GENETICS CHARACTERS OF PIGS DIFFERENT BREEDS BY DNA-POLYMORPHISM OF SWINE LEUKOCYTE ANTIGEN
Assessment of swine leukocyte antigen polymorphism (SLA–3) in different breeds pigs of Ukraine was carried out using the method of allele-specific PCR. Features of the allelic fund structure in pig breeds such as Large white, Mirgorod, Ukrainian steppe white, Ukrainian steppe speckled and Vietnamese potbellied pig were studied on four polymorphic sites: SLA–3–0602, SLA–3–0401, SLA–30101 and SLA–3–03cs01.
In the study population of Mirgorod pigs, the absence of SLA–3–03cs01 and SLA–3–0602 alleles was detected. The experimental animals were polymorphic by the SLA–3–0101 and SLA–3–0401 marker systems with the above alleles frequency of 18.2 and 81.8%, respectively. By the polymorphic site SLA–3–0401 pigs of Large white, Ukrainian steppe white and Vietnamese potbellied breeds were monomorphic, whereas the representatives of the aboriginal Ukrainian steppe speckled breed the frequency of this allele did not exceed 40%. The genetic structure of Vietnamese potbellied pigs significantly differed from the characteristics obtained for the local Ukrainian breeds by four SLA sites. The most statistically significant differences are recorded for allele frequencies SLA–3–0602 and SLA–3–0101. The SLA–3–0602 allele was absent in Vietnamese potbellied breed with its 100% presence in Large white pigs. In contrast, the SLA–3–0101 allele was found in all Vietnamese pigs and was absent in a sample of the Large white pigs (p < 0.05).
The distribution pattern of alleles in all of the samples selected for the study of polymorphisms in the pig locus of leukocyte antigen (SLA–3) showed a high genetic homogeneity of the Large white animals sample. The SLA–3–0101 and SLA–3–03cs01 alleles carriers were not detected, and by SLA–3–0602 and SLA–3–0401, 100% of the specimens had the respective alleles in their genotype. High values of the genetic homogeneity in these animals are confirmed by calculation of the total heterozygosity index, which was 0.136. The maximum genetic and, accordingly, genealogical relationship (according to the summary zootechnical account) were recorded in Vietnamese potbellied pigs for which the index of intragroup similarity was 0.960, and the calculated heterozygosity was the least among the breeds under study – 0.024.
It is expedient to consider the results of the population-genetic characteristics analysis of the autochthonous pig breeds – the Ukrainian steppe speckled and Mirgorod when further planning selection and breeding work with them. The minimum value of intragroup similarity was found in the group of the Ukrainian steppe speckled swine – 0.156, as compared to the values of this index in pigs of other breeds under study (p < 0.05), and the theoretically calculated heterozygosity for these animals sample was 0.823.
The integral assessment of breeds genetic differentiation by SLA–3 polymorphisms was obtained by performing a cluster analysis based on the calculated values of genetic distances between the breeds. The most genetically distant ones were the Mirgorod and Ukrainian steppe speckled breeds, and the value of the genetic distance between them was 0.776. In general, Ukrainian steppe speckled was characterized by the most unique distribution of SLA–3 alleles compared to other breeds under study, which has influenced the configuration of the obtained dendrogram by the UPGMA method.
By means of molecular genetic, population and cluster analysis, the singularity and specificity of the Ukrainian steppe white and speckled pigs are shown. The genetic characteristics of the Mirgorod breed obtained by us can be useful in the process of recreating these animals using biotechnological methods, since the only gene pool herd of these pigs was eliminated due to the African plague infection.
The generative material from the Mirgorod breed pigs has only been preserved in the Bank of Genetic Resources of the M.V.Zubets Institute of Animal Breeding and Genetics, NAAS. Determining genetic characteristics of the SLA allelic fund breed specificity of the local pig breeds reveals the prospects for using this information as an additional tool for their genetic certification, in special programs for conservation and restoration of their gene pool.
Convention on biological diversity. Rio de Janeiro, 5 June 1992 .– 214p. (https://treaties.un.org/doc/Treaties/1992/06/19920605%2008–44%20PM/Ch_XXVII_08p.pdf). (in English).
Pro koncepciyu zberezhennya biologichnogo riznomanittya Ukrayiny. Postanova Kabinetu ministriv Ukrayiny vid 12.05.1997., № 439, iz zminamy i dopovnennyamy vid 12.10.2011., № 1048 – About the concept of conservation of biodiversity in Ukraine. Resolution of the Cabinet of Ministers of Ukraine dated May 12, 1997, No. 439, as amended and supplemented dated 12.10.2011, No. 1048. (http://search.ligazakon.ua/l_doc2.nsf/link1/KP970439.htm) (in Ukrainian).
Shuhua, F., W. Yanan, W. Song, W. Zhenbao, J. Bo, L. Yanjie, L. Ruiying, Z. Wenzhong, Z. Nianzhi, X. Chun. 2016. Structural and Biochemical Analyses of Swine Major Histocompatibility Complex Class I Complexes and Prediction of the Epitope Map of Important Influenza A Virus Strains –Journal of virology. 90(15):6625 – 6641(in English).
Soe, O., Y. Ohba, N. Imaeda, N. Nishii, M. Takasu, G. Yoshioka, H. Kawata, A. Shigenari, H. Uenishi, H. Inoko, A. Ando, H. Kitagawa. 2008. Assignment of the SLA alleles and reproductive potential of selective breeding Duroc pig lines – Xenotransplantation.15(6):390-397(in English).
Lunney, J. K., C. Ho, M. Wysocki, D. Smith. 2009. Molecular genetics of the swine major histocompatibility complex, the SLA complex – Dev. Comp. Immunol. 33:362–374 (in English).
Smith, D. M., J. K. Lunney, C. S. Ho, G. W. Martens, A. Ando, J. H. Lee, L. Schook, C. Renard, P. Chardon. 2005. Nomenclature for factors of the swine leukocyte antigen class II system – Tissue Antigens. 66:623–639 (in English).
Ellis, S. A, R. E. Bontrop, D. F. Antczak, K. Ballingall, C. J. Davies, J. Kaufman, L. J. Kennedy, J. Robinson, D. M. Smith, M. J. Stear, R. J. Stet, M. J. Waller, L. Walter, S. G. Marsh. 2006. ISAG/IUIS–VIC Comparative MHC Nomenclature Committee report – Immunogenetics. 57:953–958 (in English).
Rudoman, G. S., V. M. Balacz`kyj, V. Yu. Nor. 2016. Analiz polimorfizmu gena MUC4, asocijovanogo iz stijkistyu svynej vitchyznyanoyi i zarubizhnoyi selekciyi do kolibakteriozu – Analysis of the polymorphism of the gene MUC4 associated with the resistance of pigs of domestic and foreign breeding to colibacillosis. Rozvedennya i genetyka tvaryn. Mizhvidomchyj naukovyj zbirnyk – Animal breeding and genetics. Interdepartmental scientific collection. 55:200–205 (in Ukrainian).
Vykoukalová, Z., A. Knoll, J. Dvořák. 2006. New SNPs in the IGF2 gene and backfat thickness and lean meat content in Large White pigs – J. Anim. Breed. Genet. 123:204–207 (in English).
Balacz`kyj, V. M., K. F. Pochernyaev. 2005. Vykorystannya DNK–typuvannya v praktyci selekcijno–pleminnoyi roboty – The use of DNA is typified in the practice of breeding and breeding work. Visnyk Poltavs`koyi derzhavnoyi agrarnoyi akademiyi – Newsletter of the Poltava State Agrarian Academy. 3:25–26 (in Ukrainian).
Lyads`kyj, I. K, K. F. Pochernyaev. 2009. Polimorfizm gena hmga1 v riznyx populyaciyax svynej velykoyi biloyi porody Ukrayiny – Polymorphism of the hmga1 gene in different populations of large white pigs in Ukraine. Naukovyj visnyk Nacional`nogo universytetu bioresursiv i pryrodokorystuvannya Ukrayiny – Scientific herald of the National University of Bioresources and Nature Management of Ukraine. 138:269–272 (in Ukrainian).
Mrode, R., J. Ojango, A. Okeyo, J. Mwacharo. 2018. Genomic Selection and Use of Molecular Tools in Breeding Programs for Indigenous and Crossbred Cattle in Developing Countries: Current Status and Future Prospects – Front Genet. 9:694-705 (in English).
Piyasatian, N., R. L. Fernando, J. C. M. Dekkers. 2012. QTL detection and marker–assisted composite line development – Livestock Sci. 143:233–241 (in English).
Walsh, P. S., D. A. Metzger, R. Higuchi. 1991. Chelex 100 as a Medium for Extraction of DNA for PCR–Based Typing from Forensic Material – BioTechniques. 10:506–509 (in English).
Ho, C. S., E. S. Rochelle, G. W. Martens, L. B. Schook, D. M. Smith. 2006. Characterization of swine leukocyte antigen polymorphism by sequence–based and PCR–SSP methods in Meishan pigs – Immunogenetics. 58:873–882 (in English).
Maniatis, T., E. Frich, and D. Sembruk. 1984. Molekulyarnoe klonirovanie – Molecular cloning. Moscow, Mir, 479 (in Russian).
Peacall, R., P. E. Smouse. 2006. GENALEX 6 : genetic analisys in Excel Population genetic software and research – Molecula Ecology Notes. 6:288–295 (in English).
Rogstad, S., S. Pelican. 1996. GELSTATS : a computer program for population genetics analyses using VNTR multilocus probe data – Bio Techniques. 21:187–196 (in English).
Kalendar', R. N. 1994. Komp'yuternaya prohramma dlya postroenyya evolyutsyonnykh derevev na osnove elektroforehramm DNK i belkov – Computer program for building evolutionary trees on the sound electrophoregram of DNA and proteins. Materyaly konferentsyy «Molekulyarno–henetycheskye markery v selektsii rastenyy» – Materials of the conference "Molecular Genetic Markers and Plant Selection". 1:25–26 (in Russian).
Tamura, K., J. Dudley, M. Nei, S. Kumar. 2004. MEGA 4 : Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 – Molecular Biology and Evolution. 24:1596–1599 (in English).
Plokhynskyy, N. A. 1969. Rukovodstvo po byometryy dlya zootekhnykov – Biometrics guide for livestock breeders. Moscow, 255 (in Russian).
Lenormand, T. 2002. Gene flow and the limits to natural selection – Trends Ecol. Evol. 17:183–189 (in English).
Hu, X, F. Yeh, 2014. Assessing postzygotic isolation using zygotic disequilibria in natural hybrid zones – PLoS ONE. 9:1–15 (in English).
Pochernyayev, K. F. 2012. Ocinka genety`chnoyi riznomanitnosti lokal`ny`x porid svy`nej Ukrayiny` za polimorfizmom mitoxondrial`noyi DNK – Svy`narstvo. 60:71–76 (in Ukraine).
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