Differential gene expression in soybean leaf tissues at late developmental stages under drought stress revealed by genome-wide transcriptome analysis.

Dung Tien Le,Maho Tanaka,Yasuko Watanabe,Lam-Son Phan Tran,Le Huy Ham,Rie Nishiyama,Kazuko Yamaguchi-Shinozaki,Kazuo Shinozaki,Motoaki Seki,Shin-Han Shiu

doi:10.1371/journal.pone.0049522

Abstract

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 46093 soybean genes, which were predicted with high confidence among approximately 66000 putative genes, 41059 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.

Highlights

Cultivated soybean (Glycine max L.) has been known as one of the major legume crops in the world, providing an abundant source of oil and protein-rich food for both human and animal consumption
Transcriptome Analysis of Soybean V6 and R2 Leaves under Normal and Drought Conditions using Microarray With the availability of the whole genomic sequence of soybean and the Glyma1 annotation, which predicted 46430 proteincoding genes with high confidence out of approximately 66000 putative genes [15], Affymetrix has designed the newest version of the Soybean Array GeneChip covering all of the soybean putative genes
To gain a comprehensive overview of the transcriptomewide regulation in soybean leaves under drought stress during the critical period spanning from late V6 stage toward the end of R2 stage, we performed microarray analyses to compare the transcriptome changes of drought-stressed V6 leaves vs. wellwatered V6 leaves and drought-stressed R2 leaves vs. well-watered R2 leaves using this 66 K Affymetrix Soybean Array GeneChip

Summary

Introduction

Cultivated soybean (Glycine max L.) has been known as one of the major legume crops in the world, providing an abundant source of oil and protein-rich food for both human and animal consumption. In response to drought stress, plants, including soybean, activate a wide range of defense mechanisms that function to increase tolerance to water limiting conditions. With the availability of genomic sequences from various plant species and recent advances in microarray technologies, genes associated with drought/dehydration responses have been identified in a number of plant species, including both model plants, such as Arabidopsis [12], and crops, such as rice (Oryza sativa) [13,14]. Despite that the soybean genomic sequence was completed several years ago [15], and subsequently the 66 K Affymetrix soybean array platform, which covers all of the soybean genes annotated by the Glyma model, was designed by a US consortium, comprehensive genome-wide analysis of the soybean transcriptome under drought stress remained to be determined

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