity) against the background of a decrease in variability within individual herds, as well as a significant deficit of heterozygotes and an increase in the role of negative genetic and demographic processes. Thus, the existence of genetic heterogeneity within commercial pig breeds should be considered as an essential element in the history of their formation and breeding.