ArticlePloS one2014
De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Integrating genomics, multi-omics, CRISPR and speed breeding for stress-resilient vegetable legume improvement.Functional & integrative genomics · 2026Review
- Comprehensive physiological and transcriptomic insights into drought stress responses in faba bean (Vicia Faba L.).BMC plant biology · 2025Article
- De Novo Transcriptome Assembly of Rice Bean (Plants (Basel, Switzerland) · 2024Article
- Screening for Drought Tolerance Within a Common Bean (Plants (Basel, Switzerland) · 2024Article
- Comprehensive Proteomic Analysis of Common Bean (Biomolecules · 2024Article
- Unraveling the drought-responsive transcriptomes in nodules of two common bean genotypes during biological nitrogen fixation.Frontiers in plant science · 2024Article
- Identification of quantitative trait loci for drought tolerance in Bukoba/Kijivu Andean mapping population of common bean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Integrated transcriptomics and metabolomics analysis reveals key regulatory network that response to cold stress in common Bean (Phaseolus vulgaris L.).BMC plant biology · 2023Article
- Comparative Transcriptome Analysis of Tolerant and Sensitive Genotypes of Common Bean (Plants (Basel, Switzerland) · 2023Article
- CkREV Enhances the Drought Resistance ofInternational journal of molecular sciences · 2022Article
- Recent advancement in OMICS approaches to enhance abiotic stress tolerance in legumes.Frontiers in plant science · 2022Review
- CkREV regulates xylem vessel development inFrontiers in plant science · 2022Article
- Review
- Genetic dissection of drought resistance based on root traits at the bud stage in common bean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Differential Regulation of Drought Responses in TwoPlants (Basel, Switzerland) · 2020Article
- Pod and Seed Trait QTL Identification To Assist Breeding for Peanut Market Preferences.G3 (Bethesda, Md.) · 2020Article
- Transcriptomic Response to Water Deficit Reveals a Crucial Role of Phosphate Acquisition in a Drought-Tolerant Common Bean Landrace.Plants (Basel, Switzerland) · 2020Article
- Genome-wide analysis of the transcriptional response to drought stress in root and leaf of common bean.Genetics and molecular biology · 2020Article
- Identification of Differentially Expressed Drought-Responsive Genes in Guar [International journal of genomics · 2020Article
- Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (International journal of genomics · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The common bean (Phaseolus vulgaris L.) is one of the most important food legumes, far ahead of other legumes. The average grain yield of the common bean worldwide is much lower than its potential yields, primarily due to drought in the field. However, the gene network that mediates plant responses to drought stress remains largely unknown in this species. The major goals of our study are to identify a large scale of genes involved in drought stress using RNA-seq. First, we assembled 270 million high-quality trimmed reads into a non-redundant set of 62,828 unigenes, representing approximately 49 Mb of unique transcriptome sequences. Of these unigenes, 26,501 (42.2%) common bean unigenes had significant similarity with unigenes/predicted proteins from other legumes or sequenced plants. All unigenes were functionally annotated within the GO, COG and KEGG pathways. The strategy for de novo assembly of transcriptome data generated here will be useful in other legume plant transcriptome studies. Second, we identified 10,482 SSRs and 4,099 SNPs in transcripts. The large number of genetic markers provides a resource for gene discovery and development of functional molecular markers. Finally, we found differential expression genes (DEGs) between terminal drought and optimal irrigation treatments and between the two different genotypes Long 22-0579 (drought tolerant) and Naihua (drought sensitive). DEGs were confirmed by quantitative real-time PCR assays, which indicated that these genes are functionally associated with the drought-stress response. These resources will be helpful for basic and applied research for genome analysis and crop drought resistance improvement in the common bean.
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