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Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish

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Abstract

The tuberous root of radish is an important vegetable, but insufficient transcriptomic and genomic data are currently available to understand the molecular mechanisms underlying tuberous root formation and development. High-throughput transcriptomic sequencing is essential to generate a large transcript sequence data set for gene discovery and molecular marker development. In this study, a total of 107.3 million clean reads were generated using Illumina paired-end sequencing technology. De novo assembly generated 61,554 unigenes with an average length of 820 bp. Based on a sequence similarity search with known proteins or nucleotides, 85.51 % (52,634), 90.18 % (55,507) and 54 % (33,242) consensus sequences showed homology with sequences in the Nr, Nt and Swiss-Prot databases, respectively. Of these annotated unigenes, 21,109 and 17,343 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. A total of 27,809 unigenes were assigned to 123 pathways in the Kyoto Encyclopedia of Genes and Genomes database. Analysis of transcript differences between libraries from the early and late seedling developmental stages demonstrated that starch and sucrose metabolism and phenylpropanoid biosynthesis may be the dominant metabolic events during tuberous root formation and plant hormones probably play critical roles in regulation of this developmental process. In total, 14,641 potential EST-SSRs were identified among the unigenes, and 12,733 primer pairs for 2,511 SSR were obtained. Summarily, this study gave us a clue to understand the radish tuberous root formation and development, and also provided us with a valuable sequence resource for novel gene discovery and marker-assisted selective breeding in radish.

Key message

De novo assembled and characterized the radish tuberous root transcriptome; explored the mechanism of radish tuberous root formation; development of EST-SSR markers in radish.

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Acknowledgments

This work was supported by the Modern Agricultural Industrial Technology System Funding of Shandong Province, China (2010sdxdcyjstxshucai); National Nature Science Foundation of China (31101553); Prospect of Shandong Seed Project, China (2011lzgcshucaizy) and the Promotive Research Fund for Excellent Young and Middle-aged Scientists of Shandong Province, China (BS2010SW027).

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Authors and Affiliations

  1. Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, 250100, China

    Shufen Wang, Qiwei He, Xianxian Liu, Wenling Xu, Libin Li, Jianwei Gao & Fengde Wang

  2. College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, 271018, China

    Xiufeng Wang

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  1. Shufen Wang
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Correspondence to Jianwei Gao or Fengde Wang.

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Communicated by W. Harwood.

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Wang, S., Wang, X., He, Q. et al. Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish. Plant Cell Rep 31, 1437–1447 (2012). https://doi.org/10.1007/s00299-012-1259-3

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  • DOI: https://doi.org/10.1007/s00299-012-1259-3

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