Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)
Joint Authors
Ding, Qian
Li, Jingjuan
Wang, Fengde
Zhang, Yihui
Li, Huayin
Zhang, Jiannong
Gao, Jianwei
Source
International Journal of Genomics
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-10-04
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Ding, Qian& Li, Jingjuan& Wang, Fengde& Zhang, Yihui& Li, Huayin& Zhang, Jiannong…[et al.]. 2015. Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). International Journal of Genomics،Vol. 2015, no. 2015, pp.1-11.
https://search.emarefa.net/detail/BIM-1066019
Modern Language Association (MLA)
Ding, Qian…[et al.]. Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). International Journal of Genomics No. 2015 (2015), pp.1-11.
https://search.emarefa.net/detail/BIM-1066019
American Medical Association (AMA)
Ding, Qian& Li, Jingjuan& Wang, Fengde& Zhang, Yihui& Li, Huayin& Zhang, Jiannong…[et al.]. Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). International Journal of Genomics. 2015. Vol. 2015, no. 2015, pp.1-11.
https://search.emarefa.net/detail/BIM-1066019
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1066019