Journal article
Molecular marker information from de novo assembled transcriptomes of chilli pepper (Capsicum annuum L.) varieties based on next-generation sequencing technology
Plant genetic resources: characterization and utilization, v 12(S1), pp S83-S86
01 Jul 2014
Featured in Collection : UN Sustainable Development Goals @ Drexel
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.
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Details
- Title
- Molecular marker information from de novo assembled transcriptomes of chilli pepper (Capsicum annuum L.) varieties based on next-generation sequencing technology
- Creators
- Yul-Kyun Ahn - Rural Development AdministrationSwati Tripathi - Rural Development AdministrationYoung-Il Cho - Rural Development AdministrationJeong-Ho Kim - Natl Inst Hort & Herbal Sci, Vegetable Res Div, Rural Dev Adm, Suwon 440706, South KoreaHye-Eun Lee - Natl Inst Hort & Herbal Sci, Vegetable Res Div, Rural Dev Adm, Suwon 440706, South KoreaDo-Sun Kim - Rural Development AdministrationJong-Gyu Woo - Rural Development Administration
- Publication Details
- Plant genetic resources: characterization and utilization, v 12(S1), pp S83-S86
- Publisher
- Cambridge Univ Press
- Number of pages
- 4
- Grant note
- PJ008024 / Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center), Rural Development Administration, Republic of Korea
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Mechanical Engineering and Mechanics
- Web of Science ID
- WOS:000342621700021
- Scopus ID
- 2-s2.0-84904466629
- Other Identifier
- 991020547433504721
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InCites Highlights
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Genetics & Heredity
- Plant Sciences