RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean

Authors: Horvath, David; HANSEN, STEPHANIE - South Dakota State University; MORILES-MILLER, JANET - South Dakota State University; PIERIK, RONALD - Utrecht University; YAN, CHANGHUI - North Dakota State University; CLAY, DAVID - South Dakota State University; Scheffler, Brian; CLAY, SHARON - South Dakota State University

Submitted to: New Phytologist
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/30/2015
Publication Date: 7/1/2015
Citation: Horvath, D.P., Hansen, S.A., Moriles-Miller, J.C., Pierik, R., Yan, C., Clay, D.E., Scheffler, B., Clay, S.A. 2015. RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean. New Phytologist. 207:196-210. https://doi.org/10.1111/nph.13351.
DOI: https://doi.org/10.1111/nph.13351

Interpretive Summary: We have investigated how weeds turn genes on and off in soybeans in the field to cause loss of yield and reduced growth. We used different weeds each year and controlled weeds in our weed free plots using different herbicides so we would only detect general responses to weeds rather than any responses that might be caused by a specific weed species. We determined first that our treatments caused leaf area , plant height, and yield. After examining more than 30,000 different genes, we identified 55 that had lower concentrations and 14 that higher concentrations of corresponding transcripts (mRNA) when the soybeans were grown with weeds. Among the genes that were “turned on” by weeds was a particular gene that codes for a transcription factor (a protein that turns other genes on or off) that is called PHYTOCHROME INTERACTING FACTOR 3 (PIF3 for short). PIF genes (but not PIF3) are known to play a role in altering the development of a model plant called arabidopsis when it is grown in dense populations or when treated with excess far red light. We surmise the soybean PIF3 may act in a similar way to the arabidopsis PIFs to alter soybean growth and development in response to weeds. Since recent studies have shown that weeds could inhibit soybean growth even when they are physically separated from them and thus not competing for resources, we believe that by turning this gene off, we may be able to make soybeans blind to weeds and thus reduce the negative impact that they have on soybean growth.

Technical Abstract: Research conducted, including the rationale: Weeds reduce yield in soybeans through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate growing seasons. Methods: RNASeq data were collected from 6 biological samples of soybeans growing with or without weeds. Weed species and the methods to maintain weed free controls varied between years to mitigate treatment effects and to allow detection of general soybeans weed responses. Key results: Soybean plants were not visibly nutrient or water stressed. We identified 55 consistently down-regulated genes in weedy plots. Many of the down-regulated genes were heat shock genes. Fourteen genes were consistently up-regulated. Several transcription factors including a PHYTOCHROME INTERACTING FACTOR 3-like gene (PIF3) were included among the up-regulated genes. Gene set enrichment analysis indicated roles for increased oxidative stress and jasmonic acid signaling responses during weed stress. Main conclusion: The relationship of this weed-induced PIF3 gene to genes involved in shade avoidance responses in arabidopsis provide evidence that this gene may be important in the response of soybean to weeds. These results suggest the weed-induced PIF3 gene will be a target for manipulating weed tolerance in soybean.