Molecular analysis of buckwheat using gene specific markers
DOI:
https://doi.org/10.5219/954Keywords:
Fagopyrium esculentum, SCoT technique, genetic variability, DNA polymorphism, dendrogramAbstract
Buckwheat (Fagopyrium esculentum) is a pseudo-cereal which has spread troughout the world and nowadays it represents cultural, economic and nutritionally important pseudocereal. It´s enviromentally friendly, characterized by high fiber, routine, protein and B vitamins, and is general-purpose. The goal of the present study was to analyze 17 genotypes of buckwheat by using 7 SCoT markers. In total, 52 fragments were detected, of which 38 were polymorphic. The average number of polymorphic fragments was 5.43. The most polymorphic fragments were detected in SCoT 26 and SCoT 29 markers, and the average percentage of polymorphism was 73.36 %. SCoT 29 reached the highest percentage of polymorphism (87.5 %) and SCoT 36 was lowest (60 %). The DI values ”‹”‹ranged from 0.625 (SCoT 36) to 0.887 (SCoT 26) and the average DI value was 0.749. The average PIC value was 0.729 with PIC values ranging from 0.386 (SCoT 36) to 0.831 (SCoT 26). To determine the genetic diversity of 17 genotypes of the buckwheat, a dendrogram was created using the hierarchical cluster analysis. The genotypes were divided into two major clusters (I and II). Cluster I was divided into three other subgroups. Sixteen genotypes were included in cluster I and the genotype of Madawaska (USA) was genetically the farthest in cluster II. Genetically the closest were the varieties of Ballada (Russia) and Bamby (Austria). Used SCoT markers were sufficiently polymorphic, were able identify and differentiate chosen set of buckwheat genotypes.
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Agarwal, A., Gupta, V., Haq, S. U., Pradeep Kumar Jatav, P. K., Kothari, S.L. 2018. Assessment of genetic diversity in 29 rose germplasms using SCoT marker. Journal of King Saud University. https://doi.org/10.1016/j.jksus.2018.04.022 DOI: https://doi.org/10.1016/j.jksus.2018.04.022
Al-Qurainy, F., Khan, S., Nadeem, M., Tarroum, M. 2015. SCoT marker for the assessment of genetic diversity in Saudi Arabian date palm cultivars. Pak. J. Bot., vol. 47, no. 2, p. 637-640.
Amirmoradi, B., Talebi, R., Karami, E. 2012. Comparison of genetic variation anddifferentiation among annual Cicer species using start codon targeted (SCoT) polymorphism, DAMD-PCR, and ISSR markers. Plant Syst. Evol., vol. 298, p. 1679-1688. https://doi.org/10.1007/s00606-012-0669-6 DOI: https://doi.org/10.1007/s00606-012-0669-6
Bhawna, M., Abdin, Z., Arya, L., Verma, M. 2017. Use of SCoT markers to assess the gene flow and population structure among two different populations of bottle gourd. Plant Gene. vol. 9, p. 80-86. https://doi.org/10.1016/j.plgene.2016.09.001 DOI: https://doi.org/10.1016/j.plgene.2016.09.001
Boczkowska, M., Tarczyk, E. 2013. Genetic diversity among Polish landraces of common oat (Avena sativa L.). Genet Resour Crop Evol., vol. 60, p. 2157. https://doi.org/10.1007/s10722-013-9984-1 DOI: https://doi.org/10.1007/s10722-013-9984-1
Collard, B. C. Y., Mackill, D. J. 2009. Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol. Biol. Rep., vol. 27, p. 86-93. https://doi.org/10.1007/s11105-008-0060-5 DOI: https://doi.org/10.1007/s11105-008-0060-5
Fang-Yong, Ch., Ji-Honga, L. 2014. Germplasm genetic diversity of Myrica rubra in Zhejiang Province studied using inter-primer binding site and start codon-targetedpolymorphism markers. Scientia Horticulturae, vol. 170, p. 169-175. DOI: https://doi.org/10.1016/j.scienta.2014.03.010
https://doi.org/10.1016/j.scienta.2014.03.010 DOI: https://doi.org/10.1016/j.scienta.2014.03.010
Gajera, H. P., Bambharolia, R. P., Domadiya, R. K., Patel, S. V., Golakiya, B. A. 2014. Molecular characterization and genetic variability studies associated with fruit quality of indigenous mango (Mangifera indica L.) cultivars. Plant Syst Evol, vol. 300, p. 1011-1020. https://doi.org/10.1007/s00606-013-0939-y DOI: https://doi.org/10.1007/s00606-013-0939-y
Gorji, A. M., Poczai, P., Polgar, Z., Taller, J. 2011. Efficiency of arbitrarily amplified dominant markers (SCoT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato. Am. J. Potato Res., vol. 88, p. 226-237. https://doi.org/10.1007/s12230-011-9187-2 DOI: https://doi.org/10.1007/s12230-011-9187-2
Gupta, P. K., Y. S. Chyi, J. Romero-Severson, and J. L. Owen. 1994. Amplification of DNA markers from evolutionary diverse genomes using single primers of simple-sequence repeats. Theoretical and Applied Genetics, vol. 89, p. 998-1006. PMid:24178116 DOI: https://doi.org/10.1007/BF00224530
Hajibarat, Z., Saidi, A. Hajibarat, Z., Talebi, R. 2015. Characterization of genetic diversity in chickpea using SSR. Physiol. Mol. Biol. Plants, vol. 21, no. 3, p. 365-373. https://doi.org/10.1007/s12298-015-0306-2 DOI: https://doi.org/10.1007/s12298-015-0306-2
Hao, J., Jiao, K., Yu, C., Guo, H., Zhu, Y., Yang, X., Zhang, S., Zhang, L., Feng, S., Song, Y., Dong, M., Wang, H., Shen, C. 2018. Development of SCoT-based SCAR marker for rapid authentication of Taxus media. Biochem. Genet., vol. 56, p. 255-266. https://doi.org/10.1007/s10528-018-9842-0 DOI: https://doi.org/10.1007/s10528-018-9842-0
Huang, L., Huang, X., Yan, H., Yin, G., Zhang, X., Tian, Y., Zhang, Y., Jiang, X., Yan, Y., Ma, X., Peng, Y., Zhou, J., Nie, G. 2014. Constructing DNA fingerprinting of Hemarthria cultivars using EST-SSR and SCoT markers. Genet Resour Crop Evol., vol. 61, p. 1047-1055. https://doi.org/10.1007/s10722-014-0107-4 DOI: https://doi.org/10.1007/s10722-014-0107-4
Chen, X., Min, D., Yasir, T. A., Hu, Y.-G., 2012. Genetic diversity, population structure and linkage disequilibrium in elite Chinese winter wheat investigated with SSR markers. PLoS One. vol. 7, No. 9, e44510. https://doi.org/10.1371/journal.pone.0044510 DOI: https://doi.org/10.1371/journal.pone.0044510
Chrungoo, N. K., Dohtdong, L., Chettry, U. 2016. Genome Plasticity in Buckwheat. In V. R. Rajpal et al. (eds.). Gene Pool Diversity and Crop Improvement, Springer International Publishing Switzerland. Sustainable Development and Biodiversity 10, p. 227-239. https://doi.org/10.1007/978-3-319-27096-8_7 DOI: https://doi.org/10.1007/978-3-319-27096-8_7
Jiang, L. F., Qi, X., Zhang, X. Q., Huang, L. K., Ma, X., Xie, W. G. 2014. Analysis of diversity and relationships among orchardgrass (Dactylis glomerata L.) accessions using start codon-targeted markers. Genet. Mol. Res, vol. 13, no. 2, p. 4406-4418. https://doi.org/10.4238/2014.June.11.4 DOI: https://doi.org/10.4238/2014.June.11.4
Kallamadi, P. R., Ganga, R., Nadigatlab, V. P. R., Mulpurib, S. 2015. Molecular diversity in castor (Ricinus communis L.). Industrial Crops and Products, vol. 66, p. 271-281. https://doi.org/10.1016/j.indcrop.2014.12.061 DOI: https://doi.org/10.1016/j.indcrop.2014.12.061
Kishore, G., Pandey, A., Dobhal, R., Gupta, S. 2013. Population Genetic Study of Fagopyrum tataricum from Western Himalaya Using ISSR Markers. Biochem Genet. vol. 51, p. 750-765. https://doi.org/10.1007/s10528-013-9604-y DOI: https://doi.org/10.1007/s10528-013-9604-y
Luo, C., He, X. H., Chen, H., Ou, S. J., Gao, M. P. 2010. 2010. Analysis of diversity and relationships among mango cultivars using start codon targeted (SCoT) markers. Biochem. Syst. Ecol., vol. 38, p. 1176-1184. https://doi.org/10.1016/j.bse.2010.11.004 DOI: https://doi.org/10.1016/j.bse.2010.11.004
Mahjbi, A., Baraket, G., Oueslati, A., Salhi-Hannachi, A. 2015. Start Codon Targeted (SCoT) markers provide new insights into the genetic diversity analysis and characterization of Tunisian Citrus species. Biochemical Systematics and Ecology, vol. 61, p. 390-398. https://doi.org/10.1016/j.bse.2015.07.017 DOI: https://doi.org/10.1016/j.bse.2015.07.017
Paetkau, D., Calvert, W., Stirling, I., Strobeck, C. 1995. Microsatellite analysis of population structure in Canadian polar bears. Molecular Ecology, vol. 4, no. 3, p. 347-354. PMiD:7663752 DOI: https://doi.org/10.1111/j.1365-294X.1995.tb00227.x
Petrovičová, L., Balážová, Ž., Vivodík, M., Gálová, Z. 2017. Detection genetic variability of Secale cereale L. by SCoT markers. Potravinarstvo. vol. 11, no. 1, p. 197-202. https://doi.org/10.5219/726 DOI: https://doi.org/10.5219/726
Poczai, P., Varga, I., Laos, M., Cseh, A., Bell, N., Valkonen, J. P., Hyvonen, J. 2013. Advances in plant gene-targeted and functional markers: a review. Plant Methods., vol. 9, no. 1, p. 6. https://doi.org/10.1186/1746-4811-9-6 DOI: https://doi.org/10.1186/1746-4811-9-6
Przybylski, R., Gruczynska, E. 2009. A review of nutritional and nutraceutical components of buckwheat. Eur. J. Plant Sci. Biotechnol., vol. 3, p. 10-22.
Que, Y., Pan, Y., Lu, Y., Yang, C., Yang, Y., Huang, N., Xu, L. 2014. Genetic Analysis of Diversity within a Chinese Local Sugarcane Germplasm Based on Start Codon Targeted Polymorphism. BioMed Research International, vol. 2014, Article ID 468375, 10 pages. https://doi.org/10.1155/2014/468375 DOI: https://doi.org/10.1155/2014/468375
Rahimi, M., Nazari, L., Kordrostami, M., Safari, P., 2018. SCoT marker diversity among Iranian Plantago ecotypes and their possible association with agronomic traits. Sci. Hort. vol. 233, p. 302-309. https://doi.org/10.1016/j.scienta.2018.01.009 DOI: https://doi.org/10.1016/j.scienta.2018.01.009
Rajesh, M. K., Sabana, A. A., Rachana, K. E., Rahman, S., Jerard, B. A., Karun, A. 2015. Genetic relationship and diversity among coconut (Cocos nucifera L.) accessions revealed through SCoT analysis. Biotech vol. 5, p. 999-1006. https://doi.org/10.1007/s13205-015-0304-7 DOI: https://doi.org/10.1007/s13205-015-0304-7
Satya, P., Karana, M., Jana, S., Mitraa, S., Sharma, A., Karmakar, P. G., Rayb, D.P. 2015. Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species. Meta Gene, vol. 3, p. 62-70. https://doi.org/10.1016/j.mgene.2015.01.003 DOI: https://doi.org/10.1016/j.mgene.2015.01.003
Shahlaei, A., Torabi, S., Khosroshahli, M. 2014. Efficiacy of SCoT and ISSR marekers in assesment of tomato (Lycopersicum esculentum Mill.) genetic diversity. International Journal of Biosciences, vol. 5, no. 2, p. 14-22. https://doi.org/10.12692/ijb/5.2.14-22 DOI: https://doi.org/10.12692/ijb/5.2.14-22
Sharma, R., Jana, S. 2002. Species relationships in Fagopyrum revealed by PCR based DNA fingerprinting. Theor Appl Genet. vol. 105, p. 306-312. https://doi.org/10.1007/s00122-002-0938-9 DOI: https://doi.org/10.1007/s00122-002-0938-9
Shi, T., Li, R., Chen, Q., Li, Y., Pan, F., Chen, Q. 2017. De novo sequencing of seed transcriptome and development of genic-SSR markers in common buckwheat (Fagopyrum esculentum). Mol Breeding. Vol. 37, p. 147. https://doi.org/10.1007/s11032-017-0743-4 DOI: https://doi.org/10.1007/s11032-017-0743-4
Singh, S. K. Sidhika, CH., Rakesh, P., Bhatt, R. K., Kalia, R. K. 2017. Genetic diversity of Indian jujube cultivars using SCoT, ISSR, and rDNA markers. Tree Genetics & Genomes. 13 : 12. https://doi.org/10.1007/s11295-016-1092-x DOI: https://doi.org/10.1007/s11295-016-1092-x
Stibilj, V., Kreft, I., Smrkolj, P., Osvald, J. 2004. Enhanced selenium content in buckwheat (Fagopyrum esculentum Moench) and pumpkin (Cucurbita pepo L.) seeds by foliar fertilization. Eur Food Res Technol. vol. 219, no. 2, p. 142-144. https://doi.org/10.1007/s00217-004-0927-0 DOI: https://doi.org/10.1007/s00217-004-0927-0
Tsaballa, A., Ganopoluos, I., Timplalexi, A., liki, X., Bosmali, I., Irini, N. O., Athanasios, T. Madesis, P. 2015. Molecular characterization of Greek pepper (Capsicum annuum L) landraces with neutral (ISSR) and gene-based (SCoT and EST-SSR) molecular markers. Biochemical Systematics and Ecology, vol. 59, p. 256-263. https://doi.org/10.1016/j.bse.2015.02.005 DOI: https://doi.org/10.1016/j.bse.2015.02.005
Vivodík, M., Gálová, Z., Balážová, Ž., Petrovičová, L. 2016. Start codon targeted (scot) polymorphism reveals genetic diversity in European old maize (Zea mays l.) genotypes. Potravinarstvo, vol. 10, no. 1, p. 563-569. https://doi.org/10.5219/660 DOI: https://doi.org/10.5219/660
Vivodík, M., Saadaoui, E., Balážová, Ž., Gálová, Z., Petrovičová, L. 2018. Genetic diversity and population structure in tunisian castor genotypes (Ricinus communis L.) detected using scot markers. Potravinarstvo Slovak Journal of Food Sciences. vol. 12, no. 1, p. 143-149. https://doi.org/10.5219/873 DOI: https://doi.org/10.5219/873
Vyhnánek, T., Trojan, V., Štiasna, K., Presinszká, M., Hřivna, L., Mrkvicová, E., Havel, L. 2015. Testing of DNA isolation for the identification of Hemp. Potravinarstvo, vol. 9, no. 1, p. 393-397. https://doi.org/10.5219/509 DOI: https://doi.org/10.5219/509
Weber, J. L. 1990. Informativeveness of human (dC-dA)n x (dG-dT)n polymorphism. Genomics, vol. 7, p. 524-530. DOI: https://doi.org/10.1016/0888-7543(90)90195-Z
Wei, Y., Hu, X., Zhang, G., Ouyang, S. 2003. Studies on the amino acid and mineral content of buckwheat protein fractions. Nahrung/Food. vol. 47, p. 114-116. https://doi.org/10.1002/food.200390020 DOI: https://doi.org/10.1002/food.200390020
Weir, B. S. Genetic data analysis. Sinauer Associated, Sunderland, UK : Massachusetts, 1990, 445 p. ISBN 0 87893 871 00 87893.
Xiong, F., Zhong, R., Han, Z., Jiang, J., He, L., Zhuang, W., Tang, R. 2011. Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes. Mol. Biol. Rep., vol. 38, p. 3487-3494. https://doi.org/10.1007/s11033-010-0459-6 DOI: https://doi.org/10.1007/s11033-010-0459-6
Yasui, Y., Wang, Y., Ohnishi, O., Campbell, C. G. 2004. Amplified fragment length polymorphism linkage analysis of common buckwheat (Fagopyrum esculentum) and its wild selfpollinated relative Fagopyrum homotropicum. Genome. vol. 47, p. 345-351. https://doi.org/10.1139/g03-126 DOI: https://doi.org/10.1139/g03-126
Zhang, J., Xie, W., Wang, Y., Zhao, X. 2015. Potential of Start Codon Targeted (SCoT) Markers to Estimate Genetic Diversity and Relationships among Chinese Elymus sibiricus Accessions. Molecules, vol. 20, p. 5987-6001. https://doi.org/10.3390/molecules20045987 DOI: https://doi.org/10.3390/molecules20045987
Zhang, P., Li, J., Li, X., Liu, X., Zhao, X., 2011. Population structure and genetic diversity in a rice core collection (Oryza sativa L.) investigated with SSR markers. PLoS One, vol. 6, no. 12, e27565. https://doi.org/10.1371/journal.pone.0027565 DOI: https://doi.org/10.1371/journal.pone.0027565
Žiarovská, J., Grygorieva, O., Zeleňáková, L., Bežo, M., Brindza, J. 2015. Identification of sweet chesnut pollen in bee pollen pellet using molecular analysis. Potravinarstvo, vol. 9, no. 1, p. 352-358. https://doi.org/10.5219/497 DOI: https://doi.org/10.5219/497
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