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Molecular marker information from de novo assembled transcriptomes of chilli pepper (Capsicum annuum L.) varieties based on next-generation sequencing technology

Published online by Cambridge University Press:  16 July 2014

Yul-Kyun Ahn ,
Swati Tripathi ,
Young-Il Cho ,
Jeong-Ho Kim ,
Hye-Eun Lee ,
Do-Sun Kim  and
Jong-Gyu Woo
Yul-Kyun Ahn*
Affiliation:
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon440-706, Republic of Korea
Swati Tripathi
Affiliation:
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon440-706, Republic of Korea
Young-Il Cho
Affiliation:
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon440-706, Republic of Korea
Jeong-Ho Kim
Affiliation:
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon440-706, Republic of Korea
Hye-Eun Lee
Affiliation:
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon440-706, Republic of Korea
Do-Sun Kim
Affiliation:
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon440-706, Republic of Korea
Jong-Gyu Woo
Affiliation:
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon440-706, Republic of Korea
*
* Corresponding author. E-mail: aykyun@korea.kr
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Abstract

Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

Keywords

Capsicum annuumpyrosequencingsimple sequence repeatssingle-nucleotide polymorphismstranscriptome assembly
Type
Research Article
Information
Plant Genetic Resources , Volume 12 , Issue S1: Special issue on the 3rd International Symposium on “Genomics of Plant Genetic Resources” , July 2014 , pp. S83 - S86
Copyright
Copyright © NIAB 2014 

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