RNA-Seq based transcriptomic analysis revealed genes associated with seed-flooding tolerance in wild soybean (Glycine soja Sieb. & Zucc.)

Seed-flooding stress is one of the most important constraints that affects the yield and quality of soybean. However, very little is known about the molecular mechanisms underlying seed-flooding tolerance. Hence, the present study investigated the transcriptome profile in root tissues of two contrasting soybean genotypes viz., PI342618B/SFT-tolerant, and NN86-4/SFS-sensitive under seed-flooding stress using RNA-Seq approach. A total of 1563 and 1958 differentially expressed genes (DEGs) were identified in SFT-tolerant and SFS-sensitive, respectively suggesting that the former is less affected by flooding stress. Both Gene ontology (GO) enrichment and MapMan pathway analyses revealed that response to seed-flooding stress was mostly enriched in the DEGs that are involved in the cell wall, antioxidant activity, catalytic and transcription factor activities as well as protein metabolism and signaling. Based on gene annotation, GO enrichment and protein-protein interaction (PPI) network analysis, a total of 807 DEGs were screened from the above terms related to the stress including response to stress, defense response and response to stimulus for candidate gene prediction analysis. Out of them, 51 genes revealing significant opposite gene expression pattern between tolerant and sensitive genotypes along with GmERFVII1, GmERFVII2 & GmERFVII3 and MAPK1 were predicted as the possible candidate genes for further analysis. Using quantitative real-time RT-PCR (qRT-PCR) and sequencing analysis, five of the randomly selected ten genes viz., Glyma.01G231200, Glyma.08G083300, Glyma.06G045400, Glyma.05G215900, and Glyma.15G015100 revealed both significant opposite expression pattern and nucleotide differences, respectively between SFT-tolerant and SFS-sensitive. Hence, these genes will be of great value for breeding seed-flooding tolerance in soybean after their proper functional validation. Overall, the transcriptome profiling indicates that all the three major processes viz., biological process (BP), cellular components (CC), and molecular functions (MF) are altered in the soybean in response to seed-flooding stress. In conclusion, these findings provide in-depth insights that will be of great utility for the exploration of candidate gene functions for seed-flooding tolerance in soybean.