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Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68

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Abstract

Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) using 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of expressed sequence tag (EST) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by raw reads assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. All unigenes have an approximately equal distribution on chromosomes by aligning with tomato (Solanum lycopersicum) pseudomolecules. Furthermore, 1,536 high quality single nucleotide discrepancies were discovered using the Bukang mature fruit cDNA collection (dbEST ID: 23667) as a reference. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from 614 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research.

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Acknowledgements

This study was supported by Agenda project (Grant No. 200901OFT071942004) of the Rural Development Administration (RDA), Republic of Korea. We are grateful for and acknowledge use of the tomato genome sequence, which was generated by the International Tomato Genome Sequencing Consortium (http://solgenomics.net/tomato/).

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Authors and Affiliations

  1. Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 340-802, Republic of Korea

    Fu-Hao Lu & Yong-Jin Park

  2. Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 441-440, Korea

    Myeong-Cheoul Cho

  3. Legume Bio-Resource Center of Green Manure (LBRCGM), Kongju National University, Yesan, 340-702, Republic of Korea

    Yong-Jin Park

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  1. Fu-Hao Lu
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Correspondence to Yong-Jin Park.

Electronic supplementary material

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11033_2011_1102_MOESM1_ESM.xls

Supplementary material 1: Annotation and FunCat results of all contigs and singletons in Capsicum annuum L. TF68 by BLAST against UniProt (XLS 11.632 kb)

11033_2011_1102_MOESM2_ESM.xls

Supplementary material 2: SNP discovery by mapping Capsicum annuum L. TF68 reads to NCBI Bukang cDNA library (XLS 892 kb)

11033_2011_1102_MOESM3_ESM.xls

Supplementary material 3: SSR discovery and primer information revealed by ARGOS program from Capsicum annuum L. TF68 contigs (XLS 219 kb)

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Lu, FH., Cho, MC. & Park, YJ. Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68. Mol Biol Rep 39, 3327–3335 (2012). https://doi.org/10.1007/s11033-011-1102-x

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