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ARS Home » Southeast Area » Raleigh, North Carolina » Soybean and Nitrogen Fixation Research » Research » Publications at this Location » Publication #353688
Research Project: Exploiting Genetic Diversity through Genomics, Plant Physiology, and Plant Breeding to Increase Competitiveness of U.S. Soybeans in Global Markets

Location: Soybean and Nitrogen Fixation Research

Title: Field-grown soybean transcriptome shows diurnal patterns in photosynthesis-related processes

Author
item Locke, Anna
item SLATTERY, REBECCA - University Of Illinois
item ORT, DONALD - University Of Illinois

Submitted to: Plant Direct
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/8/2018
Publication Date: 12/4/2018
Citation: Locke, A.M., Slattery, R., Ort, D. 2018. Field-grown soybean transcriptome shows diurnal patterns in photosynthesis-related processes. Plant Direct. 2(12):1-14. http://doi.org/10.1002/pld3.99.
DOI: https://doi.org/10.1002/pld3.99

Interpretive Summary: Crop physiology continually adjusts to changing environmental conditions over the course of the day, including fluctuations in light, temperature, and humidity. In addition to diurnal environmental responses, endogenous circadian rhythms modulate gene expression and physiology over the course of the day, but studies to identify the transcriptional underpinnings of circadian rhythm are often conducted in artificial environments such as growth chambers. This study used RNA-seq to examine the transcriptome of field-grown soybean through daylight hours. Over 11,000 genes were determined to be differentially expressed over the course of the day. Seven dominant diurnal patterns of expression were identified, and among these, genes that are associated with photosynthetic processes and chlorophyll biosynthesis were especially likely to be differentially regulated and highly transcribed. Furthermore, using dynamic gene regulatory network inference, seven genes were identified as hubs of diurnal gene regulation, and these seven genes included transcription factors, which can exert direct control of gene expression, as well as an aquaporin water transport protein, which could play a central role in diurnal regulation of leaf water status that indirectly but strongly affects many other genes. Importantly, key differences in known circadian regulators were identified between the field-grown soybeans in this study and chamber-grown soybeans from previous studies, which emphasizes the importance of field-based research to thoroughly understanding diurnal plant processes.

Technical Abstract: Many plant physiological processes have diurnal patterns regulated by diurnal environmental changes and circadian rhythms, but the transcriptional underpinnings of many of these cycles have not been studied in major crop species under field conditions. Here, we monitored the transcriptome of field-grown soybean (Glycine max) during daylight hours in the middle of the growing season with RNA-seq. The analysis revealed 21% of expressed soybean genes were differentially expressed over the course of the day. Expression of some circadian-related genes in field-grown soybean differed from previously reported expression patterns measured in controlled environments. Many genes in functional groups contributing to and/or depending on photosynthesis showed differential expression, with patterns particularly evident in the chlorophyll synthesis pathway. Gene regulatory network inference also revealed seven diurnally-sensitive gene nodes involved with circadian rhythm, transcription regulation, cellular processes, and water transport. This study provides a diurnal overview of the transcriptome for an economically important field-grown crop and a basis for identifying pathways that could eventually be tailored to optimize diurnal regulation of carbon gain.