β-tubulin intron length polymorphism among forms var. glabra and var. laxa of napa cabbage
Abstract
Aim. Main aim of this research was identification of genetic distances between different genotypes of napa cabbage (B. rapa ssp. pekinensis) and diversity identification in var. glabra and var. laxa forms. Methods. Molecular genetic analysis of napa cabbage genotypes was conducted out using method of β-tubulin intron length polymorphism (TBP). Results. Molecular profiles of different napa cabbage (B. rapa ssp. pekinensis) genotypes were identified. Number of amplified β-tubulin intron fragments was significantly varying – from 12 to 24 for each genotype. Basing on obtained results a dendrogram was built, which shows genetic distances among studied accessions. Conclusions. In present study 7 genotypes of B. rapa ssp. pekinensis were analyzed, received from IPK (Gatersleben) and Crop Research Institute (Prague) gene banks. Basing on obtained results it was established that systematic diversification of two forms var. glabra and var. laxa is not being confirmed by molecular genetic methods, such as TBP, and in this case, genetic difference between populations and cultivars was more significant.
Keywords: Brassicaceae, Brassica rapa ssp. pekinensis, ILP, TBP, napa cabbage, β-tubulin intron length polymorphism.
References
Downey R.K. The origin and description of the Brassica oilseed crops, In: Kramer J.K.G., Sauer F.D., Pigden W.J. (Eds.), High and low erucic acid rapeseed oils production, usage, chemistry, and toxicological evaluation. Academic Press, Toronto, 1983. P. 1-20. doi: 10.1016/B978-0-12-425080-2.50006-2
Gugel R.K., Falk K.C. Agronomic and seed quality evaluation of Camelina sativa in western Canada. Can. J. Plant Sci. 2006. Vol. 86. P. 1047-1058. doi: 10.4141/P04-081
Warwick S.I., Francis A., Al-Shehbaz I.A. Brassicaceae: species checklist and database on CD-Rom. Plant Syst. Evol. 2006. Vol. 259. P. 249-258. doi: 10.1007/s00606-006-0422-0
Warwick S.I., Gugel R., McDonald T., Falk K.C. Genetic variation and agronomic potential of Ethiopian mustard (Brassica carinata) in western Canada. Genet. Resour. Crop. Evol. 2006. Vol. 53. P. 297-312. doi: 10.1007/s10722-004-6108-y
Warwick S.I. Brassicaceae in agriculture, In: Schmidt R., Bancroft I. (Eds), Genetics and Genomics of the Brassicaceae. Springer Science+Business Media; LLC, New York, NY, 2011. P. 33-65. doi: 10.1007/978-1-4419-7118-0_2
Warwick S.I., Simard M.J., Lйgиre A., Beckie H.J., Braun L., Zhu B., Mason P., Sйguin-Swartz G., Stewart C.N. Jr. Hybridization between transgenic Brassica napus L. and its wild relatives: Brassica rapa L, Raphanus raphanistrum L, Sinapis arvensis L., and Erucastrum gallicum (Willd.) O. E. Schulz. Theor. Appl. Genet. 2003. Vol. 107. P. 528-539. doi: 10.1007/s00122-003-1278-0
Allainguillaume J., Alexander M., Bullock J.M., Saunders M., Allender C.J., King G., Ford C.S., Wilkinson M.J. Fitness of hybrids between rapeseed (Brassica napus) and wild Brassica rapa in natural habitats. Mol. Ecol. 2006. Vol. 15 (4). P. 1175-1184. doi: 10.1111/j.1365-294X.2006.02856.x
Sohn S.I., Oh Y.J., Lee K.R., Ko H.C., Cho H.S., Lee Y.H., Chang A. Characteristics analysis of F1 hybrids between genetically modified Brassica napus and B. rapa. PLOS ONE. 2016. Vol. 11 (9). P. e0162103. doi: 10.1371/journal.pone.0162103
Rakhmetov D.B., Rakhmetova S.О. Summary of introduction and breeding of tyfon (Brassica rapa L. × B. campestris f. biennis DC.) in M.M. Gryshko National Botanical Garden of the NAS of Ukraine. Plant Introduction. 2015. Vol. 4. P. 18-30. [in Ukrainian]
Blume R.Ya., Boychuk Yu.M., Yemets A.I., Rakhmetova S.O., Blume Ya.B., Rakhmetov D.B. Comparative analysis of fatty acid composition for oils from seeds of tyfon, oil radish and camelina breeding forms and varieties as perspective source for biodiesel production. Factors Exp. Evol. Organisms. 2016. Vol. 18. P. 61-66. [in Ukrainian]
Blume R.Ya., Lantukh G.V., Levchuk I.V., Rakhmetova S.O., Rakhmetov D.B., Blume Ya.B. Evaluation of perspectivity of use of a new hybrid oil culture of Tyfon in comparison with its parental species as raw material for biodiesel production. Factors Exp. Evol. Organisms. 2019. Vol. 24. P. 33-39. [in Ukrainian] doi: 10.7124/FEEO.v24.1074
Blume R.Y., Lantukh G.V., Levchuk I.V., Rakhmetov D.B., Blume Ya.B. Evaluation of potential biodiesel feedstocks from industrial Cruciferae: camelina, turnip rape, oil radish and tyfon. The Open Agricult. J. Thematic Iss.: Sustainable biofuel production: agricultural feedstock potential and biomass transformation technologies. Open Agr. J., 2020, Vol. 14. (In Press).
Bardini M., Lee D., Donini P., Mariani A., Giani S., Toschi M., Lowe C., Breviario D. Tubulin-based polymorphism (TBP): a new tool, based on functionally relevant sequences, to assess genetic diversity in plant species. Genome. 2004. Vol. 47. P. 281-291. doi: 10.1139/g03-132
Breviario D., Giani S., Ponzoni T., Mastromauro F., Morell L. Plant tubulin intronics. Cell Biol. Int. 2008. Vol. 32. P. 571-573. doi: 10.1016/j.cellbi.2007.11.013
Rabokon A.N., Demkovych A.E., Pirko Ya.V., Blume Ya.B. Intron length polymorphism of beta-tubulin genes as an effective instrument for plant genotyping. Mol. Appl. Genetics. 2015. Vol. 19. P. 35-44. [in Russian]
Sambrook J., David W.R. Molecular Сloning: A Laboratory Manual. Cold Spring Harbor, 2001. Vol. 2. 763 p.
Benbouza H., Jean-Marie J., Jean-Pierre B. Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels. Biotechnol. Agron. Soc. Environ. 2006. Vol. 10 (2). P. 77-81.
Breviario, D., Baird, W.V., Sangoi, S., Hilu, K., Blumetti, P., Giani, S. High polymorphism and resolution in targeted fingerprinting with combined β-tubulin introns. Mol. Breed. 2007. Vol. 20. P. 249-259. doi: 10.1007/s11032-007-9087-9
Hongtrakul V., Huestis G.M., Knapp S.J. Amplified fragment length polymorphisms as a tool for DNA fingerprinting sunflower germplasm: genetic diversity among oilseed inbred lines. Theor. Appl. Genet. 1997. Vol. 95. P. 400-407. doi: 10.1007/s001220050576
Pavlicek A., Hrda S., Flegr J. FreeTree - Freeware program for construction of phylogenetic trees on the basis of distance data and bootstrap/jackknife analysis of the tree robustness. Application in the RAPD analysis of the genus Frenkelia. Folia Biol. 1999. Vol. 45. P. 97-99.
Nei M., Li W.H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA. 1979. Vol. 76. P. 5269-5273. doi: 10.1073/pnas.76.10.5269
Nei M. Genetic distance between populations. Am. Nat. 1972. Vol. 106. P. 283-292. doi: 10.1086/282771
Hillis D.M., Bull J.J. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biol. 1993. Vol. 42. P. 182-192. doi: 10.1093/sysbio/42.2.182
Rabokon A.N., Pirko Ya.V., Demkovych A.E., Blume Ya.B. Comparative analysis of the efficiency of intron-length polymorphism of β-tubulin genes and microsatellite loci for flax varieties genotyping. Cytol. Genet. 2018. Vol. 52 (1). P. 1-10. doi: 10.3103/S0095452718010115
Galasso I., Manca A., Braglia L., Martinelli T., Morello L., Breviario D. An approach based on intron-length polymorphism for the rapid isolation and characterization of the multiple members of the β-tubulin gene family in Camelina sativa (L.) Crantz. Mol. Breed. 2011. Vol. 28. P. 635-645. doi: 10.1007/s11032-010-9515-0
Zhang Y.W., Jin D., Xu C., Zhang L., Guo M.H., Fang Z.Y. Regulation of bolting and identification of the β-tubulin gene family in Brassica rapa L. ssp pekinensis. Genet. Mol. Res. 2016. Vol. 15 (1). P. gmr.15017507. doi: 10.4238/gmr.15017507
Rabokon A.M., Pirko Y.V., Demkovych A.Ye., Andreev I.O., Parnikoza I.Yu., Kozeretska I.A., Yu Z., Kunakh V.A., Blume Y.B. Intron length polymorphism of β-tubulin genes in Deschampsia antarctica E. Desv. across the western coast of the Antarctic Peninsula. Polar Sci. 2019. Vol. 19. P. 151-154. doi: 10.1016/j.polar.2018.11.001
Kawamura K., Kawanabe T., Shimizu M., Nagano A.J., Saeki N., Okazaki K., Kaji M., Dennis E.S., Osabe K., Fujimoto R. Genetic distance of inbred lines of Chinese cabbage and its relationship to heterosis. Plant Gene. 2016. Vol. 5. P. 1-7. doi: 10.1016/j.plgene.2015.10.003