Article | . 2019 Vol. 37, Issue. 1
Development of a Core Set of SSR Markers for Cultivar Identification and Seed Purity Tests in Oriental Melon (Cucumis melo L. var. makuwa)

Department of Bioresources Engineering, Sejong University1
Department of Molecular Genetics, Dong-A University2
Plant Engineering Research Institute, Sejong University3

2019.. 119:129


Oriental melon (Cucumis melo L. var. makuwa), also called ‘Korean melon’ or ‘Chamoe’, is widely grown in East Asia, including Korea, Japan, and China. We used 521 simple sequence repeats (SSRs) to develop a core set of SSR markers as an effective tool for cultivar identification and seed purity tests in oriental melon. The polymorphism test using a subset of seven cultivars identified 20 expressed sequence tag SSR (EST-SSR) and 23 genomic SSR markers that showed high levels of polymorphism and simple segregation patterns. These SSR markers were used for DNA fingerprinting in additional 46 commercial cultivars. The average number of alleles per marker was 2.95 and 4.61 for the EST-SSR and genomic SSR markers in the 53 cultivars, respectively. For polymorphic information content (PIC), we found 0.411 to 0.816 with an average of 0.536 for the EST-SSR markers and 0.453 to 0.862 with an average of 0.568 for the genomic SSR markers. The unweighted pair group mean algorithm (UPGMA) dendrograms with the three sets of SSR markers (20 EST-SSR, 23 genomic SSR, and all 43 SSR markers) revealed that the 53 cultivars were separated into 4 to 5 major clusters. Furthermore, the set of all SSR markers was more effective at identifying the 53 cultivars relative to the other two marker sets. Therefore, the 43 SSR markers as a core set will be a valuable tool for several applications, including cultivar identification and seed purity tests in oriental melon.

1. Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181-186. doi:10.1139/g93-024  

2. Aragão FA, Torres Filho J, Nunes GH, Queiroz MA, Bordallo PN, Buso GS, Ferreira MA, Costa ZP, Bezerra Neto F (2013) Genetic divergence among accessions of melon from traditional agriculture of the Brazilian Northeast. Genet Mol Res 12:6356-6371. doi:10.4238/2013.December.6.3  

3. Chiba N, Suwabe K, Nunome T, Hirai M (2003) Development of microsatellite markers in melon (Cucumis melo L.) and their application to major cucurbit crops. Breeding Sci 53:21-27. doi:10.1270/jsbbs.53.21  

4. Christenhusz MJM, Byng JW (2016) The number of known plants species in the world and its annual increase. Phytotaxa 261:201. doi:10.11646/phytotaxa.261.3.1  

5. Danin-Poleg Y, Reis N, Tzuri G, Katzir N (2001) Development and characterization of microsatellite markers in Cucumis. Theor Appl Genet 102:61-72. doi:10.1007/s001220051618  

6. Fazio G, Staub JE, Chung SM (2002) Development and characterization of PCR markers in cucumber. J Amr Soc Hort Sci 127:545-557.   

7. Fernandez-Silva I, Eduardo I, Blanca J, Esteras C, Picó B, Nuez F, Arús P, Garcia-Mas J, Monforte AJ (2008) Bin mapping of genomic and EST-derived SSRs in melon (Cucumis melo L.). Theor Appl Genet 118:139-150. doi:10.1007/s00122-008-0883-3  

8. Gonzalo MJ, Oliver M, Garcia-Mas J, Monfort A, Dolcet-Sanjuan R, Katzir N, Arus P, Monforte AJ (2005) Simple-sequence repeat markers used in merging linkage maps of melon (Cucumis melo L.). Theor Appl Genet 110:802-811. doi:10.1007/s00122-004-1814-6  

9. Guo W, Cai C, Wang C, Han Z, Song X, Wang K, Niu X, Wang C, Lu K, et al (2007) A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium. Genetics 176:527-541. doi:10.1534/genetics.107.070375  

10. Hu J, Wang L, Li J (2011) Comparison of genomic SSR and EST-SSR markers for estimating genetic diversity in cucumber. Biol Plant 55:577-580. doi:10.1007/s10535-011-0129-0  

11. Kim H-A, Shin A-Y, Lee M-S, Lee H-J, Lee H-R, Ahn J, Nahm S, Jo S-H, Park J-M, et al (2016) De novo transcriptome analysis of Cucumis melo L. var. makuwa. Mol Cells 39:141-148. doi:10.14348/molcells.2016.2264  

12. Kong Q, Xiang C, Yang J, Yu Z (2011) Genetic variations of Chinese melon landraces investigated with EST-SSR markers. Hortic Environ Biotechnol 52:163-169. doi:10.1007/s13580-011-0087-7  

13. Kong Q, Xiang C, Yu Z, Zhang C, Liu F, Peng C, Peng X (2007) Mining and charactering microsatellites in Cucumis melo expressed sequence tags from sequence database. Mol Ecol Notes 7:281-283. doi:10.1111/j.1471-8286.2006.01580.x  

14. Kwon Y-S, Choi K-J (2013) Construction of a DNA profile database for commercial cucumber (Cucumis sativus L.) cultivars using microsatellite marker. J Korean Soc Hortic Sci 31:344-351. doi:10.7235/hort.2013.13008  

15. Leida C, Moser C, Esteras C, Sulpice R, Lunn JE, de Langen F, Monforte AJ, Pico B (2015) Variability of candidate genes, genetic structure and association with sugar accumulation and climacteric behavior in a broad germplasm collection of melon (Cucumis melo L.). BMC Genet 16:28. doi:10.1186/s12863-015-0183-2  

16. Lester G (1997) Melon (Cucumis melo L.) fruit nutritional quality and health functionality. HortTechnology 7:222-227. doi:10.21273/ HORTTECH.7.3.222  

17. Lim TK (2012) Edible medicinal and non-medicinal plants, Vol 2. Fruits. Springer, Dordrecht, Netherlands, pp 219-221  

18. Liu L, Kakihara F, Kato M (2004) Characterization of six varieties of Cucumis melo L. based on morphological and physiological characters, including shelf-life of fruit. Euphytica 135:305. doi:10.1023/B:EUPH.0000013330.66819.6f  

19. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209-220  

20. Mondini L, Noorani A, Pagnotta MA (2009) Assessing plant genetic diversity by molecular tools. Diversity 1:19–35. doi:10.3390/d1010019  

21. Mujaju C, Sehic J, Nybom H (2013) Assessment of EST-SSR markers for evaluating genetic diversity in watermelon accessions from Zimbabwe. Am J Plant Sci 4:1448-1456. doi:10.4236/ajps.2013.47177  

22. Natarajan S, Kim HT, Thamilarasan SK, Veerappan K, Park JI, Nou IS (2016) Whole genome resequencing and characterization of powdery mildew disease-associated allelic variation in melon. PLoS ONE 11:e0157524. doi:10.1371/journal.pone.0157524  

23. Nunez-Palenius HG, Gomez-Lim M, Ochoa-Alejo N, Grumet R, Lester G, Cantliffe DJ (2008) Melon fruits: genetic diversity, physiology, and biotechnology features. Crit Rev Biotechnol 28:13-55. doi:10.1080/07388550801891111  

24. Park I, Kim J, Lee J, Kim S, Cho O, Yang K, Ahn J, Nahm S, Kim H (2013) Development of SSR markers by next-generation sequencing of Korean landraces of chamoe (Cucumis melo var. makuwa). Mol Biol Rep 40:6855-6862. doi:10.1007/s11033-013-2803-0  

25. Parthiban S, Govindaraj P, Senthilkumar S (2018) Comparision of relative efficiency of genomic SSR and EST-SSR markers in estimating genetic diversity in sugarcane. 3 Biotech 8:144. doi:10.1007/s13205-018-1172-8   

26. Phan NT, Kim M-K, Sim S-C (2016) Genetic variations of F1 tomato cultivars revealed by a core set of SSR and InDel markers. Sci Hortic 212:155-161. doi:10.1016/j.scienta.2016.09.043  

27. Ritschel PS, Lins TCdL, Tristan RL, Buso GSC, Buso JA, Ferreira ME (2004) Development of microsatellite markers from an enriched genomic library for genetic analysis of melon (Cucumis melo L.). BMC Plant Biol 4:9. doi:10.1186/1471-2229-4-9  

28. Rohlf FJ (2008) NTSYSpc: Numerical taxonomy system, version 2.20. Exeter Publishing, Setauket, NY, USA  

29. Sim S-C, Hong J-H, Kwon Y-S (2016) DNA profiling of commercial pumpkin cultivars using simple sequence repeat polymorphisms. Hortic Environ Biotechnol 56:811-820. doi:10.1007/s13580-015-0123-0  

30. Sim S-C., Nguyen NN, Kim N, Kim J, Park Y (2018) Whole-genome resequencing reveals genome-wide single nucleotide polymorphisms between orange-fleshed and green-fleshed melons. Hortic Environ Biotechnol 59:275. doi:10.1007/s13580-018-0030-2  

31. Sneath PHA, Sokal RR (1973) Numerical taxonomy: The principles and practice of numerical classification. W.H. Freeman and Company, San Francisco, CA, USA  

32. Tabbasam N, Zafar Y, Mehboob-ur-Rahman (2013) Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium. Plant Syst Evol 300:559–75. doi:10.1007/s00606-013-0891-x  

33. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48-55. doi:10.1016/j.tibtech.2004.11.005  

34. Vieira ML, Santini L, Diniz AL, Munhoz Cde F (2016) Microsatellite markers: what they mean and why they are so useful. Genet Mol Biol 39:312-328. doi:10.1590/1678-4685-GMB-2016-0027  

35. Wolbang CM, Fitos JL, Treeby MT (2008) The effect of high pressure processing on nutritional value and quality attributes of Cucumis melo L. Innov Food Sci Emerg Technol 9:196-200. doi:10.1016/j.ifset.2007.08.001  

36. Zeb A (2016) Phenolic profile and antioxidant activity of melon (Cucumis melo L.) seeds from Pakistan. 5:67.  doi:10.3390/foods5040067  

37. Zhang M, Mao W, Zhang G, Wu F (2014) Development and characterization of polymorphic EST-SSR and genomic SSR markers for tibetan annual wild barley. PLoS ONE 9:e94881. doi:10.1371/journal.pone.0094881