Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)
Simple sequence repeats (SSRs) are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR) markers, located in the coding regions, are potentially more efficient for QTL mapping, gene tar...
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| Format: | Article |
| Language: | English |
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Wiley
2015-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2015/473028 |
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| author | Qian Ding Jingjuan Li Fengde Wang Yihui Zhang Huayin Li Jiannong Zhang Jianwei Gao |
| author_facet | Qian Ding Jingjuan Li Fengde Wang Yihui Zhang Huayin Li Jiannong Zhang Jianwei Gao |
| author_sort | Qian Ding |
| collection | DOAJ |
| description | Simple sequence repeats (SSRs) are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR) markers, located in the coding regions, are potentially more efficient for QTL mapping, gene targeting, and marker-assisted breeding. In this study, we investigated 51,694 nonredundant unigenes, assembled from clean reads from deep transcriptome sequencing with a Solexa/Illumina platform, for identification and development of EST-SSRs in Chinese cabbage. In total, 10,420 EST-SSRs with over 12 bp were identified and characterized, among which 2744 EST-SSRs are new and 2317 are known ones showing polymorphism with previously reported SSRs. A total of 7877 PCR primer pairs for 1561 EST-SSR loci were designed, and primer pairs for twenty-four EST-SSRs were selected for primer evaluation. In nineteen EST-SSR loci (79.2%), amplicons were successfully generated with high quality. Seventeen (89.5%) showed polymorphism in twenty-four cultivars of Chinese cabbage. The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs. The EST-SSRs identified and characterized in this study have important implications for developing new tools for genetics and molecular breeding in Chinese cabbage. |
| format | Article |
| id | doaj-art-0e8c885c957f4d7685eb8aeae78c987d |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-0e8c885c957f4d7685eb8aeae78c987d2025-02-03T01:23:29ZengWileyInternational Journal of Genomics2314-436X2314-43782015-01-01201510.1155/2015/473028473028Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)Qian Ding0Jingjuan Li1Fengde Wang2Yihui Zhang3Huayin Li4Jiannong Zhang5Jianwei Gao6College of Horticulture, Gansu Agricultural University, Lanzhou 730070, ChinaInstitute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences and Shandong Key Laboratory of Greenhouse Vegetable Biology and Shandong Branch of National Vegetable Improvement Center, Jinan 250100, ChinaInstitute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences and Shandong Key Laboratory of Greenhouse Vegetable Biology and Shandong Branch of National Vegetable Improvement Center, Jinan 250100, ChinaInstitute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences and Shandong Key Laboratory of Greenhouse Vegetable Biology and Shandong Branch of National Vegetable Improvement Center, Jinan 250100, ChinaInstitute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences and Shandong Key Laboratory of Greenhouse Vegetable Biology and Shandong Branch of National Vegetable Improvement Center, Jinan 250100, ChinaCollege of Horticulture, Gansu Agricultural University, Lanzhou 730070, ChinaInstitute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences and Shandong Key Laboratory of Greenhouse Vegetable Biology and Shandong Branch of National Vegetable Improvement Center, Jinan 250100, ChinaSimple sequence repeats (SSRs) are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR) markers, located in the coding regions, are potentially more efficient for QTL mapping, gene targeting, and marker-assisted breeding. In this study, we investigated 51,694 nonredundant unigenes, assembled from clean reads from deep transcriptome sequencing with a Solexa/Illumina platform, for identification and development of EST-SSRs in Chinese cabbage. In total, 10,420 EST-SSRs with over 12 bp were identified and characterized, among which 2744 EST-SSRs are new and 2317 are known ones showing polymorphism with previously reported SSRs. A total of 7877 PCR primer pairs for 1561 EST-SSR loci were designed, and primer pairs for twenty-four EST-SSRs were selected for primer evaluation. In nineteen EST-SSR loci (79.2%), amplicons were successfully generated with high quality. Seventeen (89.5%) showed polymorphism in twenty-four cultivars of Chinese cabbage. The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs. The EST-SSRs identified and characterized in this study have important implications for developing new tools for genetics and molecular breeding in Chinese cabbage.http://dx.doi.org/10.1155/2015/473028 |
| spellingShingle | Qian Ding Jingjuan Li Fengde Wang Yihui Zhang Huayin Li Jiannong Zhang Jianwei Gao Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis) International Journal of Genomics |
| title | Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis) |
| title_full | Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis) |
| title_fullStr | Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis) |
| title_full_unstemmed | Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis) |
| title_short | Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis) |
| title_sort | characterization and development of est ssrs by deep transcriptome sequencing in chinese cabbage brassica rapa l ssp pekinensis |
| url | http://dx.doi.org/10.1155/2015/473028 |
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