ArticleMolecular biology reports2012
Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68.
Article in Molecular biology reports, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Optimized Method for the Identification of Candidate Genes and Molecular Maker Development Related to Drought Tolerance in Oil Palm (Plants (Basel, Switzerland) · 2022Article
- Estimation of genetic diversity and population structure in3 Biotech · 2020Article
- Whole Genome Resequencing of Capsicum baccatum and Capsicum annuum to Discover Single Nucleotide Polymorphism Related to Powdery Mildew Resistance.Scientific reports · 2018Article
- Mapping of fruit length related QTLs in interspecific cross (Breeding science · 2018Article
- RNA-Seq of Guar (Frontiers in plant science · 2017Article
- A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum.Scientific reports · 2016Article
- A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding.Horticulture research · 2016Article
- New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL.Frontiers in plant science · 2016Article
- Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species.G3 (Bethesda, Md.) · 2015Article
- RNA-Seq Uncovers SNPs and Alternative Splicing Events in Asian Lotus (Nelumbo nucifera).PloS one · 2015Article
- An InDel-based linkage map of hot pepper (Molecular breeding : new strategies in plant improvement · 2015Article
- Dynamics of the chili pepper transcriptome during fruit development.BMC genomics · 2014Article
- Characterization of flower-bud transcriptome and development of genic SSR markers in Asian lotus (Nelumbo nucifera Gaertn.).PloS one · 2014Article
- De novo transcriptome assembly and novel microsatellite marker information in Capsicum annuum varieties Saengryeg 211 and Saengryeg 213.Botanical studies · 2013Article
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- De novo transcriptome assembly in chili pepper (Capsicum frutescens) to identify genes involved in the biosynthesis of capsaicinoids.PloS one · 2013Article
- De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes.BMC genomics · 2012Article
- SNP marker integration and QTL analysis of 12 agronomic and morphological traits in F₈ RILs of pepper (Capsicum annuum L.).Molecules and cells · 2012Article
- RNA-Seq Assembly - Are We There Yet?Frontiers in plant science · 2012Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
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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