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

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Comparative analysis of drought-responsive transcriptome in soybean lines contrasting for canopy wilting Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of abiotic stress molecular pathways. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of contrasting slow wilting lines to quantify transcript abumdance under drought stress condition Overall design: Methods: The three biological replicates of DS line, Pana (control and drought samples) and DT line, PI 567690 (control and drought samples) leaf sample RNA were multiplexed and s......[More] Digital Biology Lab, Computer Science, University of Missouri 4
Gene Expression Changes during embryo and seed maturation, quiescence and germination in soybean To understand the molecular events underlying seed maturation, quiescence and germination, we performed transcriptome analysis of soybean (Glycine max) embryos at four seed developmental stages (cotyledon, early, mid and late maturation), mature dry seeds, and seedlings, eight days after seed sowing. Overall design: mRNA profiling was performed on embryos at 4 stages of development, dry seeds and seedlings. Three biological replicates were collected for each developmental stage. Harada lab, Plant Biology, University of California
Mutations in Argonaute5 Illuminate Epistatic Interactions of the K1 and I Loci Leading to Saddle Seed Color Patterns in Glycine max The soybean (Glycine max) seed coat has distinctive, genetically programmed patterns of pigmentation and the recessive k1 mutation can epistatically overcome the dominant I and i-i alleles, which inhibit seed color by producing small interfering RNAs (siRNAs) targeting chalcone synthase (CHS) mRNAs. Small RNA sequencing of dissected regions of immature seed coats demonstrated that CHS siRNA levels cause the patterns produced by the i-i and i-k alleles of the I locus, which restrict pigment to th......[More] Lila Vodkin, Crop Sciences, University of Illinois 2
Transcriptional profiling of mechanically and genetically sink-limited soybeans 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 obser......[More] Crop Production and Pest Control, USDA-ARS 14
Large-scale analysis of soybean embryonic axis in five time points during germination Purpose: This RNA-Seq study aims on elucidate the major trends in the transcriptional profile of soybean embryonic axes during germination. Methods: Soybean seeds were germinated in soaked cotton at 28ºC. In addition to dry seeds, seeds were harvested at 3, 6, 12, 24 hours after imbibition. Then the embryonic axes were separated from the cotyledons for RNA extraction. For each biological sample, 20 seeds were used. Results: Identification of genes and pathways involved in metabolism, hormone sig......[More] LQFPP, CBB, Universidade Estadual do Norte Fluminense Darcy Ribeiro 5
Whole genome-wide transcript profiling to identify differentially expressed genes associated with seed field emergence in two soybean low phytate mutants Seed germination is important to soybean (Glycine max) growth and development, ultimately affecting soybean yield. A lower seed field emergence has been the main hindrance for breeding soybeans low in phytate. Although this reduction could be overcome by additional breeding and selection, the mechanisms of seed germination in different low phytate mutants remain unknown. In this study, we performed a comparative transcript analysis of two low phytate soybean mutants (TW-1 and TW-1-M), which have......[More] Zhejiang Academy of Agricultural Sciences
Transcriptome Profile of Near-Isogenic Soybean Lines for Beta-Conglycinin Alpha-Subunit Deficiency during Seed Maturation To identify Alpha-null-related transcriptional changes, the gene expressions of cgy-2-NIL and its recurrent parent DN47 were compared using Illumina high-throughput RNA-sequencing on samples at 25, 35, 50, and 55 days after flowering (DAF). Seeds at 18 DAF served as the control. Overall design: Compare gene quantity and expression between the cgy-2-NIL and DN47 in five stages of soybean seeds collected at 18, 25, 35, 50, and 55 day after flowering Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University 10
Transgenic and conventional cultivar comparison in response to salt stress Soybean is one of the main sources of oil worldwide. Salinity severely affect its yield. GmSIN1 is a NAC transcription factor coding gene. Its overexpression (OE) transgenic lines greatly improved the yield in both common and saline fields. This study focuses on founding changes genes between GmSIN1 OE transgenic seedlings and control seedlings under salt stress or non-salt stress conditions. Illumina Solexa sequencing platform was used for the comparative analysis of transcriptome profiles in t......[More] School of life science, Shandong University 4
Transcriptomics of weed stress in soybean 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 ......[More] Bioscience Research Lab, Agr. Research Service, US Dept. Agriculture 8
Glycine max Gene expression Analysis of Iron Stress Response RNAseq was used to compare gene expression in soybean grown in iron sufficient and deficient conditions, one and six hours after transfer into iron stress conditions USDA-ARS 8
Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit The purpose of this study is to compare transcriptome profiles of one fast wilting and two slow wilting genotypes under low- and high- vapor pressure deficit Experiments: Five differential expression analyses were performed. 1. Differences within the Hutchesen line for slow and fast wilting; 2. Differences within the PI471938 line for slow and fast wilting; 3. Differences within the PI416937 line for slow and fast wilting; Differences between Hutchesen, PI471938 and PI416937 (regardless of pheot......[More] BCSC, BRC, NC State University 6
Distinct transcriptional profiles of ozone stress in soybean (Glycine max) flowers and pods The sustainability of soybean growth is being significantly affected by increases in ozone concentration. Current increases in ozone concentrations have decreased soybean yields by ~15-25%. Furthermore, soybean plants differentiate many more floral buds than survive to mature pods. Studies have found that pod set can be as low as 20-40% under normal conditions. Generally, it is assumed that abortion rates can vary based on location in the canopy, source-sink relationship, hormone levels, shade, ......[More] University of Illinois Urbana Champaign 4
Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos Soybean (Glycine max) seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential me......[More] GBCB, virginia Tech 10
RNA-seq analysis reveals genetic response and tolerance mechanisms to ozone exposure in soybean Oxidative stress caused by ground level ozone is a major contributor to yield loss in a number of important crop plants. Soybean (Glycine max) is especially ozone sensitive, and research into its response to oxidative stress is limited. To better understand the genetic response in soybean to oxidative stress, an RNA-seq analysis of two soybean cultivars was performed comparing an ozone intolerant cultivar and an ozone resistant cultivar after being exposed to ozone. A cursory analysis of the tra......[More] Schlueter, Bioinformatics and Genomics, UNCC 4
Transcriptomic comparison reveals genetic variation potentially underlying seed developmental evolution of soybeans Soybean (Glycine max) was domesticated from its wild relative Glycine soja. However, the genetic variations underlying soybean domestication are not well known. Comparative transcriptomics revealed that a small portion of the orthologous genes might have been fast-evolving. In contrast, three gene expression clusters were identified as divergent by their expression patterns, which occupied 37.44% of the total genes, hinting at an essential role for gene expression alteration in soybean domestica......[More] Chinese Academy of Sciences 20
Transcriptomic study of soybean (Glycine max) in response to zinc deficiency (soybean) We conducted a genome-wide transcriptomic analysis in soybean leaves and roots treated with zinc (Zn) deficiency using RNA sequencing (RNA-seq) technology. Two biological replicates of RNA-seq were included for Zn-sufficient leaves (ZSL), Zn-deficient leaves (ZDL), Zn-sufficient roots (ZSR), and Zn-deficient roots (ZDR). Therefore a total of eight libraries were constructed. Using a 2-fold change and a P-value ≤0.05 as the cut-off for selecting the differentially expressed transcripts, we global......[More] Hangzhou Normal University 4
RNA-seq analysis of distal gene expression changes during nodulation (soybean) Legume plants form symbiotic relationships with diazotrophic bacteria called rhizobia. During such symbiosis, plants provide bacteria with preferred carbon sources such as malate and succinate in return for essential reduced nitrogen. Compatible interactions result in a series of plant root modifications that eventually result in nodule formation. Bacteria living in the nodule cells fix nitrogen via the nitrogenase enzyme complex. Interestingly, as in plant-pathogen interactions, incompatibility......[More] Iowa State University 3