Genetic diversity of Ukrainian local pig breeds based on microsatellite markers

A S Kramarenko,A V Lykhach,S I Lugovoy,S S Kramarenko,V R Kharzinova,V Y Lykhach

doi:10.15421/021826

A S Kramarenko, A V Lykhach + Show 4 more

Open Access

https://doi.org/10.15421/021826

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Abstract

Preserving the current diversity of the living material on Earth is fundamental for the survival of future generations . A study was conducted to investigate the genetic diversity of Ukrainian local pig breeds. A total of 350 pigs representing five local pig breeds from Ukraine (Mirgorod – MIR, Poltava Meat – PM, Ukrainian Meat – UM, Ukrainian White Steppe – UWS and Ukrainian Spotted Steppe – USS) and one commercial breed (Duroc, DUR) were sampled. Twelve microsatellite loci (SW24, S0155, SW72, SW951, S0386, S0355, SW240, SW857, S0101, SW936, SW911 and S0228) were selected and belong to the list of microsatellite markers recommended by ISAG. The results indicate that there exists, in general, a high degree of genetic variability within the five Ukrainian local pig breeds. However, the genetic variability in the MIR and PM breeds was significantly lower (mean Na = 2.92–3.92; Ho = 0.382–0.411; FIS = 0.178–0.184) than in the other three Ukrainian local pig breeds – UM, UWS and USS (mean Na = 5.00–8.42; Ho = 0.549–0.668; FIS = 0.027–0.066). Thirty-four private alleles were identified among the six analyzed genetic groups which were distributed between 11 of the 12 loci. A high number of alleles typical for the breed (private alleles) was observed in Duroc pigs – 9 alleles did not occur in Ukrainian local pig breeds. The HWE test showed that all of the polymorphic loci deviated from HWE (P < 0.05) in at least one population. Loci S0355 (5), S0386 (4) and SW24 (4) presented a higher number of populations in imbalance. The mean FST showed that approximately 77.8% of the genetic variation was within-population and 12.2% was across the populations. The five Ukrainian local breeds were classified into two major groups, according to the phylogenetic tree, which was based on standard genetic distance. Overall, we found that 92.6% of the individual pigs were correctly assigned (324 out of 350) to the respective breed of origin, which is likely a consequence of the well-defined breed structure. Probabilities from the allocation test of individuals for the six pig genetic groups were estimated with Structure Harvester. In cluster 1 the highest grouping probabilities were found for the MIR (0.917) and PM (0.750) breeds. Local breeds UM (0.824) and USS (0.772) were grouped in cluster 2. Cluster 3 was related to the local pig breed USW (0.873). Cluster 4 presented high allocation probabilities for the commercial pig breed Duroc (0.924). The obtained results are important for the future conservation of Ukrainian local pig breeds.

Highlights

Preserving the current diversity of the living material on Earth is fundamental for the survival of future generations
For the UM and UWS pig breeds higher total alleles (101 and 88, respectively) and rare alleles lower than 5% numbers (43 and 41, respectively) were detected across the 12 microsatellite loci analyzed
The six pig populations considered in our study showed substantial genetic diversity, with an overall mean of 6.23 alleles per locus and an average expected heterozygosity of 0.572 for the 12 short tandem repeats (STR) loci

Summary

Introduction

Preserving the current diversity of the living material on Earth is fundamental for the survival of future generations. In the case of animals, in the recent past, more and more effective breeding programmes have been implemented, and have led to an emphasis on a few specialised stocks. Breeds that are less suited to current needs tend to see their numbers decline and to be eventually lost. Conservation of variation, is necessary to meet future agricultural challenges and food needs, as well as to preserve the rich agricultural heritage of the various regions of the world (SanCristobal et al, 2003). In the process of evaluating genetic diversity to develop conservation programmes, it is of interest to assess genetic variation between domestic stocks by using powerful tools such as genetic markers (Berthouly et al, 2008)

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