SSR analysis to assess genetic diversity and population structure in parthenocarpy cucumber (Cucumis sativus L.)
DOI:
https://doi.org/10.24154/jhs.v18i1.2146Keywords:
Cucumber, Genetic diversity, Polymorphism, Population structure, SSR MarkersAbstract
The genetic diversity and population relationship was determined in 14 genotypes of parthenocarpic cucumber (Cucumis sativus L.) using simple sequence repeats (SSR) markers. In this study, fifty-nine SSR markers comprehensively showed polymorphism among cucumber genotypes. Total 252 alleles were identified with an average of 4.27 alleles per locus, while the polymorphism information content (PIC) of the primers ranged from 0.34 to 0.84 with a mean value of 0.62. The major allele frequency and heterozygosity ranged from 0.21 to 0.75 and from 0.43 to 0.89, respectively. Maximum major allele frequency was reported with primer Cs- Female-4, whereas the maximum value of polymorphic information content was found with the primer SSR11742. The dendrogram clustered genotypes into two main groups A and B with 8 and 6 genotypes, respectively. Jaccard’s similarity coefficient ranged from 0.63 to 0.86 with maximum similarity between genotypes DDPCG3 and PLP-1, whereas minimum similarity was observed between DDPCG8 and PLP Gy-1-08B. The population structure revealed three sub-populations with some admixtures. Principal coordinate analysis (PCoA) with SSR markers revealed that the genotypes were uniformly distributed across the two axes in both the plots with 41.76% of cumulative variation. The genetic divergence within indigenous genotypes allow genotypic identification, gene mapping and cloning for improvement in cucumber breeding.
References
Dar, A. A., Mahajan, R., Lay, P. and Sharma, S. 2017. Genetic diversity and population structure of Cucumis sativus L. by using SSR markers. 3 Biotech., 7: 307. DOI: https://doi.org/10.1007/s13205-017-0944-x
Doyle, J. J. and Doyle, J. L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull., 19: 11-15.
Evanno, G., Regnaut. S. and Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol., 14: 2611-2620. DOI: https://doi.org/10.1111/j.1365-294X.2005.02553.x
Falush, D., Stephens, M. and Pritchard, J. K. 2003. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics, 164: 1567-1587. DOI: https://doi.org/10.1093/genetics/164.4.1567
Garzon-Martinez, G. A., Osorio-Guarin, J. A., Delgadillo-Duran, P., Mayorga, F., Enciso- Rodriguez, F. E., Landsman, D., Marino- Ramirez, L. and Barrero, L. S. 2015. Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers. Plant Gene, 4: 29-37. DOI: https://doi.org/10.1016/j.plgene.2015.09.003
Hu, J., Wang, L. and Li, J. 2011. Comparison of genomic SSR and EST-SSR markers for estimating genetic diversity in cucumber. Biol. Plant., 55: 577-580. DOI: https://doi.org/10.1007/s10535-011-0129-0
Kaur, M. and Sharma, P. 2021. Recent advances in cucumber (Cucumis sativus L.). J. Hortic. Sci. Biotechnol., DOI: https://doi.org/10.1080/14620316.2021.1945956
Lv, J., Qi, J., Shi, Q., Shen, D., Zhang, S., Treuren, R., Dooijeweert, W. and Zhang, Z. 2012. Genetic diversity and population structure of cucumber (Cucumis sativus L.). PLoS One, 7: e46919. DOI: https://doi.org/10.1371/journal.pone.0046919
Mahajan, R., Zargar, S. M., Singh, R., Salgotra, R. K., Farhat, S. and Sonah, H. 2016. Population structure analysis and selection of core set among common bean genotypes from Jammu and Kashmir., India. Appl. Biochem., 182: 16-28. DOI: https://doi.org/10.1007/s12010-016-2307-1
Normohamadi, S., Solouki, M. and Heidari, F. 2017. Diversity in cucumber genotypes based on morphological traits and SSR molecular markers. Biosci Biotech. Res. Asia 14: 775-782. DOI: https://doi.org/10.13005/bbra/2507
Pandey, S., Ansari, W.A., Atri, N., Singh, B., Gupta, S. and Bhat, K.V. 2016. Standardization of screening technique and evaluation of muskmelon genotypes for drought tolerance. Plant Genet Resour Charact Util. DOI: https://doi.org/10.1017/S1479262116000253
Pandey, S., Ansari, W.A., Mishra, V. K., Singh, A.K. and Singh, M. 2013. Genetic diversity in Indian cucumber based on microsatellite and morphological markers. Biochem. Syst. Ecol., 51: 19-27. DOI: https://doi.org/10.1016/j.bse.2013.08.002
Pandey, S., Ansari, W. A., Pandey, M. and Singh, B. 2017. Genetic diversity of cucumber estimated by morpho-physiological and EST-SSR markers. Physiol. Mol. Biol. Plants.
Pandey, S., Ansari, W.A., Pandey, M. and Singh, B., 2018. Genetic diversity of cucumber estimated by morpho-physiological and EST-SSR markers. Physiol. Mol. Biol. Plants, 24: 135-146. DOI: https://doi.org/10.1007/s12298-017-0489-9
Park, G., Choi, Y., Jung, J. K., Shim, E. J., Kang, M. Y., Sim, S. C., Chung, S. M., Lee, G. P. and Park, Y. 2021. Genetic diversity assessment and cultivar identification of cucumber (Cucumis sativus L.) using the fluidigm single nucleotide polymorphism assay. Plants, 10: 395. DOI: https://doi.org/10.3390/plants10020395
Perrier, X. and Jacquemoud, C. 2006. DARwin software.
Pritchard, J. K., Stephens, M. and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155: 945-959. DOI: https://doi.org/10.1093/genetics/155.2.945
Sensoy, S., Buyukalaca, S. and Abak, K. 2007. Evaluation of genetic diversity in Turkish melons (Cucumis melo L.) based on phenotypic characters and RAPD markers. Genet. Resour. Crop Evol., 54: 1351-1365. DOI: https://doi.org/10.1007/s10722-006-9120-6
Someh, M., Kiani, G., Ranjbar, G. A. and Alavi, S. M. 2016. Assessment of genetic diversity in cucumber varieties using RAPD markers. J. Appl. Hortic., 18: 64-67. DOI: https://doi.org/10.37855/jah.2016.v18i01.14
Spooner, D. M., Anderson, G. J. and Jansen, R. K. 1993. Chloroplast DNA evidence for the inter- relationships of tomatoes, potatoes, and pepinos (Solanaceae). Am. J. Bot., 80: 676. DOI: https://doi.org/10.1002/j.1537-2197.1993.tb15238.x
Valcarcel, J. V., Perez-de-Castro, A., Diez, M. J. and Peiro, R. 2018. Molecular characterization of the cucumber (Cucumis sativus L.) accessions held at the COMAV’s genebank. Spanish J. Agric. Res., 16: 2171-9292. DOI: https://doi.org/10.5424/sjar/2018161-12351
Yang, Y. T., Liu, Y., Qi, F., Xu, L. L. and Li, X. Z. 2015. Assessment of genetic diversity of cucumber cultivars in China based on simple sequence repeats and fruit traits. Genet. Mol. Res., 14: 19028-19039 DOI: https://doi.org/10.4238/2015.December.29.10
Yuan, X. J., Pan, J. S., Cai, R., Guan, Y., Liu, L. Z., Zhang, W. W., Li, Z., He, H. L., Zhang, C., Si, L. T. and Zhu, L. H. 2008. Genetic mapping and QTL analysis of fruit and flower related traits in cucumber (Cucumis sativus L.) using recombinant inbred lines. Euphytica, 164: 473-491. DOI: https://doi.org/10.1007/s10681-008-9722-5
Downloads
Published
Issue
Section
License
Copyright (c) 2023 Manpreet Kaur, Parveen Sharma, Akhilesh Sharma , Hem Lata , Nimit Kumar
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
Authors retain copyright. Articles published are made available as open access articles, distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. 
This journal permits and encourages authors to share their submitted versions (preprints), accepted versions (postprints) and/or published versions (publisher versions) freely under the CC BY-NC-SA 4.0 license while providing bibliographic details that credit, if applicable.
How to Cite
. 
