Molecular Biology Reports

, Volume 40, Issue 12, pp 6855–6862 | Cite as

Development of SSR markers by next-generation sequencing of Korean landraces of chamoe (Cucumis melo var. makuwa)

  • Inkyu Park
  • Jungeun Kim
  • Jeongyeo Lee
  • Sewon Kim
  • Okhee Cho
  • Kyungbong Yang
  • Jongmoon Ahn
  • Seokhyeon Nahm
  • HyeRan KimEmail author


The oriental melon (Cucumis melo var. makuwa), called ‘chamoe’ in Korean, is a popular fruit crop cultivated mainly in Asia and a high-market value crop in Korea. To provide molecular breeding resources for chamoe, we developed and characterized genomic SSR markers from the preliminary Illumina read assemblies of Gotgam chamoe (one of the major landraces; KM) and SW3 (the breeding parent). Mononucleotide motifs were the most abundant type of markers, followed by di-, tri-, tetra-, and pentanucleotide motifs. The most abundant dinucleotide was AT, followed by AG and AC, and AAT was the most abundant trinucleotide motif in both assemblies. Following our SSR-marker development strategy, we designed a total of 370 primer sets. Of these, 236 primer sets were tested, exhibiting 93 % polymorphism between KM and SW3. Those polymorphic SSRs were successfully amplified in the netted and Kirkagac melons, which respectively exhibited 81 and 76 % polymorphism relative to KM, and 32 and 38 % polymorphism relative to SW3. Seven selected SSR markers with a total of 17 alleles (2–3 alleles per locus) were used to distinguish between KM, SW3, and four chamoe cultivars. Our results represent the first attempt to provide genomic resources for Korean landraces for the purposes of chamoe breeding, as well as to discover a set of SSR markers capable of discriminating chamoe varieties from Korea and the rest of Asia, which possess little genetic diversity. This study establishes a highly efficient strategy for developing SSR markers from preliminary Illumina assemblies of AT-rich genomes.


Illumina preliminary assembly Oriental melon SSR Genetic diversity 



This work was financially supported by grants from the Next-Generation Bio Green 21 Program (No. PJ008200) funded by the Rural Development Administration of the Republic of Korea, and the Cabbage Genomics Assisted-Breeding Support Center (CGC), funded by the Ministry for Food, Agriculture, Forestry, and Fisheries of the Republic of Korea.

Supplementary material

11033_2013_2803_MOESM1_ESM.docx (21 kb)
Supplementary material 1 (DOCX 20 kb)
11033_2013_2803_MOESM2_ESM.docx (33 kb)
Supplementary material 2 (DOCX 33 kb)
11033_2013_2803_MOESM3_ESM.docx (60 kb)
Supplementary material 3 (DOCX 59 kb)
11033_2013_2803_MOESM4_ESM.xlsx (12.4 mb)
Supplementary material 4 (XLSX 12656 kb)
11033_2013_2803_MOESM5_ESM.doc (44 kb)
Supplementary material 5 (DOC 44 kb)


  1. 1.
    Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB (2011) The real cost of sequencing: higher than you think! Genome Biol 12(8):125PubMedCrossRefGoogle Scholar
  2. 2.
    Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27(9):522–530PubMedCrossRefGoogle Scholar
  3. 3.
    Collard BC, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philosophical transactions of the Royal Society of London Series B. Biological sciences 363(1491):557–572PubMedCrossRefGoogle Scholar
  4. 4.
    Moose SP, Mumm RH (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147(3):969–977PubMedCrossRefGoogle Scholar
  5. 5.
    Paux E, Sourdille P, Mackay I, Feuillet C (2012) Sequence-based marker development in wheat: advances and applications to breeding. Biotechnol Adv 30(5):1071–1088PubMedCrossRefGoogle Scholar
  6. 6.
    Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12(10):4127–4138PubMedCrossRefGoogle Scholar
  7. 7.
    Saha MC, Cooper JD, Mian MA, Chekhovskiy K, May GD (2006) Tall fescue genomic SSR markers: development and transferability across multiple grass species. TAG Theoretical and applied genetics Theoretische und angewandte Genetik 113(8):1449–1458PubMedCrossRefGoogle Scholar
  8. 8.
    Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, Singh L (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. TAG Theoretical and applied genetics Theoretische und angewandte Genetik 114(2):359–372PubMedCrossRefGoogle Scholar
  9. 9.
    Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11(1):31–46PubMedCrossRefGoogle Scholar
  10. 10.
    Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, McCown B, Harbut R, Simon P (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 99(2):193–208PubMedCrossRefGoogle Scholar
  11. 11.
    Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23(1):48–55PubMedCrossRefGoogle Scholar
  12. 12.
    Kim J, Choi J-P, Ahmad R, Oh S-K, Kwon S-Y, Hur C-G (2012) RISA: a new web-tool for Rapid Identification of SSRs and Analysis of primers. Genes Genom 34(6):583–590CrossRefGoogle Scholar
  13. 13.
    Sebastian P, Schaefer H, Telford IR, Renner SS (2010) Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia. Proc Natl Acad Sci USA 107(32):14269–14273PubMedCrossRefGoogle Scholar
  14. 14.
    Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, Gonzalez VM, Henaff E, Camara F, Cozzuto L, Lowy E, Alioto T, Capella-Gutierrez S, Blanca J, Canizares J, Ziarsolo P, Gonzalez-Ibeas D, Rodriguez-Moreno L, Droege M, Du L, Alvarez-Tejado M, Lorente-Galdos B, Mele M, Yang L, Weng Y, Navarro A, Marques-Bonet T, Aranda MA, Nuez F, Pico B, Gabaldon T, Roma G, Guigo R, Casacuberta JM, Arus P, Puigdomenech P (2012) The genome of melon (Cucumis melo L.). Proc Natl Acad Sci USA 109(29):11872–11877PubMedCrossRefGoogle Scholar
  15. 15.
    van Leeuwen H, Monfort A, Zhang H-B, Puigdomenech P (2003) Identification and characterisation of a melon genomic region containing a resistance gene cluster from a constructed BAC library. Microcolinearity between Cucumis melo and Arabidopsis thaliana. Plant Mol Biol 51(5):703–718PubMedCrossRefGoogle Scholar
  16. 16.
    Diaz A, Fergany M, Formisano G, Ziarsolo P, Blanca J, Fei Z, Staub JE, Zalapa JE, Cuevas HE, Dace G, Oliver M, Boissot N, Dogimont C, Pitrat M, Hofstede R, van Koert P, Harel-Beja R, Tzuri G, Portnoy V, Cohen S, Schaffer A, Katzir N, Xu Y, Zhang H, Fukino N, Matsumoto S, Garcia-Mas J, Monforte AJ (2011) A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.). BMC Plant Biol 11:111PubMedCrossRefGoogle Scholar
  17. 17.
    Deleu W, Esteras C, Roig C, Gonzalez-To M, Fernandez-Silva I, Gonzalez-Ibeas D, Blanca J, Aranda MA, Arus P, Nuez F, Monforte AJ, Pico MB, Garcia-Mas J (2009) A set of EST-SNPs for map saturation and cultivar identification in melon. BMC Plant Biol 9:90PubMedCrossRefGoogle Scholar
  18. 18.
    Fernandez-Silva I, Eduardo I, Blanca J, Esteras C, Pico B, Nuez F, Arus P, Garcia-Mas J, Monforte AJ (2008) Bin mapping of genomic and EST-derived SSRs in melon (Cucumis melo L.). TAG Theoretical and applied genetics Theoretische und angewandte Genetik 118(1):139–150PubMedCrossRefGoogle Scholar
  19. 19.
    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.). TAG Theoretical and applied genetics Theoretische und angewandte Genetik 110(5):802–811PubMedCrossRefGoogle Scholar
  20. 20.
    Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24(5):713–714PubMedCrossRefGoogle Scholar
  21. 21.
    Smit AF (1999) Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 9(6):657–663PubMedCrossRefGoogle Scholar
  22. 22.
    Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386PubMedGoogle Scholar
  23. 23.
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410PubMedGoogle Scholar
  24. 24.
    Kent WJ (2002) BLAT–the BLAST-like alignment tool. Genome Res 12(4):656–664. doi: 10.1101/gr.229202 Article published online before March 2002PubMedGoogle Scholar
  25. 25.
    Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SE et al (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138(4):1251–1274PubMedGoogle Scholar
  26. 26.
    Lawson MJ, Zhang L (2006) Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol 7(2):R14PubMedCrossRefGoogle Scholar
  27. 27.
    Hong Y, Chen X, Liang X, Liu H, Zhou G, Li S, Wen S, Holbrook CC, Guo B (2010) A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome. BMC Plant Biol 10:17PubMedCrossRefGoogle Scholar
  28. 28.
    Xin D, Sun J, Wang J, Jiang H, Hu G, Liu C, Chen Q (2012) Identification and characterization of SSRs from soybean (Glycine max) ESTs. Mol Biol Rep 39(9):9047–9057PubMedCrossRefGoogle Scholar
  29. 29.
    Wang Z, Yan H, Fu X, Li X, Gao H (2012) Development of simple sequence repeat markers and diversity analysis in alfalfa (Medicago sativa L.). Mol Biol Rep. doi: 10.1007/s11033-012-2404-3 Google Scholar
  30. 30.
    Biswas MK, Chai L, Mayer C, Xu Q, Guo W, Deng X (2012) Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus. Mol Biol Rep 39(5):5373–5386PubMedCrossRefGoogle Scholar
  31. 31.
    Cloutier S, Miranda E, Ward K, Radovanovic N, Reimer E, Walichnowski A, Datla R, Rowland G, Duguid S, Ragupathy R (2012) Simple sequence repeat marker development from bacterial artificial chromosome end sequences and expressed sequence tags of flax (Linum usitatissimum L.). TAG Theoretical and applied genetics Theoretische und angewandte Genetik 125(4):685–694PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Inkyu Park
    • 1
    • 2
  • Jungeun Kim
    • 1
    • 3
  • Jeongyeo Lee
    • 1
  • Sewon Kim
    • 1
  • Okhee Cho
    • 1
  • Kyungbong Yang
    • 1
    • 3
  • Jongmoon Ahn
    • 4
  • Seokhyeon Nahm
    • 5
  • HyeRan Kim
    • 1
    • 3
    Email author
  1. 1.Plant Systems Engineering Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)DaejeonRepublic of Korea
  2. 2.College of Agriculture and Life ScienceChungnam National UniversityDaejeonRepublic of Korea
  3. 3.Systems and BioengineeringUniversity of Science and Technology (UST)DaejeonRepublic of Korea
  4. 4.Breeding Institute, Nongwoo Bio Co., LTD.YeojuRepublic of Korea
  5. 5.Biotechnology Institute, Nongwoo Bio Co., LTD.YeojuRepublic of Korea

Personalised recommendations