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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
Article

Abstract

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.

Keywords

Illumina preliminary assembly Oriental melon SSR Genetic diversity 

Notes

Acknowledgments

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

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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

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