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	Transcriptional profiling of mechanically and genetically sink-limited soybeans
Description	Soybean plants that do not produce a sink, such as depodded or male sterile plants, exhibit physiological and morphological changes during the reproductive stages, including increased levels of nitrogen and starch in the leaves and a delayed senescence. To identify transcriptional changes that occur in leaves of sink-limited plants, we used RNAseq to compare gene expression levels in trifoliate leaves from depodded and ms6 male sterile plants and control plants. In sink-limited tissues, we observed a deferral of the expression of senescence-associated genes and a continued high expression of genes associated with the maturity phase of leaf development. We identified GO-terms associated with growth and development and storage protein in sink limited tissues. We also identified that the bHLH. ARFs, and SBP transcription factors were expressed in sink limited tissues while the senescing control leaves expressed WRKY and NAC transcription factors. We identified genes that were not expressed during normal leaf development but highly expressed in sink-limited plants, including the D4 “non-yellowing” gene. These changes highlighted several metabolic pathways that were involved in distinct modes of resource parttioning in the “stay green” leaves. Overall design: Timecourse gene expression analysis of sink-limited soybean leaves. Gene expression was profiled from R2 growth stage (flowering) until the onset of leaf seenscence, and contrasted between mechanically and genetically sink-limited soybeans.
Contact	Crop Production and Pest Control, USDA-ARS
Xref	PRJNA339152
Reference	Brown AV & Hudson KA. 2017;
Conditions	14
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
T295H_Sterile_Control2	Line T295H		35 days after planting	leaf	Control			T295H_Sterile_Control2_1 T295H_Sterile_Control2_2 T295H_Sterile_Control2_3	SRR4036066 SRR4036067 SRR4036068	.bam .bai .csi .bam .bai .csi .bam .bai .csi
T295H_Sterile_Control3	Line T295H		63 days after planting	leaf	Control			T295H_Sterile_Control3_1 T295H_Sterile_Control3_2 T295H_Sterile_Control3_3	SRR4036072 SRR4036073 SRR4036074	.bam .bai .csi .bam .bai .csi .bam .bai .csi
T295H_Sterile2	Line T295H		35 days after planting	leaf	Sterile			T295H_Sterile2_1 T295H_Sterile2_2 T295H_Sterile2_3	SRR4036069 SRR4036070 SRR4036071	.bam .bai .csi .bam .bai .csi .bam .bai .csi
T295H_Sterile3	Line T295H		63 days after planting	leaf	Sterile			T295H_Sterile3_1 T295H_Sterile3_2 T295H_Sterile3_3	SRR4036075 SRR4036076 SRR4036077	.bam .bai .csi .bam .bai .csi .bam .bai .csi
T295H_SterileAP1	Line T295H		28 Days after planting (R2 growth stage)	leaf	Initial timepoint			T295H_SterileAP1_1 T295H_SterileAP1_2 T295H_SterileAP1_3	SRR4036063 SRR4036064 SRR4036065	.bam .bai .csi .bam .bai .csi .bam .bai .csi
Williams82_AP1	Line Williams 82		38 days after planting (R2 growth stage)	leaf	Initial timepoint			Williams82_AP1_1 Williams82_AP1_2 Williams82_AP1_3	SRR4036078 SRR4036079 SRR4036080	.bam .bai .csi .bam .bai .csi .bam .bai .csi
Williams82_Depodding_Control2	Line Williams 82		45 days after planting	leaf	Control			Williams82_Depodding_Control2_1 Williams82_Depodding_Control2_2 Williams82_Depodding_Control2_3	SRR4036081 SRR4036082 SRR4036083	.bam .bai .csi .bam .bai .csi .bam .bai .csi
Williams82_Depodding_Control3	Line Williams 82		54 days after planting	leaf	Control			Williams82_Depodding_Control3_1 Williams82_Depodding_Control3_2 Williams82_Depodding_Control3_3	SRR4036087 SRR4036088 SRR4036089	.bam .bai .csi .bam .bai .csi .bam .bai .csi
Williams82_Depodding_Control4	Line Williams 82		64 days after planting	leaf	Control			Williams82_Depodding_Control4_1 Williams82_Depodding_Control4_2 Williams82_Depodding_Control4_3	SRR4036093 SRR4036094 SRR4036095	.bam .bai .csi .bam .bai .csi .bam .bai .csi
Williams82_Depodding_Control5	Line Williams 82		76 days after planting	leaf	Control			Williams82_Depodding_Control5_1 Williams82_Depodding_Control5_2 Williams82_Depodding_Control5_3	SRR4036099 SRR4036100 SRR4036101	.bam .bai .csi .bam .bai .csi .bam .bai .csi
Williams82_Depodding2	Line Williams 82		45 days after planting	leaf	Depodded			Williams82_Depodding2_1 Williams82_Depodding2_2 Williams82_Depodding2_3	SRR4036084 SRR4036085 SRR4036086	.bam .bai .csi .bam .bai .csi .bam .bai .csi
Williams82_Depodding3	Line Williams 82		54 days after planting	leaf	Depodded			Williams82_Depodding3_1 Williams82_Depodding3_2 Williams82_Depodding3_3	SRR4036090 SRR4036091 SRR4036092	.bam .bai .csi .bam .bai .csi .bam .bai .csi
Williams82_Depodding4	Line Williams 82		76 days after planting	leaf	Depodded			Williams82_Depodding4_1 Williams82_Depodding4_2 Williams82_Depodding4_3	SRR4036102 SRR4036103 SRR4036104	.bam .bai .csi .bam .bai .csi .bam .bai .csi
Williams82_Depodding5	Line Williams 82		64 days after planting	leaf	Depodded			Williams82_Depodding5_1 Williams82_Depodding5_2 Williams82_Depodding5_3	SRR4036096 SRR4036097 SRR4036098	.bam .bai .csi .bam .bai .csi .bam .bai .csi