TSitologiya i Genetika 2021, vol. 55, no. 1, 62-74
Cytology and Genetics 2021, vol. 55, no. 1, 53–62, doi: https://www.doi.org/10.3103/S0095452721010023

Associations of QTL region genes of chromosome 2 with meat quality traits and productivity of ukrainian large white pig breed

Balatsky V.N., Oliinychenko Y.K., Buslyk T.V., Bankovska I.B., Korinnyi S.N., Saienko A.M., Pochernyaev K.F.

  • Інститут свинарства і агропромислового виробництва Національної академії аграрних наук України, вул. Шведська Могила, 1, 36013, Полтава, Україна

SUMMARY. In recent decades, selection in pig farming has been aimed at obtaining animals with high growth rate and increased meat yield in the carcass, resulting in a tendency to deteriorating the quality characteristics of pork. One way to solve this problem is to develop genetic markers of pig meat quality and to use them in breeding programs along with the markers of other productive traits. The article presents the results of the analysis of the association of genes IGF2 (SNP
g.3072G > A), CTSD (SNP g.70G > A) and CTSF (SNP g.22G > C), localized in the QTL region of the distal end of the p-shoulder of chromosome 2, with the indicators of meat quality and carcass structure of Ukrainian Large White breed (UVB) pigs. According to these SNPs, all genes were characterized by a high level of polymorphism (PIC = 0,343–0,371). The association of CTSD (SNP g.70G > A) with the content of intramuscular fat (p = 0,02), moisture in meat (p = 0,03) and its moisture holding capacity (p = 0,03) was established. CTSD (SNP g.70G > A) also had an additive effect on an important selection trait - the thickness of spinal fat (p = 0,05), it was the highest in pigs of the g.70GG genotype. The connection of CTSF (SNP g.22G > C) with the moisture content in the meat (p = 0,01) and the association of IGF2 (SNP g.3072G > A) with the loss of moisture during its heat treatment (p = 0,01)was determined. The polymorphisms of the studied genes can be used as genetic markers in marker-associated selection of Ukrainian Large White pig breed.

Keywords: Ukrainian Large White pig breed, SSC2, CTSF, CTSD, IGF2, SNP, meat quality, association analysis

TSitologiya i Genetika
2021, vol. 55, no. 1, 62-74

Current Issue
Cytology and Genetics
2021, vol. 55, no. 1, 53–62,
doi: 10.3103/S0095452721010023

Full text and supplemented materials


1. Balatsky, V., Oliinychenko, Y., Sarantseva, N., et al., Association of single nucleotide polymorphisms in leptin (LEP) and leptin receptor (LEPR) genes with backfat thickness and daily weight gain in Ukrainian Large White pigs, Livestock Sci., 2018, vol. 217, pp. 157–161. https://doi.org/10.1016/j.livsci.2018.09.015

2. Balatsky, V.M., Vovk, V.O., Buslyk, T.V., et al., The genetic-associated analysis of g. 22 G > C single-nucleotide polymorphism in F cathepsin gene of different pig breeds, Bull. Poltava State Agrar. Acad., 2018, vol. 4, pp. 137–141. https://doi.org/10.31210/visnyk2018. 04.20

3. Balatsky, V.N., Saienko, A.M., Pena, R.N., et al., Genetic diversity of pig breeds on ten production quantitative traits loci, Cytol. Genet., 2015, vol. 49, no. 5, pp. 299–307. https://doi.org/10.3103/S0095452715050023

4. Boccard, R., Buchter, L., Casteels, M., et al., Procedures for measuring meat quality characteristics in beef production experiments, Report of a Working Group in the Commission of the European Communities (CEC) Beef Production Research Programme, Li-vest Prod. Sci., 1981, vol. 8, pp. 385–397. https://doi.org/10.1016/0301-6226 (81)90061-0

5. Bohrer, B.M., Clark, D.L, Tavárez, M.A., et al., Effect of an insulin-like growth factor 2 single nucleotide polymorphism on fresh belly characteristics and bacon slicing yields of finishing pigs, Meat Sci., 2015, vol. 101, pp. 109–110. https://doi.org/10.1016/j.meatsci.2014.09.029

6. Burgos, S.C., Llambн, D.S., Hidalgo, G.J., et al., Selection markers in Pampa Rocha pigs: a comparison with autochthonous breeds of Spain and Portugal, J. MVZ Cordoba, 2019, vol. 24, no. 2, pp. 7198–7202. https://doi.org/10.21897/rmvz.1642

7. Clark, D.L., Bohrer, B.M., Tavárez, M.A., et al., Effects of the porcine igf2 intron 3-g3072a mutation on carcass cutability, meat quality, and bacon processing, J. Anim. Sci., 2014, vol. 92, no. 12, pp. 5778–5788. https://doi.org/10.2527/jas.2014-8283

8. Cobanovic, N., Stajkovic, S., Grkovic, N., et al., Effects of RYR1 gene mutation on the health, welfare, carcass and meat quality in slaughter pigs, IOP Conf. Ser.: Earth Environ. Sci., 2019, vol. 333. https://doi.org/10.1088/1755-1315/333/1/012051

9. Criado-Mesas, L., Ballester, M., Crespo-Piazuelo, D., et al., Analysis of porcine IGF2 gene expression in adipose tissue and its effect on fatty acid composition, PLoS One, 2019, vol. 14, no. 8, pp. e0220708. https://doi.org/10.1371/journal.pone0220708

10. Danley, R.L., New heat flux DSC measurement technique, Thermochim. Acta, 2002, vol. 395, nos. 1–2, pp. 201–208. https://doi.org/10.1016/S0040-6031(02)00212-5

11. Davoli, R., Schivazappa, C., Zambonelli, P., et al., Association study between single nucleotide polymorphisms in porcine genes and pork quality traits for fresh consumption and processing into Italian dry-cured ham, Meat Sci., 2016, vol. 126, pp. 73–81. https://doi.org/10.1016/j.meatsci.2016.11.01

12. Fontanesi, L., Speroni, C., Buttazzoni, L., et al., The insulin-like growth factor 2 (IGF2) gene intron3-g.3072G>A polymorphism is not the only Sus scrofa chromosome 2p mutation affecting meat production and carcass traits in pigs: evidence from the effects of a cathepsin D (CTSD) gene polymorphism, J. Anim. Sci., 2010, vol. 88, pp. 2235–2245. https://doi.org/10.2527/jas.2009-2560

13. Fontanesi, L., Scotti, E., Speroni, C., et al., A selective genotyping approach identifies single nucleotide polymorphisms in porcine chromosome 2 genes associated with production and carcass traits in Italian heavy pigs, Ital. J. Anim. Sci., 2011, vol. 10, no. 2, pp. 72–77. https://doi.org/10.4081/ijas.2011.e15

14. Fontanesi, L., Speroni, C., Buttazzoni, L., et al., Association between polymorphisms in cathepsin and cystatin genes with meat production and carcass traits in Italian Duroc pigs: confirmation of the effects of a cathepsin L (CTSL) gene marker, Mol. Biol. Rep., 2012, vol. 39, no. 1, pp. 109–115. https://doi.org/10.1007/s11033-011-0715-4

15. Grau, R. and Hamm, R., Über das Wasserbin-dungsvermgen des Sugetiermuskels. II. Mitteilung. Über die Bestimmung der Wasserbindung des Muskels, Zeitschrift Lebensmittel-Intersuchung Forschung, 1957, vol. 105, no. 6, pp. 446–460. https://doi.org/10.1007/BF011-26901

16. Hao, L.L., Yu, H., Zhang, Y., et al., Single nucleotide polymorphism analysis of exons 3 and 4 of IGF-1 gene in pigs, Genet. Mol. Res., 2011, vol. 10, pp. 1689–1695. https://doi.org/10.4238/vol10-3gmr1328

17. Official Methods of Analysis of the AOAC, 13th ed., Horwitz, W., Ed., The Association of Official Analytical Chemists, 1111 N. 19th St., Arlington, VA 22209, 1980. https://doi.org/10.1002/jps.2600700437

18. Hu, Zhi-L., Park, C.A., and Reecy, J.M., Building a livestock genetic and genomic information knowledge base through integrative developments of Animal QTLdb and CorrDB, Nucleic Acids Res., 2019, vol. 47 (D1), pp. D701–D710. https://doi.org/10.1093/nar/gky1084

19. Karpushkina, T.V., Kostyunina, O.V., Sizareva, E.I., et al., Productive traits of large white pigs depending on IGF2 and CTSD genotypes, Dostizh. Nauki Tekhn. APK, 2016, vol. 30, no. 6, pp. 82.

20. Kenchaiwong, W., Duangjinda, M., and Boonkum, W., Polymorphisms of candidate genes associated with feed efficiency and growth traits in commercial crossbred pigs, J. Sci. Technol., 2019, vol. 41, no. 5, pp. 1069–1075.

21. Kostyunina, O.V., Kramarenko, S.S., Svezhentseva, N.A., et al., The association of IGF2 with productive traits of pigs of large white breed in the aspect of sexual differentiation, Agric. Biol., 2015, vol. 50, no. 6, pp. 736–745. https://doi.org/10.15389/agrobiology.2015.6.736rus

22. Martínez-Montes, M., Fernández, A., Mucoz, M., et al., Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed, PLoS One, 2018, 2018, vol. 13, no. 3. e0190184. https://doi.org/10.1371/journal.pone.0190184

23. Nezer, C., Moreau, L., Brouwers, B., et al., An imprinted QTL with major effect on muscle mass and fat deposition maps to the IGF2 locus in pigs, Nat. Genet., 1999, vol. 21, pp. 155–156. https://doi.org/10.1038/593

24. Oczkowicz, M., Tyra, M., Walinowicz, K., et al., Known mutation (A3072G) in intron 3 of the IGF2 gene is associated with growth and carcass composition in Polish pig breeds, J. Appl. Genet., 2009, vol. 50, no. 3, pp. 257–259. https://doi.org/10.1007/BF03195681

25. Peakall, R. and Smouse, P.E., GenAlEx 6.5: genetic analysis in Excel, population genetic software for teaching and research—an update, Bioinformatics, 2012, vol. 28, no. 19, pp. 2537–2539. https://doi.org/10.1093/bioinformatics/bts460

26. Pena, R.N., Ros-Freixedes, R., Tor, M., et al., Genetic marker discovery in complex traits: a field example on fat content and composition in pigs, Int. J. Mol. Sci., 2016, vol. 17, no. 12, p. 2100. https://doi.org/10.3390/ijms17122100

27. Piyrkowska, K.L., Ropka-Molik, K., Eckert, R., et al., The association between polymorphisms of three cathepsins and economically important traits in pigs raised in Poland, Livestock Sci., 2012, vol. 150, pp. 316–323. https://doi.org/10.1016/j.livsci.2012.09.022

28. Qiao, R., Gao, J., Zhang, Zh., et al., Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations, Genet. Select. Evol., 2015, vol. 47, p. 17. https://doi.org/10.1186/s12711-015-0089-5

29. Ramos, A.M., Glenn, K.L., Serenius, T.V., et al., Genetic markers for the production of US country hams, J. Anim. Breed. Genet., 2008, vol. 128, pp. 248–257.https://doi.org/10.1111/j.1439-0388.2007.00710.x

30. Russo, V., Davoli, R., Nanni Costa, L., et al., Association of the CTSB, CTSF and CSTB genes with growth, carcass and meat quality traits in heavy pigs, Ital. J. Anim. Sci., 2003, vol. 2, no. 1, pp. 67–69. https://doi.org/10.4081/ijas.2003.11675917

31. Russo, V., Fontanesi, L., Davoli, R., et al., Linkage mapping of the porcine cathepsin F (CTSF) gene close to the QTL regions for meat and fat deposition traits on pig chromosome 2, Anim. Genet., 2004, vol. 35, pp. 155–157. https://doi.org/10.1111/j.1365-2052.2004.01105.x

32. Russo, V., Fontanesi, L., Scotti, E., et al., Single nucleotide polymorphisms in several porcine cathepsin genes are associated with growth, carcass, and production traits in Italian Large White pigs, J. Anim. Sci., 2008, vol. 86, pp. 3300–3314. https://doi.org/10.2527/jas.2008-0920

33. Simonetti, A., Rando, A., Di Gregorio, P., et al., Variability of the IGF2 locus in the Suino Nero Lucano pig population and its effects on meat quality, Anim. Prod. Sci., 2017, vol. 58, no. 11, pp. 1976–1982. https://doi.org/10.1071/AN17051

34. Tocci, A.M. and Mascheroni, R.H., Characteristics of differential scanning calorimetry determination of thermophysical properties of meats, Lebensmittel-Wissenschaft und-Technologie, 1998, vol. 31, no. 5, pp. 418–426. https://doi.org/10.1006/fstl.1998.0319

35. Untergasser, A., Nijveen, H., Rao, X., et al., Pri-mer3Plus, an enhanced web interface to Primer3, Nucleic Acids Res., 2007, vol. 35, no. 2, pp. W71–W74. https://doi.org/10.1093/nar/gkm306

36. Van Laere, A.S., Nguyen, M., Braunschweig, M., et al., A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig, Nature, 2003, vol. 425, no. 6960, pp. 832–836. https://doi.org/10.1038/nature02064

37. Zhang, C., Bruce, H., Yang, T., et al., Genome Wide Association Studies (GWAS) identify QTL on SSC2 and SSC17 affecting loin peak shear force in crossbred commercial pigs, PLoS One, 2016, vol. 11, no. 2. e0145082. https://doi.org/10.1371/journal.pone.0145082