Name | Transcriptomics of weed stress in soybean |
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Description | 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 gR1.fastqing seasons. Methods: RNASeq data were collected from 6 biological samples of soybeans gR1.fastqing 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. Overall design: Samples were collected from two treatments ("Control" and "Weedy") with six biological replicates (2008, 2009, and twop each for 2010 and 2011) for each treatment. |
Contact | Bioscience Research Lab, Agr. Research Service, US Dept. Agriculture |
Xref | PRJNA256960 |
Reference | |
Conditions | 8 |
Species | Glycine max |
Metadata export | .CSV .JSON |
Mapped Genomes | Gm275Wm82a2V1 Gm508Wm82a4V1 |
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Expression Analysis | Expression Profile / Differential Expression / Co-expression |
Name | Genotype | Mutation | Stage | Tissue | Treatment | Level | Time | Samples | Xref | Download alignments |
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Control_2008 | AG1631 | Newly emerged unfolded trifoliate less than 2 cm in length from at least 8 plants per plot | "Control" with weeds controlled by application of Dual II Magnum (S-metolachlor) (1.9 L ha-1) on May 22 |
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Control_2009 | AG1631 | Newly emerged unfolded trifoliate less than 2 cm in length from at least 8 plants per plot | "Control" with weeds controlled by application of Poast (sethoxydim) (1.8 L ha-1) on June 26 |
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Control_2010 | AG1631 | Newly emerged unfolded trifoliate less than 2 cm in length from at least 8 plants per plot | "Control" with weeds controlled by application of Glyphosate was used at 1.2 L ha-1 |
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Control_2011 | AG1631 | Newly emerged unfolded trifoliate less than 2 cm in length from at least 8 plants per plot | "Control" with weeds controlled by application of Roundup Weather Max (glyphosate)\, Dual II Magnum (s-metolachlor)\, Poast (sethoxydim)\, and Pursuit (imazethapyr) were used at suggested ra |
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Weedy_2008 | AG1631 | Newly emerged unfolded trifoliate less than 2 cm in length from at least 8 plants per plot | "Weedy" with weeds being a natural population of velvetleaf and buckwheat at denisties of about 300 m-2 |
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Weedy_2009 | AG1631 | Newly emerged unfolded trifoliate less than 2 cm in length from at least 8 plants per plot | "Weedy" with weeds being a natural population of velvetleaf and buckwheat at denisties of about 48 m-2 |
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Weedy_2010 | AG1631 | Newly emerged unfolded trifoliate less than 2 cm in length from at least 8 plants per plot | "Weedy" with weeds being flax at denisties of about 600 m-2 |
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Weedy_2011 | AG1631 | Newly emerged unfolded trifoliate less than 2 cm in length from at least 8 plants per plot | "Weedy" with weeds being naturally occurring velvetleaf and weedy common sunflower (Helianthus annuus) at denisties of about 160 m-2 |
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