Analysis of diversity and genetic interactions of potato varieties (Solanum tuberosum L.) based on morphological characteristics and SSR markers

Authors

DOI:

https://doi.org/10.21498/2518-1017.14.3.2018.145292

Keywords:

potatoes, genetic polymorphism, cluster analysis, Mantel test, correlation links

Abstract

Purpose. To estimate a correlation between SSR-markers and morphological features by genetic distances on the basis of polymorphism of potato varieties.

Methods. PCR analysis, cluster and correlation-regression analysis.

Results. The results of analysis of potatoes varieties polymorphism based on molecular genetic and morphological marker features are presented. Varieties polymorphism was assessed on four microsatellite markers: STM0019, STM3009, STM3012, STM5136 and 42 morphological markers. According to the results of PCR analysis, it was determined that the frequency of identified alleles ranged from 0.021 to 0.33, the index of polymorphism on the average for studied markers was 0.76. Using cluster analysis, the genetic distances between varieties based on SSR and morphological markers were determined, and similar varieties and varieties that differ among themselves were identified. According to the obtained distribution, the correlation between the genetic distances by Mantel test are estimated, namely, a regression, in which the variables are similarity matrices, summing the pairwise similar values between the sampling points was defined. As a result of the estimation of genetic distances between the investigated genotypes of potatoes, it was revealed that the varieties ‘Skarbnytsia’ and ‘Yavir’ were the most similar by markers STM0019, STM3009, STM3012, STM5136. The distance between these varieties was 2.45, while the greatest distance – 3.74 was found among the varieties ‘Levada’ and ‘Dovira’, ‘Fantaziia’ and ‘Dovira’. According to marker morphological signs, the least value of genetic distances was 8.9 for varieties ‘Slovianka’ and ‘Poliske Dzherelo’, the most distant ones were ‘Okolytsia’ and ‘Dovira’, with values of 18.2. It was revealed that the potato variety ‘Dovira’ with the value of genetic distances of 18.2 and 3.74 for morphological and SSR markers respectively was the most distant from other investigated genotypes. The correlations were not found by Mantel test as a result of the analysis of genetic distances based on SSR-markers and morphological signs.

Conclusions. The use of a complex of studies containing a description of morphological features and microsatellite markers is promising for identifying potato varieties, creating collections of well-known varieties and determining their differences.

Author Biographies

Л. М. Присяжнюк, Ukrainian Institute for Plant Variety Examination

Larysa Prysiazhniuk

О. Л. Кляченко, National University of Life and Environmental Sciences of Ukraine

Oksana Klyachenko

І. О. Діхтяр, Ukrainian Institute for Plant Variety Examination

Iryna Dikhtiar (Sihalova)

Н. В. Симоненко, Ukrainian Institute for Plant Variety Examination

Natalia Symonenko

References

Bellumori, M., Innocenti, M., Michelozzi, M., Cerretani, L., & Mulinacci, N. (2017). Coloured-fleshed potatoes after boiling: Promising sources of known antioxidant compounds. J. Food Compos. Anal., 59, 1–7. doi: 10.1016/j.jfca.2017.02.004

Oliinyk, T. M., Slobodian, S. O., & Hrytsai, R. V. (2012). The use of microsatellite markers for phylogenetic analysis potato varieties of domestic and foreign breeding. Kartopliarstvo [Potato Production], 41, 41–48. [in Ukrainian]

Zaviriukha, P., & Lishchynska, N. (2013). Studying of a initial material for potato breeding on a complex of valuable economic signs. Visnyk Lvivskoho natsionalnoho ahrarnoho universytetu. Ahronomiia [Bulletin of Lviv National Agrarian University. Agronomy], 17(2), 220–232. [in Ukrainian]

Chung, Y. S., Palta, J., Bamberg, J., & Jansky, S. (2016). Potential molecular markers associated with tuber calcium content in wild potato germplasm. Crop Sci., 56(2), 576–584. doi: 10.2135/cropsci2015.06.0370

Ramakrishnan, A. P., Ritland, C. E., Sevillano, R. H. B., & Riseman, A. (2015). Review of potato molecular markers to enhance trait selection. Am. J. Potato Res., 92(4), 455–472. doi: s12230-015-9455-7

Burstin, J., & Charcosset, A. (1997). Relationship between phenotypic and marker distances: theoretical and experimental investigations. Heredity, 79(5), 477–483. doi: 10.1038/sj.hdy.6882270

Geng, Y., van Klinken, R. D., Sosa, A., Li, B., Chen, J., & Xu, C. Y. (2016). The relative importance of genetic diversity and phenotypic plasticity in determining invasion success of a clonal weed in the USA and China. Front. Plant Sci., 7, 213–216. doi: 10.3389/fpls.2016.00213

Valliyodan, B., Ye, H., Song, L., Murphy, M., Shannon, J. G., & Nguyen, H. T. (2016). Genetic diversity and genomic strategies for improving drought and waterlogging tolerance in soybeans. J. Exp. Bot., 68(8), 1835–1849. doi: 10.1093/jxb/erw433

Riday, H., Brummer, E. C., Campbell, T. A., Luth, D., & Cazcarro, P. M. (2003). Comparisons of genetic and morphological distance with heterosis between Medicago sativa subsp. sativa and subsp. falcata. Euphytica, 131(1), 37–45. doi: 10.1023/A:1023050126901

Volkova, N. E. (2015). Molecular markers in genetics, breeding and seed production of legumes (review). Zbirnyk naukovykh prats SHI – NTsNS [Collected Scientific Articles of PBGI – NCSCI], 26, 99–106. [in Ukrainian]

Shen, Z., Zhang, K., Ma, L., Duan, J., & Ao, Y. (2017). Analysis of the genetic relationships and diversity among 11 populations of Xanthoceras sorbifolia using phenotypic and microsatellite marker data. Electron. J. Biotechnol., 26, 33–39. doi: 10.1016/j.ejbt.2016.12.008

Kwon, Y. S., Lee, J. M., Yi, G. B., Yi, S. I., Kim, K. M., Soh, E. H., … Kim, B. D. (2005). Use of SSR markers to complement tests of distinctiveness, uniformity, and stability (DUS) of pepper (Capsicum annuum L.) varieties. Mol. Cells, 19(3), 428–435.

Tkachyk, S. O. (Ed.). (2016). Metodyka provedennia ekspertyzy sortiv roslyn hrupy ovochevykh, kartopli ta hrybiv na vidminnist, odnoridnist i stabilnist [Method of examination of plant varieties of vegetable, potato and mushroom groups for distinctness, uniformity and stability]. Vinnytsia: Nilan-LTD. [in Ukrainian]

Côté, M. J., Leduc, L., & Reid, A. (2013). Evaluation of simple sequence repeat (SSR) markers established in Europe as a method for the identification of potato varieties grown in Canada. Am. J. Potato Res., 90(4), 340–350. doi: 10.1007/s12230-013-9310-7

Tkachyk, S. O. (Ed.). (2015). Metodyka provedennia kvalifikatsiinoi ekspertyzy sortiv roslyn na prydatnist do poshyrennia v Ukraini. Metody vyznachennia pokaznykiv yakosti produktsii roslynnytstva [Method of conducting qualification examination of plant varieties for suitability of their distribution in Ukraine. Methods of determining the quality indices of crop production]. Vinnytsia: Nilan-LTD. [in Ukrainian]

Rocha, E. A., Paiva, L. V., Carvalho, H. H. D., & Guimarães, C. T. (2010). Molecular characterization and genetic diversity of potato cultivars using SSR and RAPD markers. Crop Breed. Appl. Biotechnol., 10(3), 204–210. doi: 10.1590/S1984-70332010000300004

Ghebreslassie, B. M., Githiri, S. M., Mehari, T., Kasili, R. W., Ghislain, M., & Magembe, E. (2016). Genetic diversity assessment of farmers’ and improved potato (Solanum tuberosum) cultivars from Eritrea using simple sequence repeat (SSR) markers. Afr. J. Biotechnol., 15(35), 1883–1891. doi: 10.5897/AJB2016.15237

Reid, A., Hof, L., Felix, G., Rücker, B., Tams, S., Milczynska, E., … Weitz, A. (2011). Construction of an integrated microsatellite and key morphological characteristic database of potato varieties on the EU common catalogue. Euphytica, 182(2), 239–249. doi: 10.1007/s10681-011-0462-6

Reid, A., Hof, L., Esselink, D., & Vosman, B. (2009). Potato Cultivar Genome Analysis. In R. Burns (Ed.), Plant Pathology. Methods in Molecular Biology (vol. 508, pp. 295–308). New York, N.Y.: Humana Press. doi: 10.1007/978-1-59745-062-1_2

Roik, M. V., Syvolap, Yu. M., Petiukh, H. P., Shaiuk, L. V., Babiazh, A. I., & Bilous, N. V. (2007). Vyznachennia molekuliarno-henetychnoho polimorfizmu rodu Beta L. za dopomohoiu polimeraznoi lantsiuhovoi reaktsii [Detection of molecular-genetic polymorphism of the genus Beta L. by polymerase chain reaction]. Kyiv: PolihrafKonsaltynh. [in Ukrainian]

Fortin, M. J., Dale, M. R., & Ver Hoef, J. M. (2002). Spatial analysis in ecology. In A. H. El-Shaarawi, & W. W. Piegorsch (Eds.), Encyclopedia of Environmetrics (Vol. 4, pp. 2051–2058). Chichester: John Wiley & Sons Ltd.

Drozdov, V. I. (2010). Instruktsiya po ispolzovaniyu paketa Statistica 6.0 [Manual for using Statistica 6.0]. Kursk: Izdatelstvo YuZGU. [in Russian]

Everitt, B. S., Landau, S., Leese, M., & Stahl, D. (2011). Cluster Analysis. (5th ed.). Chichester: John Wiley & Sons Ltd. doi: 10.1002/9780470977811

Kishine, M., Tsutsumi, K., & Kitta, K. (2017). A set of tetra-nucleotide core motif SSR markers for efficient identification of potato (Solanum tuberosum) cultivars. Breed. Sci., 67(5), 544–547. doi: 10.1270/jsbbs.17066

Legendre, P., & Fortin, M. J. (2010). Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data. Mol. Ecol. Resour., 10(5), 831–844. doi: 10.1111/j.1755-0998.2010.02866.x

Diniz-Filho, J. A. F., Soares, T. N., Lima, J. S., Dobrovolski, R., Landeiro, V. L., Telles, M. P. D. C., … Bini, L. M. (2013). Mantel test in population genetics. Genet. Mol. Biol., 36(4), 475–485. doi: 10.1590/S1415-47572013000400002

Zhang, Q., Peters, J. L., Visser, E. J., Kroon, H., & Huber, H. (2016). Hydrologically contrasting environments induce genetic but not phenotypic differentiation in Solanum dulcamara. J. Ecol., 104(6), 1649–1661. doi: 10.1111/1365-2745.12648

Muhinyuza, J. B., Shimelis, H., Melis, R., Sibiya, J., Gahakwa, D., & Nzaramba, M. N. (2015). Assessment of genetic relationship of promising potato genotypes grown in Rwanda using SSR markers. Aust. J. Crop Sci., 9(8), 696–700.

Karuri, H. W., Ateka, E. M., Amata, R., Nyende, A. B., Muigai, A. W. T., Mwasame, E., & Gichuki, S. T. (2010). Evaluating diversity among Kenyan sweet potato genotypes using morphological and SSR markers. Int. J. Agr. Biol., 12(1), 33–38.

Darvishzadeh, R. (2012). Phenotypic and molecular marker distance as a tool for prediction of heterosis and F1 performance in sunflower (Helianthus annuus L.) under well-watered and water-stressed conditions. Aust. J. Crop Sci., 6(4), 732–738.

Downloads

Published

2018-10-23

How to Cite

Присяжнюк, Л. М., Кляченко, О. Л., Діхтяр, І. О., & Симоненко, Н. В. (2018). Analysis of diversity and genetic interactions of potato varieties (Solanum tuberosum L.) based on morphological characteristics and SSR markers. Plant Varieties Studying and Protection, 14(3), 277–284. https://doi.org/10.21498/2518-1017.14.3.2018.145292

Issue

Section

GENETICS

Most read articles by the same author(s)

1 2 3 > >>