Genetic diversity of modern lines of hybrid pigs based on variations in mitochondrial DNA sequence

Ye. O. Budakva¹, K. F. Pochernyaev¹, S. M. Korinnyi², M. G. Povod³

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¹Institute of Pig Breeding and Agricultural Production NAAS,
1 Shvedska Mohyla str., Poltava, 36013, Ukraine

²Poltava State Agrarian University,
1/3 Skovorody str., Poltava, 36003, Ukraine

³Sumy National Agrarian University,
160 Gerasima Kondratieva str., Sumy, 40021, Ukraine

In the study, we evaluated the genetic specificity of haplotypes in the population of hybrid gilts (Large White × Landrace), (Landrace × Large White) from the SPE “Globinsky Pig Complex” LLC and breeding sows of the Large White breed from the SE “DG named after January 9^th” using polymorphism of the lengths of the restricted fragments of mtDNA. The purpose of the study was to determine if the process of creating specialized parent lines (of modern cross-border breeds) reduces haplotype diversity. As a genetic material, bristles from sows of the Large White breed (n=7) were used and epithelial tissue of pigs (Large White × Landrace), (Landrace × Large White) — (n=37). DNA release from bristle samples was carried out using ion exchange resin Chelex-100. For the study of the D-loop of the mitochondrial genome of hybrid pigs (n=37) from the epithelial tissue of the auricle, a set of DNA-sorb-B nucleic acid extraction kit from “InterLabService-Ukraine” LLC was used. The samples of epithelial tissue of pigs’ ears were treated with fire from fuel tablet. For the analysis of the mitochondrial genome, the method of polymorphism of the lengths of restricted fragments was used, amplified with PCR. Genotyping of DNA samples of experimental pigs according to mitochondrial markers was carried out with the involvement of the polysite method in accordance with the methodological recommendations of K. F. Pochernyaev and M. D. Berezovsky (2014). The use of maternal inheritance type markers (mtDNA) allowed to identify 2 maternal lines with specific haplotypes, which participated in the creation of hybrid pigs and the formation of their haplogroup. The genetic diversity of mtDNA subspecies of wild and domesticated pigs is limited by the existing lines. Therefore, one haplotype of the mitochondrial genome does not indicate a specific breed, since, several breeds have the same haplotype mtDNA — A, G, C, N, and O. The concentration of haplotype A in tribal sows of Large White breed with a frequency (16%). In the hybrid gilts (Large White × Landrace), (Landrace × Large White) the concentration of detected haplotypes is: C (n=9) — Landrace, Hampshire, Wales, wild pig (20.5%); G — (n=5) Wales, wild pig (11.4%); O (n=5) — Landrace, wild pig (11.4%); N (n=11) — Large White, Berkshire, Asian wild pig (25%); D 9%, K 6.8% (n=7) — unknown among the breeds of domestic pig. We assume that pigs of a Large White breed with haplotype A and hybrid pigs (Large White × Landrace), (Landrace × Large White) with haplotype G, O, in particular D, K contain aboriginal genetic resources. However, in the middle of the XX century, subspecies of wild and domesticated pig breeds became less population-like due to decrease in the area of cultivation and increased pressure from foreign breeds with high growth rates and breeding grounds. Thus, there is a risk of extinction — existing haplotypes and those which have not yet been identified among domesticated pigs (D, K). This suggests that the study should focus on classifying and identifying the phylogenetic origin of pigs and the creation of a molecular genetic bank of producer boars for environmental activities. The domestication process puts strong selective pressure on Sus scrofa species through genetic processes such as inbreeding, genetic drift, natural and artificial selection according to the desired signs. Over the past 9–10,000 years, human intervention has led to domesticated species that are morphologically, behaviorally, and genetically different from their ancestors’ relatives. We believe that the “hybrid” subspecies of wild pigs with some morphological features of a domesticated pig had a higher proportion of the full-genomic ancestors of a domestic pig compared to the morphologically pure subspecies of wild pigs. Animals with haplotypes D, K are the result of hybridization with European boars. Representatives of haplotypes A (Large White, European-type Duroc, Mangalica); G (Wales, wild pig) — Italy; C (Landrace, Wales, Hampshire, wild pig) — Ukraine, Poland, France; O (landrace, wild pig) — Sweden, grouped into the European cluster of “mt-E” haplogroup. Pigs with the haplotype N — Large White (Asian type), Berkshire, a wild pig belongs to the Asian cluster of “mt-A” haplogroup. Over time, this led to almost complete disappearance of primary Middle Eastern ancestors in the nuclear genomes of European domesticated pigs. Phylogenetic reconstruction of mitochondrial genome data from hybrid pigs reflects a clear geographical division of mtDNA data — Eastern Europe and Asia. In particular, the subspecies of European and Asian wild pigs is the ancestral foundation on the maternal line, which preceded domestication and breeding pigs by hybridization. European and Asian haplotypes of wild pigs have shown that wild pigs from regions such as Italy, Poland, France, Scandinavia, and Ukraine were also either domesticated or at least initially included in domesticated pigs. The results of the study of the S. s. domestica mitochondrial genome showed an intra-breed genetic diversity of hybrid gilts. This is due to the selection strategy of international genetic centers, where, despite the consolidation of the genetic structure in the inside of the center, significant general genetic diversity of the breed is ensured. In addition, the above results indicate a connection between the frequency distribution of mtDNA haplotypes and adaptation to different climate conditions. As a whole, the presented results are an incentive to continue research on the study of the mitochondrial genome of modern lines of hybrid pigs. Carriers of haplotype C, O, G, and N are the basis of maternal breeding and improvement of the lines of hybrid pigs of the XXI century. It is necessary to take into account the fact that the cleanest mother nuclei (Wild pig, Great Yorkshire, Landrace) are really clean foundation for use in hybridization schemes, in the crossing over, in the formation and development of modern hybrid lines of pigs. Despite this, the diversity of the mitochondrial genome in the population of transboundary breeds persists.

Key words: origin, mtDNA, D-loop, haplotype, haplogroup, clade, cluster, breeding sows of the Large White, hybrid gilts (Large White × Landrace), (Landrace × Large White), PCR-RFLP analysis

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