Genome-wide transcriptional analysis of two soybean genotypes under dehydration and rehydration conditions
| Autor: | Ai H Sha, Li M Chen, Cheng Wang, Zhi H Shan, Wei Chang, Xin A Zhou, Chan J Zhang, De Z Qiu, Wen B Li, Zhong L Yang, Rong Zhou, Shui L Chen |
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| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
Digital gene expression tag profile
Genotype Transcription Genetic Sequence analysis Drought tolerance Quantitative RT-PCR Biology Plant Roots Protein kinases Gene Expression Regulation Plant Gene expression Genetics Transcription factors Cluster Analysis Gene Illumina dye sequencing Gene Library Plant Proteins Genes Essential Dehydration cDNA library Reverse Transcriptase Polymerase Chain Reaction Gene Expression Profiling fungi Electric Conductivity food and beverages Reproducibility of Results Water Regulatory proteins Sequence Analysis DNA Rehydration Adaptation Physiological Droughts Gene expression profiling Plant Leaves Gene Ontology Phenotype Differentially expressed genes Soybeans DNA microarray Soybean Genome Plant Biotechnology Research Article Signal Transduction |
| Zdroj: | BMC Genomics |
| ISSN: | 1471-2164 |
| Popis: | Background Soybean is an important crop that provides valuable proteins and oils for human use. Because soybean growth and development is extremely sensitive to water deficit, quality and crop yields are severely impacted by drought stress. In the face of limited water resources, drought-responsive genes are therefore of interest. Identification and analysis of dehydration- and rehydration-inducible differentially expressed genes (DEGs) would not only aid elucidation of molecular mechanisms of stress response, but also enable improvement of crop stress tolerance via gene transfer. Using Digital Gene Expression Tag profiling (DGE), a new technique based on Illumina sequencing, we analyzed expression profiles between two soybean genotypes to identify drought-responsive genes. Results Two soybean genotypes—drought-tolerant Jindou21 and drought-sensitive Zhongdou33—were subjected to dehydration and rehydration conditions. For analysis of DEGs under dehydration conditions, 20 cDNA libraries were generated from roots and leaves at two different time points under well-watered and dehydration conditions. We also generated eight libraries for analysis under rehydration conditions. Sequencing of the 28 libraries produced 25,000–33,000 unambiguous tags, which were mapped to reference sequences for annotation of expressed genes. Many genes exhibited significant expression differences among the libraries. DEGs in the drought-tolerant genotype were identified by comparison of DEGs among treatments and genotypes. In Jindou21, 518 and 614 genes were differentially expressed under dehydration in leaves and roots, respectively, with 24 identified both in leaves and roots. The main functional categories enriched in these DEGs were metabolic process, response to stresses, plant hormone signal transduction, protein processing, and plant-pathogen interaction pathway; the associated genes primarily encoded transcription factors, protein kinases, and other regulatory proteins. The seven most significantly expressed (|log2 ratio| ≥ 8) genes— Glyma15g03920, Glyma05g02470, Glyma15g15010, Glyma05g09070, Glyma06g35630, Glyma08g12590, and Glyma11g16000—are more likely to determine drought stress tolerance. The expression patterns of eight randomly-selected genes were confirmed by quantitative RT-PCR; the results of QRT-PCR analysis agreed with transcriptional profile data for 96 out of 128 (75%) data points. Conclusions Many soybean genes were differentially expressed between drought-tolerant and drought-sensitive genotypes. Based on GO functional annotation and pathway enrichment analysis, some of these genes encoded transcription factors, protein kinases, and other regulatory proteins. The seven most significant DEGs are candidates for improving soybean drought tolerance. These findings will be helpful for analysis and elucidation of molecular mechanisms of drought tolerance; they also provide a basis for cultivating new varieties of drought-tolerant soybean. |
| Databáze: | OpenAIRE |
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