| Title |
Development of SSR markers by next-generation sequencing of Korean landraces of chamoe (Cucumis melo var. makuwa)
|
|---|---|
| Published in |
Molecular Biology Reports, October 2013
|
| DOI | 10.1007/s11033-013-2803-0 |
| Pubmed ID | |
| Authors |
Inkyu Park, Jungeun Kim, Jeongyeo Lee, Sewon Kim, Okhee Cho, Kyungbong Yang, Jongmoon Ahn, Seokhyeon Nahm, HyeRan Kim |
| 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. |
Mendeley readers
The data shown below were compiled from readership statistics for 12 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Malaysia | 1 | 8% |
| Chile | 1 | 8% |
| Unknown | 10 | 83% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 4 | 33% |
| Researcher | 2 | 17% |
| Student > Bachelor | 1 | 8% |
| Other | 1 | 8% |
| Student > Master | 1 | 8% |
| Other | 1 | 8% |
| Unknown | 2 | 17% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 7 | 58% |
| Business, Management and Accounting | 1 | 8% |
| Earth and Planetary Sciences | 1 | 8% |
| Engineering | 1 | 8% |
| Unknown | 2 | 17% |
Attention Score in Context
This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 03 January 2024.
All research outputs
#7,455,523
of 22,792,160 outputs
Outputs from Molecular Biology Reports
#390
of 2,908 outputs
Outputs of similar age
#69,642
of 208,038 outputs
Outputs of similar age from Molecular Biology Reports
#9
of 47 outputs
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So far Altmetric has tracked 2,908 research outputs from this source. They receive a mean Attention Score of 2.3. This one has gotten more attention than average, scoring higher than 73% of its peers.
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We're also able to compare this research output to 47 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 57% of its contemporaries.