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Title 

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

 

한국재래종 참외의 NGS 염기서열 분석을 통한 SSR 마커 개발

Authors 

Inkyu ParkJungeun KimJeongyeo LeeS KimO ChoKyungbong YangJ AhnS NahmHyeran Kim

Publisher 

Springer Verlag (Germany)

Issue Date 

2013

Citation 

Molecular Biology Reports, vol. 40, no. 12, pp. 6855-6862

Keywords 

Genetic diversityIllumina preliminary assemblyOriental melonSSR

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.

ISSN 

0301-4851

Link 

http://dx.doi.org/10.1007/s11033-013-2803-0

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2017-04-19


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