Genotyping of Ukrainian Large White pigs by intronic polymorphism in HMGA1 gene

V. Teniaiev¹, A. Saienko¹, M. Peka^1,2, O. Tsereniuk¹
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¹Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla str, Poltava, 36013, Ukraine
²V. N. Karazin Kharkiv National University, 4 Svobody sq., Kharkiv, 61022, Ukraine

The HMGA1 (High Mobility Group AT-hook 1) gene is considered a candidate locus for growth- and fatness-related traits in pigs due to its involvement in transcriptional regulation and energy metabolism and its localization within a quantitative trait locus (QTL) region on Sus scrofa chromosome 7. The aim of this study was to characterize a previously described intronic polymorphism of the HMGA1 gene in the population of Ukrainian Large White pig breed and to evaluate its population genetic parameters for potential application in marker-assisted selection. An in silico analysis based on the Sscrofa11.1 reference genome was performed to define the genomic localization of the amplified fragment, describe the polymorphism according to Ensembl nomenclature, and identify its rsID in the European Variation Archive. Genotyping of 30 Ukrainian Large White pigs was carried out using the polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) method with the restriction endonuclease NaeI. The polymorphic site was localized at position 7:30,326,531 and identified as rs80981303 (c.220-170C>T). Population analysis revealed genotype frequencies of 0.10 (CC), 0.40 (CT), and 0.50 (TT), with allele frequencies of 0.30 for C and 0.70 for T. The distribution of genotypes did not deviate from Hardy–Weinberg equilibrium (χ₂ = 0.068, P=0.794). The polymorphic information content value (PIC = 0.3318) indicated that the locus is sufficiently informative. The obtained results confirm the polymorphic nature of the HMGA1 gene in the Ukrainian Large White pig breed and support the potential utility of rs80981303 as a genetic marker. Further association studies with productive traits could substantiate its practical application in pig breeding programs.

Key words: HMGA1 gene; pig; Ukrainian Large White breed; intronic polymorphism; PCR–RFLP; population genetics; marker-assisted selection