Dataset Information

Transcriptome-Wide Identification of Reference Genes for Expression Analysis of Soybean Responses to Drought Stress along the Day.

ABSTRACT: The soybean transcriptome displays strong variation along the day in optimal growth conditions and also in response to adverse circumstances, like drought stress. However, no study conducted to date has presented suitable reference genes, with stable expression along the day, for relative gene expression quantification in combined studies on drought stress and diurnal oscillations. Recently, water deficit responses have been associated with circadian clock oscillations at the transcription level, revealing the existence of hitherto unknown processes and increasing the demand for studies on plant responses to drought stress and its oscillation during the day. We performed data mining from a transcriptome-wide background using microarrays and RNA-seq databases to select an unpublished set of candidate reference genes, specifically chosen for the normalization of gene expression in studies on soybean under both drought stress and diurnal oscillations. Experimental validation and stability analysis in soybean plants submitted to drought stress and sampled during a 24 h timecourse showed that four of these newer reference genes (FYVE, NUDIX, Golgin-84 and CYST) indeed exhibited greater expression stability than the conventionally used housekeeping genes (ELF1-? and ?-actin) under these conditions. We also demonstrated the effect of using reference candidate genes with different stability values to normalize the relative expression data from a drought-inducible soybean gene (DREB5) evaluated in different periods of the day.

SUBMITTER: Marcolino-Gomes J

PROVIDER: S-EPMC4583485 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Transcriptome-Wide Identification of Reference Genes for Expression Analysis of Soybean Responses to Drought Stress along the Day.

Marcolino-Gomes Juliana J Rodrigues Fabiana Aparecida FA Fuganti-Pagliarini Renata R Nakayama Thiago Jonas TJ Ribeiro Reis Rafaela R Bouças Farias Jose Renato JR Harmon Frank G FG Correa Molinari Hugo Bruno HB Correa Molinari Mayla Daiane MD Nepomuceno Alexandre A

PloS one 20150925 9

The soybean transcriptome displays strong variation along the day in optimal growth conditions and also in response to adverse circumstances, like drought stress. However, no study conducted to date has presented suitable reference genes, with stable expression along the day, for relative gene expression quantification in combined studies on drought stress and diurnal oscillations. Recently, water deficit responses have been associated with circadian clock oscillations at the transcription level ...[more]

PMID: 26407065

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Project description:To investigate soybean responses to drought stress and growth through metabolism compensation after rehydration, and for the establishment of an optimal water-saving irrigation model, we used the soybean variety Suinong 14 as experimental material and adopted a weighing method for water control in potted plants. We exposed soybean plants to stress treatments at different growth stages using different stress levels and durations. We then studied the effects of drought stress and rehydration on soybean growth and development, osmoregulation, and endogenous hormonal regulations, as well as antioxidant systems. The results showed that drought stress inhibited increases in the soybean plant height and leaf area. This inhibition became more significant as the level, duration, and frequency of the drought stress increased. After rehydration, the soybean plant heights and leaf areas exhibited rapid increases and partial compensation for their decreased sizes. As the level, duration, and frequency of drought stress increased, the compensation effect decreased, but it did not return to the control level. Drought stress reduced the chlorophyll content and relative water content in the soybean leaves and increased the osmolyte contents, antioxidant potential, and peroxidation of the membrane lipids. In addition, the changes mentioned above became more dramatic as the drought stress level, duration, and frequency increased. Upon rehydration, various levels of growth compensation were observed in each physio-biochemical parameter. As the drought stress level, duration, and frequency increased, the compensation effect also increased. Overall, the compensation effect for drought stress that occurred at the early growth stages was higher than that at the later growth stages. Drought stress led to decreases in the ZR/IAA and ZR/ABA ratios in soybean leaves and an increase in the ABA/(IAA + GA + ZR) ratio; thus, the plant growth was inhibited. These hormone ratios exhibited more dramatic changes when the drought stress level became more severe and the stress duration was prolonged. After rehydration, these hormone ratios produced equal compensation effects. Therefore, the compensatory effect of rewatering after drought stress is conditional. Severe stress, especially long-term severe stress, will reduce the compensatory effect. At the same time, drought resistance treatment at seedling stage can improve the adaptability and compensatory effect of re-drought at grain filling stage.

Project description:The availability of complete genome sequence of soybean has allowed research community to design the 66 K Affymetrix Soybean Array GeneChip for genome-wide expression profiling of soybean. In this study, we carried out microarray analysis of leaf tissues of soybean plants, which were subjected to drought stress from late vegetative V6 and from full bloom reproductive R2 stages. Our data analyses showed that out of 46,093 soybean genes, which were predicted with high confidence among approximately 66,000 putative genes, 41,059 genes could be assigned with a known function. Using the criteria of a ratio change > = 2 and a q-value<0.05, we identified 1458 and 1818 upregulated and 1582 and 1688 downregulated genes in drought-stressed V6 and R2 leaves, respectively. These datasets were classified into 19 most abundant biological categories with similar proportions. There were only 612 and 463 genes that were overlapped among the upregulated and downregulated genes, respectively, in both stages, suggesting that both conserved and unconserved pathways might be involved in regulation of drought response in different stages of plant development. A comparative expression analysis using our datasets and that of drought stressed Arabidopsis leaves revealed the existence of both conserved and species-specific mechanisms that regulate drought responses. Many upregulated genes encode either regulatory proteins, such as transcription factors, including those with high homology to Arabidopsis DREB, NAC, AREB and ZAT/STZ transcription factors, kinases and two-component system members, or functional proteins, e.g. late embryogenesis-abundant proteins, glycosyltransferases, glycoside hydrolases, defensins and glyoxalase I family proteins. A detailed analysis of the GmNAC family and the hormone-related gene category showed that expression of many GmNAC and hormone-related genes was altered by drought in V6 and/or R2 leaves. Additionally, the downregulation of many photosynthesis-related genes, which contribute to growth retardation under drought stress, may serve as an adaptive mechanism for plant survival. This study has identified excellent drought-responsive candidate genes for in-depth characterization and future development of improved drought-tolerant transgenic soybeans.

Dataset Information

Transcriptome-Wide Identification of Reference Genes for Expression Analysis of Soybean Responses to Drought Stress along the Day.

Publications

Transcriptome-Wide Identification of Reference Genes for Expression Analysis of Soybean Responses to Drought Stress along the Day.

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