Transferability of Microsatellite Markers from Cucumber (Cucumis sativus) to Seven Cultivated Cucurbit Crops
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Published:
Feb 19, 2020
Keywords:
Cucumber Microsatellites Transferability Cucurbit
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Abstract
Plant breeding relies heavily on genetic resources with high genetic diversity presence in nature. Lack of genomic resources can slow down molecular characterization of any plant species. Transferability of SSR markers is when SSRs developed in one species can cross amplify in other species. Cucumber is an economically important fruit crop in the family Cucurbitaceae with many already developed Simple Sequence Repeat (SSR). We evaluated 515 cucumber-derived SSR markers in seven less studied cucurbit crops consisting of fifty one accessions. The transferability rate was 6.94% in pumpkin, 17.09% in wax gourd, 19.81% in bottle gourd, 13.27% in luffa, 45.05% in melon, 18.55% in watermelon and 8.76% in bitter gourd. Genetic diversity analysis classified tested plant species into five clades corresponding to four tribes. The result indicated that cucumber derived genetic tools are applicable to decipher genetic information in other cucurbit species.
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Natenuch, S., Nguyen, C., Jantasuriyarat, C., & Samipak, S. (2020). Transferability of Microsatellite Markers from Cucumber (Cucumis sativus) to Seven Cultivated Cucurbit Crops. Applied Science and Engineering Progress, 13(1), 86–93. Retrieved from https://ph02.tci-thaijo.org/index.php/ijast/article/view/240019
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References
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[37] J. Wang, P. Sun, Y. Li, Y. Liu, N. Yang, J. Yu, X. Ma, S. Sun, R. Xia, X. Liu, D. Ge, S. Luo, Y. Liu, Y. Kong, X. Cui, T. Lei, L. Wang, Z. Wang, W. Ge, L. Zhang, X. Song, M. Yuan, D. Guo, D. Jin, W. Chen, Y. Pan, T. Liu, G. Yang, Y. Xiao, J. Sun, C. Zhang, Z. Li, H. Xu, X. Duan, S. Shen, Z. Zhang, S. Huang, and X. Wang, “An overlooked paleotetraploidization in Cucurbitaceae,” Molecular Biology and Evolution, vol. 35, no. 1, pp.16–26, Jan. 2018.
[2] H. S. Paris, “Overview of the origins and history of the five major cucurbit crops: Issues for ancient DNA analysis of archaeological specimens,” Vegetation History and Archaeobotany, vol. 25, no. 4, pp. 405–414, Fab. 2016.
[3] Food and Architecture Organization of the United Nation. (2019, May). Cucumber Production. FAO. Rome, Italy [Online]. Available: http://faostat.fao.org/
[4] A. Levi, C. E. Thomas, M. Newman, O. U. K. Reddy, X. Zhang, and Y. Xu, “ISSR and AFLP markers differ among american watermelon cultivars with limited genetic diversity,” Journal of the American Society for Horticultural Science, vol. 129, no. 4, pp. 553–558, Jul. 2004.
[5] T. K. Behera, A. K. Singh, and J. E. Staub, “Comparative analysis of genetic diversity in Indian bitter gourd (Momordica charantia L.) using RAPD and ISSR markers for developing crop improvement strategies,” Scientia Horticulturae, vol. 115, no. 3, pp. 209–217, Feb. 2008.
[6] T. Horejsi, J. M. Box, and J. E. Staub, “Efficiency of randomly amplified polymorphic DNA to sequence characterized amplified region marker conversion and their comparative polymerase chain reaction sensitivity in cucumber,” Journal of the American Society for Horticultural Science, vol. 124, no. 2, pp. 128–135, Mar. 1999.
[7] Y. Danin-Poleg, N. Reis, S. Baudracco-Arnas, M. Pitr, J. E. Staub, M. Oliver, P. Arus, C. M. deVicente, and N. Katzir, “Simple sequence repeats in Cucumis mapping and map merging,” Genome, vol. 43, no.6, pp. 963–974, Dec. 2000.
[8] G. Fazio, J. E. Staub, and S. M. Chung, “Development and characterization of PCR markers in cucumber (Cucumis sativus L.),” Journal of the American Society for Horticultural Science, vol. 127, no 4. , pp. 545–557, Jul. 2002.
[9] M. A. Yeboah, C. Xuehao, C. R. Feng, G. Liang, and M. Gu, “A genetic linkage map of cucumber (Cucumis sativus L) combining SRAP and ISSR markers,” African Journal of Biotechnology, vol. 6, no. 24, pp. 2784–2791, Dec. 2007.
[10] I. A. Mohammed, A. N. Gumaa, N. M. Kamal, Y. S. Alnor, and A. M. Ali, “Genetic diversity among some cucurbits species determined by random amplified polymorphic DNA RAPD Marker,” International Journal of Plant Research, vol. 2, no.4, pp. 131–137, Feb. 2012.
[11] M. L. C. Vieira, L. Santini, A .L. Diniz, and C. F. Munhoz, “Microsatellite markers: What they mean and why they are so useful,” Genetics and Molecular Biology, vol. 39, no. 3, pp. 312–328, May 2016.
[12] A. S. Mason, “SSR genotyping,” in Plant Genotyping Methods and Protocols. New York, 2015, pp. 77–89.
[13] A. Grover, B. Ramesh, and P. C. Sharma, “Development of microsatellite markers in potato and their transferability in some members of Solanaceae,” Physiology and Molecular Biology of Plants, vol. 15, no. 4, pp. 343–358, Oct. 2009.
[14] C. Jantasuriyarat, S. Ritchuay, P. Pattarawat, P. S. Huehne, and S. Kate-Ngam, “Development and transferability of EST-SSR and transferability of genomic SSR markers for genetic diversity assessment of Doritis,” Biochemical Systematics and Ecology, vol. 45, pp. 57–65, Dec. 2012.
[15] X. C. Zhu, H. W. Wu, H. Raman, D. Lemerle, R. Stanton, and G. E. Burrows, “Evaluation of simple sequence repeat (SSR) markers from Solanum crop species for Solanum elaeagnifolium,” Weed Research, vol. 52, no.3, pp. 217–223, Jun. 2012.
[16] S. I. C. Carvalho, C. F. Ragassi, I. B. Oliveira, Z. P. S. Amaral, F. J. B. Reifschneider, F. G. Faleiro, and G. S. C. Buso, “Transferability of microsatellite markers of Capsicum annuum L. to C. frutescens L. and C. chinense Jacq.,” Genetics and Molecular Research, vol. 14, no.3, pp. 7937– 7946, Jul. 2015.
[17] G. S. C. Buso, A. M. M. Reis, Z. P. S. Amaral, and M. E. Ferreira, “Novel and highly informative Capsicum SSR markers and their cross-species transferability,” Genetic and Molecular Research, vol. 15, no. 3, pp. 1–13, Sep. 2016.
[18] T. Disasa, T. Feyissa, and D. Sertse, “Transferability of Sorghum Microsatellite Markers to Bamboo and Detection of Polymorphic Markers,” The Open Biotechnology Journal, vol. 10, pp. 223–233, Jan. 2016.
[19] C. Kuleung, P. S. Baenziger, and I. Dweikat, “Transferability of SSR markers among wheat, rye, and triticale,” Theoretical and Applied Genetics, vol. 108, no. 6, pp. 1147–1150, Apr. 2004.
[20] S. Whankaew, S. Kanjanawattanawong, C. Phumichai, D. R. Smith, J. Narangajavana, and K. Triwitayakorn, “Cross-genera transferability of (simple sequence repeat) SSR markers among cassava (Manihot esculenta Crantz), rubber tree (Hevea brasiliensis Muell. Arg.) and physic nut (Jatropha curcas L.),” African Journal of Biotechnology, vol. 10, no.10, pp. 1768–1776, Mar. 2011.
[21] M. Verma and L. Arya, “Development of EST-SSRs in watermelon (Citrullus lanatus var. lanatus) and their transferability to Cucumis spp.,” Journal of Horticultural Science and Biotechnology, vol. 83, no. 6, pp. 732–736, Nov. 2008.
[22] L. Gong, G. Stift, R. Kofler, M. Pachner, and T. Lelley, “Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L.,” Theoretical and Applied Genetics, vol. 117, no.1, pp. 37–48, Jun. 2008.
[23] Y. Ji, Y. Luo, B. Hou, W. Wang, J. Zhao, L. Yang, Q. Xue, and X. Ding, “Development of polymorphic microsatellite loci in Momordica charantia (Cucurbitaceae) and their transferability to other cucurbit species,” Scientia Horticulturae, vol. 140, pp. 115–118, Jun. 2012.
[24] M. Yildiz, H. E. Cuevas, S. Sensoy, C. Erdinc, and F. S.Baloch, “Transferability of Cucurbita SSR markers for genetic diversity assessment of Turkish bottle gourd (Lagenaria siceraria) genetic resources,” Biochemical Systematics and Ecology, vol. 59, pp. 45–53, Jan. 2015.
[25] N.Watcharawongpaiboon and J. Chunwongse, “Development and characterization of microsatellite markers from an enriched genomic library of cucumber (cucumis sativus),” Plant breeding, vol. 127, no.1, pp. 74–81, Feb. 2008.
[26] Y. Ren, Z. Zhang, J. Liu, J. E. Staub, Y. Han, Z. Cheng, X. Li, J. Lu, H. Miao, H. Kang, B. Xie, X. Gu, X. Wang, Y. Du, W. Jin, and S. Huang, “An integrated genetic and cytogenetic map of the cucumber genome,” PLoS ONE, vol. 4, no. 6, pp. 1–8, Jun. 2009.
[27] M. Bhawna, Z. Abdin, L. Arya, and M. Verma, “Transferability of cucumber microsatellite markers used for phylogenetic analysis and population structure study in bottle gourd (Lagenaria siceraria (Mol.) Standl.),” Applied Biochemistry and Biotechnology, vol. 175, no. 4, pp. 2206–2223, Dec. 2014.
[28] S. Pandey, W. A. Ansari, B. R. Choudhary, M. Pandey, S. E. Jena, A. H. Singh, R. K. Dubey, and B. Singh, “Microsatllite analysis of genetic diversity and population structure of hermaphodite ridge gourd (Luffa hermaphrodita),” 3 Biotech, vol. 8, no. 1, pp. 17–25, Dec. 2017.
[29] J. J. Doyle and J. L.Doyle, “A rapid DNA isolation procedure for small quantities of fresh leaf tissue,” Phytochemical Bulletin, vol. 19, no. 1, pp. 11–15, 1987.
[30] S. Huang, R. Li, Z. Zhang, L. Li, X. Gu, W. Fan, and S. Li., “The genome of the cucumber, Cucumis sativus L.,” Nature Genetic, vol. 41, no. 12, pp. 1275–1281. Dec. 2009.
[31] P. F. Cavagnaro, D. A. Senalik, L. Yang, P. W. Simon, T. T. Harkins, C. D. Kodira, S. Huang, and Y. Weng, “Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.),” BMC Genomics, vol. 11, pp. 569–586, Oct. 2010.
[32] H. Benbouza, J. M. Jacquemin, J. P. Baudoin, and G. Mergeai, “Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels,” Biotechnology, Agronomy, Society and Environment, vol. 10, no. 2, pp. 77–81, Jan. 2006.
[33] F. J. Rohlf, “NTSYS-pc: Numerical Taxonomy System Ver. 2.2,” Exeter Software, New York, USA, 2000.
[34] I. V. Yap and R. J. Nelson, Winboot: A Program for Performing Bootstrap Analysis of Binary Data to Determine the Confidence Limits of UPGMA-based Dendrograms. Manila, Philippines: International Rice Research Institute, 1996.
[35] H. Schaefer and S. S. Renner, “Phylogenetic relationships in the order Cucurbitales and a new classification of the gourd family (Cucurbitaceae),” Taxon, vol. 60, no. 1, pp. 122–138, Feb. 2011.
[36] S. S. Renner and H. Schaefer, “Phylogeny and evolution of the Cucurbitaceae,” Genetics and Genomics of Cucurbitaceae, vol. 20, pp. 13–23, 2016.
[37] J. Wang, P. Sun, Y. Li, Y. Liu, N. Yang, J. Yu, X. Ma, S. Sun, R. Xia, X. Liu, D. Ge, S. Luo, Y. Liu, Y. Kong, X. Cui, T. Lei, L. Wang, Z. Wang, W. Ge, L. Zhang, X. Song, M. Yuan, D. Guo, D. Jin, W. Chen, Y. Pan, T. Liu, G. Yang, Y. Xiao, J. Sun, C. Zhang, Z. Li, H. Xu, X. Duan, S. Shen, Z. Zhang, S. Huang, and X. Wang, “An overlooked paleotetraploidization in Cucurbitaceae,” Molecular Biology and Evolution, vol. 35, no. 1, pp.16–26, Jan. 2018.