ArticlePloS one2016
Development of Gene-Based SSR Markers in Rice Bean (Vigna umbellata L.) Based on Transcriptome Data.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 39 citations in OpenAlex.
- Unlocking the potential of rice bean (Journal of food composition and analysis : an official publication of the United Nations University, International Network of Food Data Systems · 2026Article
- Genome analysis and introgression of multiple disease resistance into pre-breeding lines derived from greengram × ricebean crosses.Molecular biology reports · 2026Article
- Article
- Multi-environment phenotyping of ricebean (Frontiers in plant science · 2026Article
- RNA-Seq-based transcriptomics reveals differential gene expression between two Pisum sativum subspecies and uncovers their molecular marker profiles.BMC genomics · 2025Article
- Generation and characterization of novel transcriptome-derived SSR markers for genetic applications in blueberry.Scientific reports · 2025Article
- De Novo Transcriptome Assembly of Rice Bean (Plants (Basel, Switzerland) · 2024Article
- Assessment of the Diuretic Properties of Rice Bean Accessions Using a Mouse Model and Identification of Active Polyphenolic Compounds.Nutrients · 2024Article
- Article
- Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era.Frontiers in genetics · 2022Review
- Transcriptome Analysis Reveals Key Pathways and Candidate Genes Controlling Seed Development and Size in Ricebean (Frontiers in genetics · 2021Article
- De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweedPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Review
- De novo assembly and comparative transcriptome analysis: novel insights into terpenoid biosynthesis in Chamaemelum nobile L.Plant cell reports · 2019Article
- VigSatDB: genome-wide microsatellite DNA marker database of three species of Vigna for germplasm characterization and improvement.Database : the journal of biological databases and curation · 2019Article
- De novo transcriptome analysis of Rhododendron molle G. Don flowers by Illumina sequencing.Genes & genomics · 2018Article
- Unravelling a stearidonic acid-rich triacylglycerol biosynthetic pathway in the developing seeds of Buglossoides arvensis: A transcriptomic landscape.Scientific reports · 2017Article
- De novo transcriptomic analysis of cowpea (Vigna unguiculata L. Walp.) for genic SSR marker development.BMC genetics · 2017Article
- Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers.BMC genomics · 2017Article
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Authors and funding
12 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) is a warm season annual legume mainly grown in East Asia. Only scarce genomic resources are currently available for this legume crop species and no simple sequence repeat (SSR) markers have been specifically developed for rice bean yet. In this study, approximately 26 million high quality cDNA sequence reads were obtained from rice bean using Illumina paired-end sequencing technology and assembled into 71,929 unigenes with an average length of 986 bp. Of these unigenes, 38,840 (33.2%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases. Furthermore, 30,170 (76.3%) could be classified into gene ontology categories, 25,451 (64.4%) into Swiss-Prot categories and 21,982 (55.6%) into KOG database categories (E-value < 1.0E-5). A total of 9,301 (23.5%) were mapped onto 118 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. A total of 3,011 genic SSRs were identified as potential molecular markers. AG/CT (30.3%), AAG/CTT (8.1%) and AGAA/TTCT (20.0%) are the three main repeat motifs. A total of 300 SSR loci were randomly selected for validation by using PCR amplification. Of these loci, 23 primer pairs were polymorphic among 32 rice bean accessions. A UPGMA dendrogram revealed three major clusters among 32 rice bean accessions. The large number of SSR-containing sequences and genic SSRs in this study will be valuable for the construction of high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.
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