Molecular-genetic analysis of Malus sieversii – comparison of Dzungarian populations in situ and ex situ
Keywords:
Clone-varieties of Sievers apple tree, ISSR-PCR, ITS, Malus sieversii, rps16 intron, trnL intron, trnL-trnF spacer
Abstract
Malus sieversii (Ledeb.) M. Roem. is recognized as the ancestor of the cultivated apple tree. It has a valuable gene pool, and in the last decades, it becomes endangered in Kazakhstan. The genetic diversity of 13 clone-varieties of Sievers apple tree (Malus sieversii) of Dzungarian population from the introduction collection of the Main Botanical Garden in Almaty (Kazakhstan) and 31 samples from three natural populations were assessed using eight polymorphic ISSR markers. The phylogenetic relationship of the clone-varieties with the natural population was estimated using ribosomal (ITS) and chloroplast DNA (rps16 intron, trnL intron, trn L-trn F). The data revealed a high genetic diversity of various clones and samples of Sievers apple tree of the Dzungarian populations. As a result of phylogenetic and cluster analysis the studied clones and samples of M. sieversii from natural populations formed a cluster, samples of supposedly hybrid origin formed 2 clusters, and no clustering was detected depending on geographical distance. The data demonstrate that there is an active information exchange between the populations.
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References
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Bornet B., Branchard M. 2001. Nonanchored Inter Simple Sequence Repeat (ISSR) markers: reproducible and specific tools for genome fingerprinting. Plant Mol Biol Rep. 19: 209–215.
Darriba D., Taboada G. L., Doallo R., Posada D. 2012. "jModelTest 2: more models, new heuristics and parallel computing". Nature Methods 9(8): 772.
Джангалиев А. Д. Дикая яблоня Казахстана. Алма-Ата: Наука, 1977. 280 c.
Dzhangaliev A. D. 2003. The wild apple tree of Kazakhstan. Hort. Rev. 29: 65–304.
Джангалиев А. Д., Напина Л. И., Салова Т. Н., Уварова Е. И. Malus sieversii (Ledeb.) M. Roem. // Красная книга Казахской ССР. Редкие и находящиеся под угрозой исчезновения виды животных и растений. Ч. 2. Растения. Алма-Ата: Изд-во «Наука» Казахской ССР, 1981. С. 98.
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Forsline P. L., Aldwinckle H. S., Dickson E. E., Hokanson S. C. 2003. Collection, maintenance, characterization, and utilization of wild apples from central Asia. Hort. Rev. 29: 1–61.
Forte A. V., Ignatov A. N., Ponomarenko V. V., Dorokhov D. B., Savelyev N. I. 2002. Phylogeny of the Malus (apple tree) species, inferred from the morphological traits and molecular DNA analysis. Russian Journal of Genetics 38(10): 1150–1160.
Фризен Н. Молекулярные методы, используемые в систематике растений. Барнаул: АзБука, 2007. С. 33–34.
Gupta M., Chyi Y-S., Romero-Severson J., Owen J. L. 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
Hokanson S. C., Szewc-McFadden A. K., Lamboy W. F., McFerson J. R. 1998. Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus × domestica Borch. core subset collection. Theor. Appl. Genet. 97: 671–683. DOI: 10.1007/s001220050943
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Hurka G., Friesen N., German D., Franzke A., Neuffer B. 2012.‘Missing link’ species Capsella orientalis and Capsella thracica elucidate evolution of model plant genus Capsella (Brassicaceae). Molecular Ecology 21: 1223–1238. DOI: 10.1111/j.1365-294X.2012.05460.x
Исаев Е. Б. 2014. Malus sieversii (Ledeb.) M. Roem. // Красная книга Казахстана. Т. 2. Ч. 1. Растения. Алматы, 2014. С. 52.
IUCN. URL: https://www.iucn.org (Accessed 05 November 2015).
Jeanmougin F., Thompson J. D., Gouy M., Higgins D. G., Gibson T. J. 1998. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23: 403–405. DOI: 10. 1016/S0968-0004(98)01285-7
Juniper B., Mabberley D. J. 2006. The story of the apple. Timber Press, Portland, 511 pp.
Kimura M., Ohta T. 1972. On the stochastic model for estimation of mutational distance between homologous proteins. Journal of Molecular Evolution 2: 87–90.
Kumar S., Stecher G., Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33: 1870–1874. DOI:10.1093/molbev/msw054
Куцев М. Г. 2009. Фрагментный анализ ДНК растений: RAPD, DAF, ISSR. Барнаул: Артика, 2009. 164 с.
Ledebour C. F. 1830. Flora Altaica. Vol. 2. G. Geimeri, Berlin, 464 pp.
Lewsey M. G., Hardcastle T. J., Melnyk C. W., Molnar A., Valli A., Urich M., Nery J.., Baulcombe D., Ecker J. 2016. Mobile small RNAs regulate genome-wide DNA methylation. PNAS 18: 1–10. DOI: 10.1073/pnas.1515072113.
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.
Nikifirova S., Cavalieri D., Velasco R., Goremykin V. 2013. Phylogenetic analysis of 47 chloroplast genomes clarifies the contribution of wild species to the domesticated apple maternal line. Mol. Biol. Evol. 30 (8): 1751–1760.
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
Омашева М. Е., Чекалин С. В., Рябушкина Н. А., Галиакпаров Н. Н. Оценка молекулярно-генетического разнообразия популяций Malus sieversii Джунгарского Алатау и Тарбагатая // Биотехнология. Теория и практика, 2015. № 1. С. 26–34. DOI: 10.11134/btp.1.2015.3
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
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 54 (2): 176–187.
Oxelman B., Lidén M., Berglund D. 1997. Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae). Plant Syst. Evol. 206: 393–410. DOI: 10.1007/BF00987959
Richards C. M., Volk G. M., Reilley A. A., Henk A. D., Lockwood D., Reeves P. A., Forsline P. L. 2009. 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
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 Syst. Evol. 226: 35–58. DOI:10.1007/s006060170072
Roemer M. J. 1847. Familiarum naturalium regni vegetabilis Synopses monographicae. Fasc. III. Rosiflorae. Vimariae, Landes-Industrie-Comptior, 314 pp. DOI: 10.5962/bhl.title.49482
Sievers J. A. C. 1796. Briefe aus Sibirien. St. Petersburg. URL: http://www.deutschestextarchiv.de/book/view/siever_briefe_1796
Ситпаева Г. Т., Веселова П. В., Гемеджиева Н. Г., Грудзинская Л. М. Комплексные исследования диких сородичей культурных растений Западного Тянь-Шаня // Тр. Инст. ботаники и фитоинтродукции. Алматы, 2014. 194 с.
Смирнов С. B., Фризен Н. В. 2006. Использование молекулярно-генетического анализа для выявления гибридов на примере Brachanthemum baranovii (Asteraceae) // Проблемы ботаники Южной Сибири и Монголии: Материалы V Междунар. науч.-практ. конф. (Барнаул, 21–23 ноября 2006 г.). Барнаул, 2006. С. 256–258.
Sokal R. R., Michener C. D. 1958. A statistical method for evaluating relationships. University of Kansas Science Bulletin 38: 1409–1448.
Swofford D. L. 2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4.0 beta version. Sinauer Associates, Sunderland, Massachusetts, 144 pp.
Taberlet P., Gielly L., Pautou G., Bouvet J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Pl. Mol. Biol. 17: 1105–1109.
Vavilov N. I. 1931. 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. 263):132–134.
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
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 seed-based core collection for Malus sieversii. J. Amer. Soc. Hort. Sci. 130: 203–210. DOI:10.21273/JASHS.130.2.203
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. Academic Press, New York, USA, 315–322 pp. DOI: 10.1007/BF00224530
Yan G., Long H., Song W., Chen R. 2008. Genetic polymorphism of Malus sieversii populations in Xinjiang, China. Genet. Resources Crop Evol. 55: 171–181. DOI: 10.1007/s10722-007-9226-5
Zhang C., Chen X., He T., Liu X., Feng T., Yuan Z. 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
Zhang H., Zhang M., Wang L. 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
Zhou Z. Q., Li Y. N. 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
Published
2019-06-17
How to Cite
Shadmanova L. S., Sitpayeva G. T., Mukanova G. S., Friesen N. V. Molecular-genetic analysis of Malus sieversii – comparison of Dzungarian populations in situ and ex situ // Turczaninowia, 2019. Vol. 22, № 2. P. 187-198 DOI: 10.14258/turczaninowia.22.2.15. URL: http://turczaninowia.asu.ru/article/view/5801.
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