Establishing the breed composition of pigs using KASP technology
https://doi.org/10.29235/1029-8940-2025-70-1-69-79
Abstract
A high differentiating potential of seven polymorphic variants has been identified to distinguish between Yorkshire, Belarusian Large White and Belarusian Meat pig breeds bred in Belarus. For the Yorkshire pig breed, a model is proposed including three single nucleotide polymorphisms – Chr.6:g.121005974A>G, Chr.17:g.15827832G>T, Chr.10:g.30081932A>G; for the Belarusian Large White pig breed – Chr.6:g.121005974A>G, Chr.3:g.118879246C>G, Chr.7:g.52269732A>G; for the Belarusian Meat pig breed – Chr.8:g.47482649G>T, Chr.9:g.48882095A>G, Chr.10:g.30081932A>G. The models demonstrate high accuracy, specificity, and sensitivity values. The approach to differentiating pig breeds is based on the technology of сompetitive allele-specific PCR.
About the Authors
V. N. Kipen′Belarus
Vуacheslav N. Kipen′ – Ph. D. (Biol.), Associate Professor, Leading Researcher
27, Academicheskaya Str., 220072, Minsk
E. V. Snytkov
Belarus
Evgenij V. Snytkov – Researcher
27, Academicheskaya Str., 220072, Minsk
M. E. Mikhailova
Belarus
Mariya E. Mikhailova – Ph. D. (Biol.), Associate Professor, Head of Laboratory
27, Academicheskaya Str., 220072, Minsk
References
1. Dekkers J. C. M. Marker-assisted selection for commercial crossbred performance. Journal of Animal Science, 2007, vol. 85, no. 9, pp. 2104–2114. https://doi.org/10.2527/jas.2006-683
2. Fontanesi L., Schiavo G., Galimberti G., Bovo S., Russo V., Gallo M., Buttazzoni L. A genome-wide association study for a proxy of intermuscular fat level in the Italian Large White breed identifies genomic regions affecting an important quality parameter for dry-cured hams. Animal genetics, 2017, vol. 48, no. 4, pp. 459–465. https://doi.org/10.1111/age.12542
3. PorcineSNP60 DNA Analysis Kit v3. Available at: https://www.illumina.com/products/by-type/microarray-kits/porcine-snp60.html (accessed 30.06.2024).
4. Ramos A. M., Megens H. J., Crooijmans R. P. M. A., Schook L. B., Groenen M. A. M. Identification of high utility SNPs for population assignment and traceability purposes in the pig using high-throughput sequencing. Animal genetics, 2011, vol. 42, no. 6, pp. 613–620. https://doi.org/10.1111/j.1365-2052.2011.02198.x
5. Fontanesi L., Schiavo G., Gallo M., Baiocco C., Galimberti G., Bovo S., Russo V., Buttazzoni L. Genome-wide association study for ham weight loss at first salting in Italian Large White pigs: towards the genetic dissection of a key trait for dry-cured ham production. Animal Genetics, 2017, vol. 48, no. 1, pp. 103–107. https://doi.org/10.1111/age.12491
6. Zanella R., Peixoto J. O., Cardoso F. F., Cardoso L. L., Biegelmeyer P., Cantão M. E., Otaviano A., Freitas M. S., Caetano A. R., Ledur M. C. Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data. Genetics Selection Evolution, 2016, vol. 48, art. 24. https://doi.org/10.1186/s12711-016-0203-3
7. Davoli R., Luise D., Mingazzini V., Zambonelli P., Braglia S., Serra A., Russo V. Genome-wide study on intramuscular fat in Italian Large White pig breed using the PorcineSNP60 BeadChip. Journal of Animal Breeding and Genetics, 2016, vol. 133, no. 4, pp. 277–282. https://doi.org/10.1111/jbg.12189
8. Bergfelder-Drüing S., Grosse-Brinkhaus C., Lind B., Erbe M., Schellander K., Simianer H., Tholen E. A genome-wide association study in large white and landrace pig populations for number piglets born alive. PLoS One, 2015, vol. 10, no. 3, p. e0117468. https://doi.org/10.1371/journal.pone.0117468
9. Fontanesi L., Schiavo G., Galimberti G., Calò D. G., Russo V. A genomewide association study for average daily gain in Italian Large White pigs. Journal of Animal Science, 2014, vol. 92, no. 4, pp. 1385–1394. https://doi.org/10.2527/jas.2013-7059
10. Becker D., Wimmers K., Luther H., Hofer A., Leeb T. A genome-wide association study to detect QTL for commercially important traits in Swiss Large White boars. PLoS One, 2013, vol. 8, no. 2, p. e55951. https://doi.org/10.1371/journal.pone.0055951
11. Wilkinson S., Archibald A. L., Haley C. S., Megens H.-J., Crooijmans R., Groenen M., Wiener P., Ogden R. Development of a genetic tool for product regulation in the diverse British pig breed market. BMC Genomics, 2012, vol. 13, art. 580. https://doi.org/10.1186/1471-2164-13-580
12. Biffani S., Botti S., Bishop S. C., Stella A., Giuffra E. Using SNP array data to test for host genetic and breed effects on Porcine Reproductive and Respiratory Syndrome Viremia. BMC Proceedings, 2011, vol. 5, suppl. 4, art. S28. https://doi.org/10.1186/1753-6561-5-s4-s28
13. Huang Y., Bates R. O., Ernst C. W., Fix J. S., Steibel J. P. Estimation of U.S. Yorkshire breed composition using genomic data. Journal of Animal Science, 2014, vol. 92, no. 4, pp. 1395–1404. https://doi.org/10.2527/jas.2013-6907
14. Uimari P., Sironen A., Sevón-Aimonen M. L. Whole-genome SNP association analysis of reproduction traits in the Finnish Landrace pig breed. Genetics Selection Evolution, 2011, vol. 43, no. 1, art. 42. https://doi.org/10.1186/1297-9686-43-42
15. He Y., Li X., Zhang F., Su Y., Hou L., Chen H., Zhang Z., Huang L. Multi-breed genome-wide association study reveals novel loci associated with the weight of internal organs. Genetics Selection Evolution, 2015, vol. 47, art. 87. https://doi.org/10.1186/s12711-015-0168-7
16. Stratz P., Wimmers K., Meuwissen T. H. E., Bennewitz J. Investigations on the pattern of linkage disequilibrium and selection signatures in the genomes of German Piétrain pigs. Journal of Animal Breeding and Genetics, 2014, vol. 131, no. 6, pp. 473–482. https://doi.org/10.1111/jbg.12107
17. Roberts K. S., Lamberson W. R. Relationships among and variation within rare breeds of swine. Journal of Animal Science, 2015, vol. 93, no. 8, pp. 3810–3813. https://doi.org/10.2527/jas.2015-9001
18. Kipen’ V. N., Ryabtseva A. O., Kotova S. A., Zhurina N. V., Gandzha A. I., Tsybovskii I. S. Polymorphism analysis of MC1R and NR6A1 genes to evaluate the level of introgression of domestic swine (Sus scrofa domesticus) genes in wild boar (Sus scrofa scrofa) population. Molekulyarnaya i prikladnaya genetika [Molecular and applied genetics], 2019, vol. 26, pp. 83–95 (in Russian).
19. Kipen’ V. N., Snytkov E. V. GENIS – methodological approach for in silico genotyping (validation on Sus scrofa sequencing results). Matematicheskaya biologiya i bioinformatika = Mathematical Biology and Bioinformatics, 2024, vol. 19, no. 1, pp. 36–51 (in Russian).
20. Sequence Read Archive (SRA). Available at: https://www.ncbi.nlm.nih.gov/sra (accessed 20.06.2024).
21. Ritchie M. D., Hahn L. W., Roodi N., Bailey L. R., Dupont W. D., Parl F. F., Moore J. H. Multifactor–dimensionality reduction reveals high–order interactions among estrogen–metabolism genes in sporadic breast cancer. American Journal of Human Genetics, 2001, vol. 69, no. 1, pp. 138–147. https://doi.org/10.1086/321276
22. Kipen’ V. N., Ivanova E. I., Snytkov E. V., Verchuk A. N. Analysis of HEPH Gene Polymorphism on the X Chromosome for Identification of Wild Boar and Domestic Pig. Russian Journal of Genetics, 2020, vol. 56, no. 9, pp. 1099–1108. https://doi.org/10.1134/s1022795420080062
23. Building Applied Genomic Capacity for Animal Industries. Available at: https://www.animalgenome.org (accessed 20.06.2024).
24. Kipen’ V. N., Snytkov E. V., Mikhailova M. E., Sheiko R. I. Breed differentiation of domestic pigs using SNP – extended bioinformatical analysis. Doklady Natsional’noi akademii nauk Belarusi = Reports of the National Academy of Sciences of Belarus, 2022, vol. 66, no. 3, рр. 301–309 (in Russian).
25. Kipen’ V. N., Snytkov E. V., Mikhailova M. E., Sheiko R. I. Differentiation of pig breeds using KASP technology – test-system for duroc. Molekulyarnaya i prikladnaya genetika [Molecular and applied genetics], 2024, vol. 36, pp. 114–122 (in Russian).
26. Kipen’ V. N., Mikhailova M. E., Snytkov E. V., Sheiko R. I. Analysis of KDM3A and DBX2 gene polymorphism for differentiation of Sus scrofa domesticus duroc pigs. Doklady Natsional’noi akademii nauk Belarusi = Reports of the National Academy of Sciences of Belarus, 2023, vol. 67, no. 2, pp. 119–125 (in Russian).
27. Kipen’ V. N. Modelirovanie paneli porodospecifichnyh SNP-markerov dlya opredeleniya chistoporodnosti domashnih svinej porody dyurok. Biotekhnologiya: dostizheniya i perspektivy razvitiya: sbornik materialov II mezhdunarodnoi nauchno-prakticheskoi konferentsii, Pinsk, 7–8 dekabrya 2017 goda [Biotechnology: achievements and development prospects: collection of materials of the II international scientific and practical conference, Pinsk, December 7–8, 2017]. Pinsk, 2017, pp. 63–65 (in Russian).
28. Kotova S. A., Kipen’ V. N. Modelirovanie paneli porodospecifichnyh SNP-markerov dlya genotipirovaniya domashnih svinej porody landras s ispol’zovaniem MDR-analiza. Sovremennye dostizheniya i problemy biotekhnologii sel’skokhozyaistvennykh zhivotnykh BioTekhZh – 2016: materialy 11-i Vserossiiskoi konferentsii-shkoly uchenykh s mezhdunarodnym uchastiem, poselok Dubrovitsy, 13–16 dekabrya 2016 goda [Modern achievements and problems of biotechnology of agricultural animals BioTechZh – 2016: materials of the 11th All-Russian conference-school of scientists with international participation, Dubrovitsy settlement, December 13–16, 2016]. Dubrovitsy, 2016, pp. 86–91 (in Russian).
29. Snytkov E. V., Kipen’ V. N., Mikhailova M. E., Belyak O. A, Romanishko E. L., Sheiko R. I. Bioinformaticheskij ana liz genomov domashnih svinej – porodospecifichnye SNP dlya porod landras i p’etren. Geneticheskie problemy v populyatsiyakh: materialy Nauchnoi konferentsii s mezhdunarodnym uchastiem, posvyashchennoi 50-letnemu yubileyu laboratorii populyatsionnoi genetiki imeni Yu. P. Altukhova IOGen RAN i 85-letiyu so dnya rozhdeniya akademika Yuriya Petrovicha Altukhova, 11–14 noyabrya 2022 goda [Genetic Problems in Populations: Proceedings of the Scientific Conference with International Participation Dedicated to the 50th Anniversary of the Yu. P. Altukhov Laboratory of Population Genetics, Institute of Genetics of the Russian Academy of Sciences and the 85th Anniversary of the Birth of Academician Yuri Petrovich Altuk- hov, November 11–14, 2022]. Moskow, 2022, p. 56 (in Russian).