Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-Seq

Authors: CHEN, WEI - University Of Missouri; YAO, QIUMING - University Of Missouri; PATIL, GUNVANT - University Of Missouri; AGARWAL, GAURAV - University Of Missouri; DESHMUKH, RUPESH - University Of Missouri; LIN, LI - University Of Missouri; WANG, BIAO - University Of Missouri; WANG, YONGQIN - University Of Missouri; PRINCE, SILVAS - University Of Missouri; SONG, LI - University Of Missouri; XU, DONG - University Of Missouri; An, Yong-Qiang - Charles; VALLIYODAN, BABU - University Of Missouri; VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; NGUYEN, HENRY - University Of Missouri

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/4/2016
Publication Date: 7/19/2016
Publication URL: https://handle.nal.usda.gov/10113/62875
Citation: Chen, W., Yao, Q., Patil, G., Agarwal, G., Deshmukh, R.K., Lin, L., Wang, B., Wang, Y., Prince, S.J., Song, L., Xu, D., An, Y., Valliyodan, B., Varshney, R.K., Nguyen, H.T. 2016. Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-Seq. Frontiers in Plant Science. 7:1044. doi:10.3389/fpls.2016.01044.

Interpretive Summary: Soybean is the second largest crop in the US. Its yield directly impacts US agricultural economics. Drought and flooding are two major causes for soybean yield loss. In this study, we examined how soybean plants respond to drought and flooding at molecular and systems levels for developing better strategies to reduce soybean yield loss from drought and flooding. Recent availability of next-generation sequencing (NGS) technologies allows soybean researchers to measure expression of all soybean genes in a single tissue simultaneously, and therefore greatly increase our research efficiency. The study applied a NGS technology to measure expression of soybean genes in response to drought and flooding treatments, and identified 2,769 and 3,589 genes whose expression are affected by drought and flooding treatments, respectively. In addition, we showed that several biochemical pathways such as photosynthesis and starch metabolism are associated with plant response to drought and flooding treatments. We were also able to identify 289 transcription factor genes whose expression was influenced by drought and flooding treatments. Those transcription factor genes are likely to play an important regulatory role in soybean response to drought and flood treatments, and could be potentially engineered to develop better drought and flood tolerate soybean varieties.

Technical Abstract: Soybean is the second largest crop in the US. Its yield directly impacts US agricultural economics. Drought and flooding are two major causes for soybean yield loss. To better understand their underlying molecular regulatory mechanisms, we sequenced the transcriptomes of soybean grown in drought and flooding conditions. A total of 2,769 and 3,589 genes were differentially regulated by drought and flooding treatments, respectively. We observed that a number of bHLH, ERF, MYB, NAC, and WRKY transcription factor genes were highly regulated by drought and flooding treatments, suggesting their potential role in regulating soybean response to drought and flooding. The genes in photosynthesis and chlorophyll synthesis were preferentially down-regulated by both stresses, and suggesting a possibility that these extreme stress conditions may reduce plant metabolic activities, and therefore potentially prolong their survival in their stress condition. Interestingly, a number of genes in the cell wall synthesis pathway were up-regulated under drought stress, but down-regulated under flooding stress. Genes in starch and sugar metabolic pathways were also preferentially regulated by the stress treatments. Changes of cell wall precursors and starch/sugar content are both likely to serve as adaptive mechanisms for soybean survival under stress conditions.