Genetic diversity and population structure in tunisian castor genotypes (Ricinus communis L.) Detected using scot markers
DOI:
https://doi.org/10.5219/873Keywords:
castor, DNA, PCR, dendrogram, SCoT markerAbstract
Due to the chemical and physical properties of castor oil (Ricinus communis L.) that make it a valuable raw material for numerous industrial applications, including the production of biofuel, interest to develop more and better varieties has been increased. In the present study, the representatives of the genus castor collected from 12 different parts of Tunisia were differentiated by the DNA fingerprinting patterns using 37 SCoT primers. PCR amplification of DNA using 37 primers for SCoT analysis produced 268 DNA fragments that could be scored in all 56 genotypes of Tunisian castor. The number of amplified fragments varied from 4 (SCoT 45, SCoT 31 and ScoT 17) to 10 (SCoT 3, SCoT 11, SCoT 14, SCoT 18 and SCoT 12). Of the 268 amplified bands 230 were polymorphic, with an average of 6.22 polymorphic bands per primer. To determine the level of polymorphism in the analysed group of Tunisian castor genotypes polymorphic information content (PIC) was calculated. The lowest values of polymorphic information content were recorded for SCoT 17 (0.411) and the the highest PIC values were detected for SCoT 14 (0.868) with an average of 0.751. A dendrogram was constructed from a genetic distance matrix based on profiles of the 37 SCoT primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 56 Tunisian castor genotypes were clustered into two main clusters (1 and 2). Of the 56 genotypes of Tunisian castor, 2 unique genotypes were separated (BA-5 and K-4). Genetically the closest were two genotypes from Tunisian region Souassi (S-2 and S-5) in subclaster 2bc. Results showed the utility of SCoT markers for estimation of genetic diversity of castor genotypes leading to genotype identification.
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Al-Qurainy, F., Khan, S., Nadeem, M., Tarroum, M. 2015. SCoT marker for the assessment of genetic diversity in Saudi Arabian date palm cultivars. Pakistan Journal of Botany, vol. 47, no. 2, p. 637-640.
Allan, G., Williams, A., Rabinowicz, P. D., Chan, A. .P., Ravel, J., Keim P. 2008. Worldwide genotyping of castor bean germplasm (Ricinus communis L.) using AFLPs and SSRs. Genet. Resour. Crop Evol., vol. 55, p. 365-378. https://doi.org/10.1007/s10722-007-9244-3 DOI: https://doi.org/10.1007/s10722-007-9244-3
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 Systematics and Evolution, vol. 298, no. 9, p. 1679-1688. https://doi.org/10.1007/s00606-012-0669-6 DOI: https://doi.org/10.1007/s00606-012-0669-6
Anjani, K. 2012. Castor genetic resources: a primary gene pool for exploitation. Ind Crops Prod., vol. 35, p. 1-14. https://doi.org/10.1016/j.indcrop.2011.06.011 DOI: https://doi.org/10.1016/j.indcrop.2011.06.011
Balážová, Ž., Gálová, Z., Vivodík, M., Petrovičová, L., Hornyák Gregáňová, R. 2017. Molecular variability of oat based on gene specific markers. Potravinarstvo Slovak Journal of Food Sciences, vol. 11, no. 1, p. 332-337. https://dx.doi.org/10.5219/774 DOI: https://doi.org/10.5219/774
Bošeľová, D. and Žiarovská, J. 2016. Direct PCR as the platform of Hedera helix, L. genotypying without the extraction of DNA. Journal of Central European Agriculture, vol. 17, no. 4, p. 941-949. https://doi.org/10.5513/jcea01/17.4.1795 DOI: https://doi.org/10.5513/JCEA01/17.4.1795
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 Molecular Biology Report, vol. 27, p. 86-93. https://doi.org/10.1007/s11105-008-0060-5 DOI: https://doi.org/10.1007/s11105-008-0060-5
Damodaram, T., Hegde, D. M. 2010. Oilseeds Situation: A Statistical Compendium. Directorate of Oilseeds Research, Hyderabad.
Etminan, A., Pour-Aboughadareh, A., Mohammadi, R., Ahmadi-Rad, A., Noori, A., Mahdavian Z. and Moradi Z. 2016. Applicability of start codon targeted (SCoT) and inter-simple sequence repeat (ISSR) markers for genetic diversity analysis in durum wheat genotypes. Biotechnology & Biotechnological Equipment, vol. 30, no. 6, p. 1075-1081, https://doi.org/10.1080/13102818.2016.1228478 DOI: https://doi.org/10.1080/13102818.2016.1228478
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. https://doi.org/10.1016/j.scienta.2014.03.010 DOI: https://doi.org/10.1016/j.scienta.2014.03.010
Foster J. T., Allan, G. J., Chan, A. P., Rabinowicz, P. D., Ravel, J., Jackson, P. J., Keim, P. 2010. Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis). BMC Plant Biol., vol. 10, p. 13-18. https://doi.org/10.1186/1471-2229-10-13 PMid:20082707 DOI: https://doi.org/10.1186/1471-2229-10-13
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 Systematics and Evolution, vol. 300, p. 1011-1020. https://doi.org/10.1007/s00606-013-0939-y DOI: https://doi.org/10.1007/s00606-013-0939-y
Gálová, Z., Vivodík, M., Balážová, Ž., Kuťka Hlozáková, T. 2015. Identification and differentiation of Ricinus communis L. using SSR markers. Potravinarstvo, vol. 9, no. 1, p. 556-561. https://doi.org/10.5219/516 DOI: https://doi.org/10.5219/516
Chai, X., Dong, R., Liu, W., Wang, Y. and Liu, Z. 2017. Optimizing sample size to assess the genetic diversity in common Vetch (Vicia sativa L.) populations using Start Codon Targeted (SCoT) markers. Molecules, vol. 22, p. 567-577. https://doi.org/10.3390/molecules22040567 DOI: https://doi.org/10.3390/molecules22040567
Cheema, N. M., Malik, M. A., Qadir, G. and Rabbani, M. A. 2010. Characterization of castor bean genotypes under various environments using SDS-PAGE of total seed storage proteins. Pak. J. Bot., vol. 42, no. 3, p. 1797-1805.
Jiang, L. F., Qi, X., Zhang, X. Q., Huang, L. K., Ma, X. and 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
Kallamadia, P. R., Ganga Rao Nadigatlab, V. P. R., Mulpuriba, 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
Kanti, M., Anjani, K., Usha Kiran, B. and Vivekananda, K. 2015. Agro-morphological and molecular diversity in Castor (Ricinus communis L.) germplasm collected from Andaman and Nicobar Islands, India. Czech J. Genet. Plant Breed., vol. 51, no.3, p. 96-109. https://doi.org/10.17221/205/2014-cjgpb DOI: https://doi.org/10.17221/205/2014-CJGPB
Luo, C., He, X. H., Chen, H., Ou, S. J., Gao, M. P. 2010. Analysis of diversity and relationships among mango cultivars using start codon targeted (SCoT) markers. Biochemical Systematics and Ecology, vol. 38, no. 6, p. 1176-1184. https://doi.org/10.1016/j.bse.2010.11.004 DOI: https://doi.org/10.1016/j.bse.2010.11.004
Malook, I., Jamil, M., Fayyaz, M., Rehman, H., Irshad, M., Bashar, K. U., Khan, S., Akhter, N., Aslam M. M. and Rha, E. S. 2016. Biochemical and molecular characterization of Castor bean (Ricinus Communis L.) collected from different climatic zones of Pakistan. Journal of Bio-Molecular Sciences, vol. 4, no. 1, p. 16-23.
Petrovičová, L., Balážová, Ž., Vivodík, M., Gálová, Z. 2017. Detection genetic variability of Secale cereale L. by SCoT markers. Potravinarstvo Slovak Journal of Food Sciences, vol. 11, no. 1, p. 197-202. https://dx.doi.org/10.5219/726 DOI: https://doi.org/10.5219/726
Ražná, K., Bežo, M., Hlavačková, L., Žiarovská, J., Miko, M., Gažo, J., Habán, M. 2016. MicroRNA (miRNA) in food resources and medicinal plant. Potravinarstvo, vol. 10, no. 1, p. 188-194. https://doi.org/10.5219/583 DOI: https://doi.org/10.5219/583
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 PMid:2575086 DOI: https://doi.org/10.1016/j.mgene.2015.01.003
Simões, K. S., Silva, S. A., Machado, E. L. and Silva, M. S. 2017. Genetic divergence in elite castor bean lineages based on TRAP markers. Genetics and Molecular Research, vol. 16, no. 3, p. 100-112. https://doi.org/10.4238/gmr16039776 DOI: https://doi.org/10.4238/gmr16039776
Simões, K. S., Silva, S. A., Machado, E. L. and Brasileiro, H. S. 2017. Development of TRAP primers for Ricinus communis L. Genetics and Molecular Research, vol. 16, no. 2, p. 100-113. https://doi.org/10.4238/gmr16029647 DOI: https://doi.org/10.4238/gmr16029647
Scholz, V., Silva, J. N. 2008. Prospects and risks of the use of castor oil as a fuel. Biomass Bioenerg, vol. 32, p. 95-100. https://doi.org/10.1016/j.biombioe.2007.08.004 DOI: https://doi.org/10.1016/j.biombioe.2007.08.004
Tsaballa, A., Ganopoulos, I., Timplalexi, A., Aliki, X., Bosmali, I., Irini, N., 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
Que, Y., Pan, Y., Lu, Y., Yang, C., Yang, Y., Huang, N. and Xu, L. 2014. Genetic analysis of diversity within a Chinese local sugarcane germplasm based on Start Codon Targeted Polymorphism. BioMed Research International., vol. 2014, p. 150-160. https://doi.org/10.1155/2014/468375 DOI: https://doi.org/10.1155/2014/468375
Vivodík, M., Balážová, Ž., Gálová, Z. and Kuťka Hlozáková, T. 2015. Differentiation of ricin using RAPD markers. Pak. J. Bot., vol. 47, no. 4, p. 1341-1345.
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
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
Wang, Ch., Li, G., Zhang, Z., Peng, M., Shang, Y., Luo, R., Chen, Y. 2013. Genetic diversity of castor bean (Ricinus communis L.) in Northeast China revealed by ISSR markers. Biochemical Systematics and Ecology, vol. 51, p. 301-307. https://doi.org/10.1016/j.bse.2013.09.017 DOI: https://doi.org/10.1016/j.bse.2013.09.017
Weber, J. L. 1990. Informativeveness of human (dC-dA)n x (dG-dT)n polymorphism. Genomics, vol. 7, no. 4, p. 524-530. https://doi.org/10.1016/0888-7543(90)90195-Z DOI: https://doi.org/10.1016/0888-7543(90)90195-Z
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. Molecular Biology Reports, vol. 38, no. 5, p. 3487-3494. https://doi.org/10.1007/s11033-010-0459-6 PMid:21104441 DOI: https://doi.org/10.1007/s11033-010-0459-6
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
Žiarovská, J., Kyseľ, M., Cimermanová, R., Knoteková, L. 2017. Effect of DNA extraction method in the Rosa Canina L. identification under different processing temperature. Potravinarstvo Slovak Journal of Food Sciences, vol. 11, no. 1, p. 190-196. https://dx.doi.org/10.5219/717 DOI: https://doi.org/10.5219/717
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