Genetic characteristics of the last autochthonous herd of Myrhorod pig breed based on mitochondrial DNA analysis

K. F. Pochernyaev; S. M. Korinnyi; A. A. Getya; V. G. Tsybenko; P. A. Vashchenko

doi:10.15407/agrisp13.02.003

K. F. Pochernyaev The Institute of Pig Breeding and Agroindustrial production of the National Academy of Agrarian Science of Ukraine, 1, Shvedska Mohyla Str., Poltava, 36013, Ukraine https://orcid.org/0000-0001-9973-6429
S. M. Korinnyi The Institute of Pig Breeding and Agroindustrial production of the National Academy of Agrarian Science of Ukraine, 1, Shvedska Mohyla Str., Poltava, 36013, Ukraine https://orcid.org/0000-0002-1649-3079
A. A. Getya The National University of Life and Environmental Sciences of Ukraine of the Ministry of Education and Science of Ukraine, 15, Heroiv Oborony Str., Kyiv, 03041, Ukraine https://orcid.org/0000-0002-4747-9261
V. G. Tsybenko The Institute of Pig Breeding and Agroindustrial production of the National Academy of Agrarian Science of Ukraine, 1, Shvedska Mohyla Str., Poltava, 36013, Ukraine https://orcid.org/0000-0003-3932-8508
P. A. Vashchenko The Poltava State Agrarian University of the Ministry of Education and Science of Ukraine, 1/3, Hryhoriia Skovorody Str., Poltava, 36003, Ukraine https://orcid.org/0000-0002-9287-819X

DOI: https://doi.org/10.15407/agrisp13.02.003

Keywords: pigs, mitochondrial haplotypes, haplotype diversity, Myrhorod breed, local breed, breed restoration, genetic characterization

Abstract

Aim. To identify mitochondrial haplotypes in the last autochthonous herd of Myrhorod pigs, to assess haplotype diversity, evolutionary divergence, and the evolutionary history of the breed in order to adjust the strategies for its restoration. Methods. The biological material was collected in 2011 and 2017 (n = 25) and (n = 84), respectively. Mitochondrial haplotypes of pigs were determined using a multisite PCR-RFLP assay. The population and statistical analyses were performed using GENALEX 6 software. The evolutionary analysis was conducted in MEGA12. Results. Over two generations in the last autochthonous herd of the Myrhorod breed, which was raised under intensive conditions, the total number of mitochondrial haplotypes decreased from 4 to 3. The disappearance of the genealogical family with haplotype l does not eliminate the m.15714C allelic variant from the population, as it persists in sows with haplotypes A and C. The loss of the maternal line with haplotype l did not reduce the level of haplotype diversity in the Myrhorod breed population; on the contrary, it increased from (h = 0.077) in 2011 to (h = 0.153) in 2017. An analysis of the number of base substitutions per site between sequences revealed evolutionary divergence among the sequences defining the haplotypes. The lowest evolutionary divergence (number of substitutions per site, d = 0.058) was observed between the sequences defining haplotypes A and C. The greatest divergence (d = 0.298) was observed between haplotypes O, C, and haplotype J1, which was used as the outgroup. An assessment of the divergence among the haplotypes of Myrhorod pigs and their evolutionary history demonstrated their affiliation with European domestication events. The haplotype of the Asian wild boar (AF136564) and the Meishan breed (AF136567), used as an outgroup in the phylogenetic analysis, formed a separate branch on the optimal tree with a total branch length (d = 0.359) clearly demonstrating the differentiation between European and Asian domestication events. Three of the six SNPs studied — m.15616T>C, m.15714T>C, and m.15758T>C — influenced the level of haplotype diversity in the Myrhorod breed population. Among the polymorphic allelic variants of mitochondrial DNA, SNP m.15714C (q = 0.960) was the most frequent in 2011, and m.15758C (q = 0.917) — in 2017. A significant deviation was observed between the expected variance and the observed variance (Vo2011 = 0.157, Ve2017 = 0.487) and (Vo2017 = 0.161, Ve2017 = 0.509). Conclusions. 1. An assessment of the evolutionary divergence among the haplotypes of Myrhorod pigs and their evolutionary history demonstrates their connection to European domestication events. The presence of four mitochondrial haplotypes in this local breed suggests the influence of introgression from domesticated pigs or breeds that evolved in different geographic regions of Europe. 2. While developing the Myrhorod pig breed, boars of the Berkshire, Middle White, Large White, Large Black, and Tamworth breeds were used, none of which could pass on Asian mitochondrial haplotypes. 3. Over two generations in the last autochthonous herd of the Myrhorod breed, which was kept in conditions of competition with modern transboundary breeds, the total number of mitochondrial haplotypes decreased from 4 to 3. Paradoxically, the level of haplotype diversity in the Myrhorod breed population increased after the loss of the maternal line with haplotype l. In light of this, preserving maternal lines with different haplotypes is of greater practical importance for the genetic characterization and management of the local breed than haplotype diversity. 4. To preserve and restore the Myrhorod pig breed, given the current situation, the most effective approach may be one based not on searching for the original local genetic material, but rather on identifying and utilizing the marker haplotypes we have identified that have been introgressed into the Large White, Poltava Meat, and Red White-Belted breeds.

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