Genome-wide transcriptional analysis of two soybean genotypes under dehydration and rehydration conditions

Abstract

BackgroundSoybean 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.ResultsTwo 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.ConclusionsMany 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.

Transcriptome Analysis of Taxillusi chinensis (DC.) Danser Seeds in Response to Water Loss

“…In Arabidopsis , water in seeds supplies several biochemical reactions during the seed germination, such as water up-taken from outside [53, 56]. At molecular level, drought stress induced genes have been characterized in different plant species including Arabidopsis [14, 15], rice [16–18], soybean [19, 20], and other plants [21–23]. …”

“…At cellular and molecular levels, a large number of genes have been reported to respond to drought stress [11–13]. Large scale profiling methods like microarray and next-generation sequencing have been demonstrated to estimate the gene expression changes during dehydration process in several model species, such as Arabidopsis [14, 15], rice [16–18], soybean [19, 20] and other plants [21–23]. These studies have shown that the plant defense against drought stress starts with the perception of water loss, which can trigger the activation of abscisic acid (ABA)-dependent and ABA–independent regulatory systems [24].…”

“…It enables the de novo assembly and gene expression analyses for those species, of which the genome sequences are not available currently [26]. To study drought stress induced genes, RNA-Seq has been used to assemble the transcriptome and profiled gene expression in Glycine max [20], Brassica rapa L . ssp .…”

“…Pekinensis [21], Bryum argenteum [27], Brassica napus [28], and Gossypium arboretum [29]. In Jindou21 (drought-tolerant soybean genotype), 518 and 614 genes including genes ethylene-responsive factors, MYB TFs, and zinc finger proteins are differentially expressed under water deficit condition in leaves and roots, respectively [20]. Comparative transcriptome analysis of Brassica napus has shown that a total of 6,018 and 5,377 genes including AREB/ABF, NAC, WRKY and MYB/MYC TFs are induced in response to drought stress [28] in root and leaf, respectively.…”

Feed legumes for truly sustainable crop-animal systems

“…Breeding for wide or specific adaptation across contrasting cropping conditions can be facilitated by: i) progress in the understanding and exploitation of physiological strategies contributing to plant adaptation and stress tolerance (Araújo et al, 2015); ii) the adoption of managed selection environments or phenotyping platforms capable of reproducing the genotype adaptive responses that occur across agricultural regions (Annicchiarico and Piano, 2005); iii) the development of inexpensive screening procedures for tolerance to key stresses [e.g., intrinsic pea tolerance to radiant frost: Shafiq et al (2012)]; and iv) the development of molecular marker-based selection procedures for stress tolerance based on individual quantitative trait loci (e.g., Zhang et al, 2015) or the analysis of individual genes [e.g., via transcriptional analysis: Chen et al, 2013)]; and v) the combination of major-and minor-gene effects into genomic selection models for predicting yield responses in specific cropping conditions (Annicchiarico et al, 2015a). The exploration of marker-based selection for drought tolerance has been remarkably limited in feed legumes, despite the importance of this stress (Araújo et al, 2015).…”