Evaluation genetic diversity of Malus sieversii of Dzungarian populations using ISSR-PCR markers
DOI:
https://doi.org/10.26577//eb.2020.v83.i2.03Abstract
Fruit forests of Tien Shan are the centre of origin of several plant species. In this geographical region, many economically valuable species are distributed, such as Malus sieversii (Ledeb.) M. Roem. – Sievers apple tree. The natural populations of M. sieversii of Kazakhstan with a wide range of genetic and phenotypic variations of characters are increasingly subjected to anthropogenic pressure and genetic erosion. It is known that for the effective conservation and rational use of genetic resources, a thorough assessment of the genetic variation that they possess is required. The genetic diversity of 13 clone varieties of M. sieversii of the Dzungarian population of The Main botanical garden’s introduction collection in Almaty (Kazakhstan) and 31 samples from three populations was assessed using 8 polymorphic ISSR markers and iMEC program. To assess the genetic relationships between the studied samples, the expected heterozygosity and average heterozygosity of the samples were calculated. As basic measures, the polymorphism information content (PIC), distinguishing ability (D), effective multiplex ratio (E), marker index MI and resolution (R) were calculated using iMEC. The work revealed a high genetic diversity of clone varieties and samples of the Dzungarian population. As a result of PCA analysis, the studied variety clones and M. sieversii samples from natural populations formed one cloud, which indicates a genetic exchange between these populations.
Keywords: Clone-varieties of Sievers apple tree, iMEC program, ISSR-PCR, genetic diversity, Malus sieversii, PCA analysis
References
1. Crosby JA, Janick J, Pecknold PC, Korban SS, O’Connor PA, Ries SM, Goffreda S, Voordeckers A (1992) Breeding apple for scab resistance. Acta Hortic 317: 43-70
2. Vavilov N. I. (1931b) Dikie rodichi plodovyh derevev // Tr. po prikl. botan., genet. i selektsii. [The wild relatives of fruit trees of the Asian part of the USSR and Caucasus and the problem of the origin of fruit trees]. Trans. Applе Bot. Gene Breed 26(3):132–134.
3. Dzhangaliev, A.D. (2003) The wild apple tree of Kazakhstan. Hort. Rev. 29: 65–304.
4. Luby, J.; Forsline, P.; Aldwinckle, H.; Bus, V.; Geibel, M. (2001) Silk road apples—Collection, evaluation, and utilization of Malus sieversii from Central Asia. HortScience. 36: 225–231.
5. Harris S. A., Robinson J. P., Junuper D. E. (2002) Genetic clues to the origin of the apple//Trend in genetic, Vol.18, №8. P. 426-430
6. Dzhangaliev A. D. (1977) Dikaja jablonja Kazahstana [The wild apple of Kazakstan]. Nauka. Alma-Ata, 280 pp.
7. Zhou Z. Q., Y.N. Li. (2000) The RAPD evidence for the phylogenetic relationship of the closely related species of cultivated apple. Genet Res Crop Evol. 47:353–357. DOI: 10.1023/A:1008740819941
8. Robinson J. P., Harris S. A., Juniper B.E. (2001) Taxonomy of the genus Malus Mill. (Rosaceae) with emphasis on the cultivated apple, Malus domestica Borkh. Plant Systematics and Evolution. 226: 35-58. DOI:10.1007/s006060170072
9. Forsline P. L., Aldwinckle H. S., Dickson E. E., Hokanson S. C. (2003) Collection, maintenance, haracterization, and utilization of wild apples from central Asia. Hort. Rev. 29:1–61.
10. Juniper B. and D. J. Mabberley. (2006) The story of the apple. Timber Press, Portland, (OR).
11. Flora Kazakhstana / pod red. Pavlov N.V. (1956-1966) [The Flora of Kazakhstan]. Alma-Ata, Nauka, Т. 1-9. Alma-Ata, Science.
12. ICN. (2018) Turland, N. J., Wiersema, J. H., Barrie, F. R., Greuter, W., Hawksworth, D. L., Herendeen, P. S., Knapp, S., Kusber, W.-H., Li, D.-Z., Marhold, K., May, T. W., McNeill, J., Monro, A. M., Prado, J., Price, M. J. & Smith, G. F. (eds.) International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017. Regnum Vegetabile 159. Glashütten: Koeltz Botanical Books. DOI https://doi.org/10.12705/Code.2018
13. Yan G., H. Long, W. Song, and R. Chen. (2008) Genetic polymorphism of Malus sieversii populations in Xinjiang, China. Genet. Resources Crop Evol. 55:171–181. DOI: 10.1007/s10722-007-9226-5
14. Cornille A., Gladieux P., Smulders M. J. M., Roldan-Ruiz I., Laurens F., Le Cam B., Nersesyan A., Clavel J., Olonova M., Feugey L., Gabrielyan I., Zhang X.-G., Tenaillon M. I., Giraud T. (2012) New insight into the history of domesticated apple: Secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS Genet. 8: e1002703. DOI: 10.1371/journal.pgen.1002703
15. Zhang H., M. Zhang, L. Wang. (2015) Genetic structure and historical demography of Malus sieversii in the Yili Valley and the western mountains of the Junggar Basin, Xinjiang, China. J Arid Land. 7(2): 264–271. DOI: 10.1007/s40333-014-0044-2
16. Dzhangaliev A. D., Salova T. N. (2007) Unikalnoe i globalnoe znachenie genofonda yablonevyh lesov Kazakhstana // Doklady NAN RK. [Unique and global knowledge of the apple forest genefund of Kazakhstan // Reports of RK NAS]. 5: 41-47.
17. Kutsev M. G. (2009) Fragmentnyi analiz DNK rastenii: RAPD, DAF, ISSR. [Fragment analysis of plant DNA: RAPD, DAF, ISSR]. Arctika, Barnaul, 164 pp.
18. Binneck E., Nedel J.L., Dellagostin O. A. (2002) RAPD analysis on cultivar identification: a useful methodology? Rev. Bras. Sem. 24: 183-196
19. Zhang C, Chen X, He T, et al. (2007) Genetic structure of Malus sieversii population from Xinjiang, China, revealed by SSR markers. Journal of Genetics and Genomics, 34: 947−955. DOI: 10.1016/S1673-8527(07)60106-4
20. Volk G. M., Richards C.M., Henk A.D., Reilley A. A., Miller D. D., Forsline P. L. (2009) Novel diversity identified in a wild apple population from the Kyrgyz Republic. Hort. Science 44:516-518. DOI: 10.21273/HORTSCI.44.2.516
21. Sitpaeva G.T., Veselova P.V., Gemedjieva N.G., Grudzinskaya L.M. et al. (2014) Kompleksnye issledovaniya dikih sorodichei kulturnyh rastenii Zapadnogo Tyan-Shanya // Tr. inst. Botaniki i phitointroduktsii. [Сomprehensive studies of wild relatives of cultivated plants of the Western Tien Shan // Works of the Institute of Botany and Phytointroduction, Almaty, pp. 194]. Almaty, 194 pp.
22. Omasheva М., Flachowsky H., Ryabushkina N., Pozharskiy A., Galiakparov N., Hanke M. (2017) To what extent do wild apples in Kazakhstan retain their genetic integrity? Tree Genetics & Genomes.13: 52. DOI: 10.1007/s11295-017-1134-z
23. Volk G. M., Richards C. M., Reilley A. A., Henk A.D., Forsline P.L., Aldwinckle H.S. (2005) Ex situ conservation of vegetatively propagated species: Development of a seedbased core collection for Malus sieversii. J. Amer. Soc. Hort. Sci. 130: 203–210. DOI: 10.21273/JASHS.130.2.203
24. Richards C.M., Volk G.M., A.A. Reilley, A.D. Henk, D. Lockwood, P.A. Reeves, and P.L. Forsline. (2009b) Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple. Tree Genet. Genomes 5: 339–347. DOI: 10.1007/s11295-008-0190-9
25. Gupta M., Y-S. Chyi, J. Romero-Severson & J. L. Owen. (1994) Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor. Appl. Genet. 89: 998–1006. DOI: 10.1007/BF00224530
26. Friesen N. (2007) Molekuljarnye metody ispolzuemye v sistematike rastenii. [Molecular methods using in Plant taxonomy]. Azbuka, Barnaul, 33-34 pp.
27. White T. J., Bruns T., Lee S., Taylor J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: a guide to methods and applications. (Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds). Academic Press, New York, USA: 315–322. DOI: https://doi.org/10.1007/BF00224530
28. Botstein D., White R.L., Skolnick M., Davis R.W. (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 32(3): 314–331.
29. Amiryousefi A, Hyvönen J, Poczai P. (2018) iMEC: Online Marker Efficiency Calculator. Applications in Plant Sciences. 6(6): e1159. DOI:10.1002/aps3.1159
30. Chesnokov Yu.B., Artemyeva А.М. (2015) Otsenka mery informatsionnogo polimorfizma geneticheskogo raznoobrazia [Evaluation of the measure of polymorphism information of genetic diversity]. Sel’skokhozyaistvennaya biologiya [Agricultural Biology] 50(5): 571-578. doi:10.15389/agrobiology.
31. Bahtaulova A.S., Bekmanov B., Kanagatov Zh. Zh. (2017) Molekuljarno-geneticheskii analiz raznoobrazija dikoi jabloni (Malus sieversii Ledeb. M. Roem.) s pomoshh’u DNK-markerov. Vestnik Karagandinskogo universiteta. Serija “Biologja. Meditsina. Geografija” [Molecular-genetic analysis of the wild apple tree (Malus sieversii Ledeb. M. Roem.) diversity based on DNA-markers] Vestnik of KarGU. 4(88): 21-28.
32. Omasheva М., Pozharsky A. S., Smailov B. B., Ryabushkina N. A., Galiakparov N. N. (2018) Genetic Diversity of Apple Cultivars Growing in Kazakhstan. Russian Journal of Genetics, Vol. 54, No. 2, pp.176–187.
2. Vavilov N. I. (1931b) Dikie rodichi plodovyh derevev // Tr. po prikl. botan., genet. i selektsii. [The wild relatives of fruit trees of the Asian part of the USSR and Caucasus and the problem of the origin of fruit trees]. Trans. Applе Bot. Gene Breed 26(3):132–134.
3. Dzhangaliev, A.D. (2003) The wild apple tree of Kazakhstan. Hort. Rev. 29: 65–304.
4. Luby, J.; Forsline, P.; Aldwinckle, H.; Bus, V.; Geibel, M. (2001) Silk road apples—Collection, evaluation, and utilization of Malus sieversii from Central Asia. HortScience. 36: 225–231.
5. Harris S. A., Robinson J. P., Junuper D. E. (2002) Genetic clues to the origin of the apple//Trend in genetic, Vol.18, №8. P. 426-430
6. Dzhangaliev A. D. (1977) Dikaja jablonja Kazahstana [The wild apple of Kazakstan]. Nauka. Alma-Ata, 280 pp.
7. Zhou Z. Q., Y.N. Li. (2000) The RAPD evidence for the phylogenetic relationship of the closely related species of cultivated apple. Genet Res Crop Evol. 47:353–357. DOI: 10.1023/A:1008740819941
8. Robinson J. P., Harris S. A., Juniper B.E. (2001) Taxonomy of the genus Malus Mill. (Rosaceae) with emphasis on the cultivated apple, Malus domestica Borkh. Plant Systematics and Evolution. 226: 35-58. DOI:10.1007/s006060170072
9. Forsline P. L., Aldwinckle H. S., Dickson E. E., Hokanson S. C. (2003) Collection, maintenance, haracterization, and utilization of wild apples from central Asia. Hort. Rev. 29:1–61.
10. Juniper B. and D. J. Mabberley. (2006) The story of the apple. Timber Press, Portland, (OR).
11. Flora Kazakhstana / pod red. Pavlov N.V. (1956-1966) [The Flora of Kazakhstan]. Alma-Ata, Nauka, Т. 1-9. Alma-Ata, Science.
12. ICN. (2018) Turland, N. J., Wiersema, J. H., Barrie, F. R., Greuter, W., Hawksworth, D. L., Herendeen, P. S., Knapp, S., Kusber, W.-H., Li, D.-Z., Marhold, K., May, T. W., McNeill, J., Monro, A. M., Prado, J., Price, M. J. & Smith, G. F. (eds.) International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017. Regnum Vegetabile 159. Glashütten: Koeltz Botanical Books. DOI https://doi.org/10.12705/Code.2018
13. Yan G., H. Long, W. Song, and R. Chen. (2008) Genetic polymorphism of Malus sieversii populations in Xinjiang, China. Genet. Resources Crop Evol. 55:171–181. DOI: 10.1007/s10722-007-9226-5
14. Cornille A., Gladieux P., Smulders M. J. M., Roldan-Ruiz I., Laurens F., Le Cam B., Nersesyan A., Clavel J., Olonova M., Feugey L., Gabrielyan I., Zhang X.-G., Tenaillon M. I., Giraud T. (2012) New insight into the history of domesticated apple: Secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS Genet. 8: e1002703. DOI: 10.1371/journal.pgen.1002703
15. Zhang H., M. Zhang, L. Wang. (2015) Genetic structure and historical demography of Malus sieversii in the Yili Valley and the western mountains of the Junggar Basin, Xinjiang, China. J Arid Land. 7(2): 264–271. DOI: 10.1007/s40333-014-0044-2
16. Dzhangaliev A. D., Salova T. N. (2007) Unikalnoe i globalnoe znachenie genofonda yablonevyh lesov Kazakhstana // Doklady NAN RK. [Unique and global knowledge of the apple forest genefund of Kazakhstan // Reports of RK NAS]. 5: 41-47.
17. Kutsev M. G. (2009) Fragmentnyi analiz DNK rastenii: RAPD, DAF, ISSR. [Fragment analysis of plant DNA: RAPD, DAF, ISSR]. Arctika, Barnaul, 164 pp.
18. Binneck E., Nedel J.L., Dellagostin O. A. (2002) RAPD analysis on cultivar identification: a useful methodology? Rev. Bras. Sem. 24: 183-196
19. Zhang C, Chen X, He T, et al. (2007) Genetic structure of Malus sieversii population from Xinjiang, China, revealed by SSR markers. Journal of Genetics and Genomics, 34: 947−955. DOI: 10.1016/S1673-8527(07)60106-4
20. Volk G. M., Richards C.M., Henk A.D., Reilley A. A., Miller D. D., Forsline P. L. (2009) Novel diversity identified in a wild apple population from the Kyrgyz Republic. Hort. Science 44:516-518. DOI: 10.21273/HORTSCI.44.2.516
21. Sitpaeva G.T., Veselova P.V., Gemedjieva N.G., Grudzinskaya L.M. et al. (2014) Kompleksnye issledovaniya dikih sorodichei kulturnyh rastenii Zapadnogo Tyan-Shanya // Tr. inst. Botaniki i phitointroduktsii. [Сomprehensive studies of wild relatives of cultivated plants of the Western Tien Shan // Works of the Institute of Botany and Phytointroduction, Almaty, pp. 194]. Almaty, 194 pp.
22. Omasheva М., Flachowsky H., Ryabushkina N., Pozharskiy A., Galiakparov N., Hanke M. (2017) To what extent do wild apples in Kazakhstan retain their genetic integrity? Tree Genetics & Genomes.13: 52. DOI: 10.1007/s11295-017-1134-z
23. Volk G. M., Richards C. M., Reilley A. A., Henk A.D., Forsline P.L., Aldwinckle H.S. (2005) Ex situ conservation of vegetatively propagated species: Development of a seedbased core collection for Malus sieversii. J. Amer. Soc. Hort. Sci. 130: 203–210. DOI: 10.21273/JASHS.130.2.203
24. Richards C.M., Volk G.M., A.A. Reilley, A.D. Henk, D. Lockwood, P.A. Reeves, and P.L. Forsline. (2009b) Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple. Tree Genet. Genomes 5: 339–347. DOI: 10.1007/s11295-008-0190-9
25. Gupta M., Y-S. Chyi, J. Romero-Severson & J. L. Owen. (1994) Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor. Appl. Genet. 89: 998–1006. DOI: 10.1007/BF00224530
26. Friesen N. (2007) Molekuljarnye metody ispolzuemye v sistematike rastenii. [Molecular methods using in Plant taxonomy]. Azbuka, Barnaul, 33-34 pp.
27. White T. J., Bruns T., Lee S., Taylor J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: a guide to methods and applications. (Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds). Academic Press, New York, USA: 315–322. DOI: https://doi.org/10.1007/BF00224530
28. Botstein D., White R.L., Skolnick M., Davis R.W. (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 32(3): 314–331.
29. Amiryousefi A, Hyvönen J, Poczai P. (2018) iMEC: Online Marker Efficiency Calculator. Applications in Plant Sciences. 6(6): e1159. DOI:10.1002/aps3.1159
30. Chesnokov Yu.B., Artemyeva А.М. (2015) Otsenka mery informatsionnogo polimorfizma geneticheskogo raznoobrazia [Evaluation of the measure of polymorphism information of genetic diversity]. Sel’skokhozyaistvennaya biologiya [Agricultural Biology] 50(5): 571-578. doi:10.15389/agrobiology.
31. Bahtaulova A.S., Bekmanov B., Kanagatov Zh. Zh. (2017) Molekuljarno-geneticheskii analiz raznoobrazija dikoi jabloni (Malus sieversii Ledeb. M. Roem.) s pomoshh’u DNK-markerov. Vestnik Karagandinskogo universiteta. Serija “Biologja. Meditsina. Geografija” [Molecular-genetic analysis of the wild apple tree (Malus sieversii Ledeb. M. Roem.) diversity based on DNA-markers] Vestnik of KarGU. 4(88): 21-28.
32. Omasheva М., Pozharsky A. S., Smailov B. B., Ryabushkina N. A., Galiakparov N. N. (2018) Genetic Diversity of Apple Cultivars Growing in Kazakhstan. Russian Journal of Genetics, Vol. 54, No. 2, pp.176–187.
Downloads
How to Cite
Shadmanova, L. S., Sitpayeva, G. T., & Friesen, N. (2020). Evaluation genetic diversity of Malus sieversii of Dzungarian populations using ISSR-PCR markers. Experimental Biology, 83(2), 23–31. https://doi.org/10.26577//eb.2020.v83.i2.03
Issue
Section
BOTANY
