Gene expression profiling of soybean leaves and roots under salt, saline–alkali and drought stress by high-throughput Illumina sequencing

Salt, saline–alkali and drought stresses are major environmental constraints for the production and yield of soybean worldwide. To identify genes responsible for stress tolerance, the transcriptional profiles of genes in leaves and roots of seedlings (two-leaf stage) of the soybean inbred line HJ-1 were examined after 48 h under various stress conditions; salt (120 mM NaCl), saline–alkali (70 mM NaCl and 50 mM NaHCO3) and drought (2% PEG 8000). Gene expression at the transcriptional level was investigated using high-throughput Illumina sequencing technology and bioinformatics tools. Under salt, saline–alkali and drought stress, 874, 1897, and 535 genes, respectively, were up-regulated in leaves, and 1822, 1731 and 1690 genes, respectively, were up-regulated in roots, compared with expression in the corresponding organ in control plants. Comparisons among salt, saline–alkali and drought stress yielded similar results in terms of the percentage of genes classified into each GO category. Moreover, 69 genes differentially expressed in both organs with similar expression patterns clustered together in the taxonomic tree across all conditions. Furthermore, comparison of gene expression among salt, saline–alkali and drought treated plants revealed that genes associated with calcium-signaling and nucleic acid pathways were up-regulated in the responses to all three stresses, indicating a degree of cross-talk among these pathways. These results could provide new insights into the stress tolerance mechanisms of soybean.

► We analyzed gene expression profiling of soybean under stresses.
► Genes were categorized according to the number of expressed transcripts.
► 69 genes were expressed differently under salt, saline-alkali and drought stresses.
► Genes were clustered according to similarities across all stresses.
► The response to stress in soybean is a complex physiological and metabolic pathway.