LegumeIP V3: From Models to Crops - An Integrative Gene Discovery Platform for Translational Genomics in Legumes

LegumeIP V3: From Models to Crops - An Integrative Gene Discovery Platform for Translational Genomics in Legumes

[G. max (gene)]
Detail of Experiment mapped on Glycine max Wm82 Gm275Wm82a2V1

Details

Name	Transcriptomics of weed stress in soybean
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	Horvath DP et al . 2015;
Conditions	8
Species	Glycine max
Metadata export	.CSV .JSON

Analysis

Mapped Genomes	Gm275Wm82a2V1 Gm508Wm82a4V1
Expression Analysis	Expression Profile / Differential Expression / Co-expression

Conditions

Name	Genotype	Mutation	Stage	Tissue	Treatment	Level	Time	Samples	Xref	Download alignments
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			Control_2008_1	SRR1531418	.bam .bai .csi
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			Control_2009_1	SRR1531419	.bam .bai .csi
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			Control_2010_1 Control_2010_2	SRR1531421 SRR1531420	.bam .bai .csi .bam .bai .csi
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			Control_2011_1 Control_2011_2	SRR1531423 SRR1531422	.bam .bai .csi .bam .bai .csi
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			Weedy_2008_1	SRR1531424	.bam .bai .csi
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			Weedy_2009_1	SRR1531425	.bam .bai .csi
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			Weedy_2010_1 Weedy_2010_2	SRR1531426 SRR1531427	.bam .bai .csi .bam .bai .csi
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			Weedy_2011_1 Weedy_2011_2	SRR1531428 SRR1531429	.bam .bai .csi .bam .bai .csi