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

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Name Description Contact Reference Conditions
important ethylene signaling for isoflavonoid mediated resistance to Rhizoctonia solani in roots The root-infecting necrotrophic fungal pathogen Rhizoctonia solani causes significant disease to all the world’s major food crops. As a model for pathogenesis of legumes we have examined the interaction of R. solani AG8 with Medicago truncatula. RNAseq analysis of the moderately resistant M. truncatula accession A17 and highly susceptible sickle (skl) mutant (defective in ethylene sensing) identified major transcriptional reprogramming early in A17. Responses specific to A17 included components ......[More] CSIRO 8
effects of rhizobia and mycorrhizal fungi on expression in roots of model legume Study examines effects of rhizobia and mycorrhizal fungi on genome-wide expression in roots of model legume as well as the effects of rhizobia on mycorrhizal gene expression. University of Miami 4
inoculation of symbiotic fungi with medicago truncatula root and nodule Root and/or nodule tissues of four Medicago truncatula accessions were subjected to RNA-Seq. Three treatments were performed for each accession: 14 days post inoculation (dpi) using Sinorhizobium meliloti (KH46c) strain, 14 days dpi using Sinorhizobium Medicae (WSM419) strain as well as uninoculated root tissue as control. Three replications were done for each treatment. University of Minnesota
  • unpublished;
TSAR1 and TSAR2 activate triterpene saponin production in Medicago truncatula We identified two novel transcription factors ‘Triterpene Saponin Activation Regulator’ (TSAR) 1 and 2 that each activate a specific branch of saponin synthesis in M. truncatula. Therefore we generated three independent TSAR1 and three independent TSAR2 overexpression (OE) hairy root lines. As a control we raised three independent hairy root lines expressing a non-functional GUS gene. By qRT-PCR analyses and metabolite profiling of these lines, we found that TSAR1 OE leads to accumulation of non......[More] Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium Department of Plant Systems Biology,VIB, Gent, Belgium 3
importance of DNA (de)methylation and epigenetic regulations for indeterminate nodule development Epigenetic mechanisms are known to regulate gene expression but no regulators have been characterized in the context of nodule development in legumes. Here, we describe DEMETER (DME) in Medicago truncatula, a gene coding for a demethylase that is required for normal symbiosome differentiation during nodule development. MtDMEis strongly upregulated in indeterminate nodules in the differentiation zone. The role of DMEduring nodule development was analyzed by using an RNA interference approach. Thi......[More] INRA-CNRS 5
CK dependent Rhizobium LCO induced signalling in Medicago truncatula RNAseq analysis of Medicago truncatula WT and Mtcre1 3h post rhizobium LCO application 4 sample with 3 biological replicates each, sequenced in both directions Wageningen University, Laboratory of Molecular Biology 8
Expression analysis of MtTdp1 depleted plants Expression analysis of MtTdp1 depleted plants Università di Verona - Functional Genomics Centre
  • unpublished;
A17 and the ethylene insensitive sickle mutant interacting with the fungal root pathogen, Rhizoctonia solani AG8 This study compares the response of wild type (A17) and ethylene insensitive mutant (sickle) lines of the model legume Medicago truncatula to infection by the root-infecting necrotrophic fungal pathogen, Rhizoctonia solani AG8 (WAC10335). Two time points were taken, 2 and 7 days after inoculation along with corresponding mock-treated controls. CSIRO Agriculture and Food 8
transcriptome profiling of Agrobacterium-mediated infiltration of transcription factors to discover gene function and expression networks in plants Medicago truncatula leaves were infiltrated with Agrobacterium harbouring different transcription factors (compared to control infiltrations). Agroinfiltration results in specific transcription factor-mediated gene expression profiles. Transcriptome profiling of agroinfiltration of transcription factors allows the discovery of gene function and expression networks in plants University of Otago 2
Nodule Development 3 Publicly available RNA-seq dataset from UCDAVIS was collected from a time-course of rhizobial infection events within the first 48 hours post-inoculation (hpi). UCDAVIS (drcook@ucdavis.edu) 36
RNA-seq of mycorrhizal Medicago truncatula roots under K+ deprivation (barrel medic) Arbuscular mycorrhizal (AM) associations enhance the phosphorous and nitrogen nutrition of host plants, but little is known about their role in potassium (K+) nutrition. Medicago truncatula plants were co-cultured with the AM fungus Rhizophagus irregularis under high and low K+ regimes for six weeks. We determined how K+ deprivation affects plant development, mineral acquisition, and how these negative effects are tempered by the AM colonization. The transcriptional response of AM roots under K+......[More] Ané lab, Bacteriology, University of Wisconsin-Madison 4
Symbiotic Interactions 3 Publicly available RNA-seq dataset from INRA-CNRS was collected from root epidermis after 4 or 24h treatment with Nod factors or mock treatment in n order to analyze very early symbiotic stages. Pascal Gamas (pascal.gamas@toulouse.inra.fr) 4
Transcriptomic response to Nod Factor treatments on Medicago NGS2013-04: Transcriptomic response to Nod Factor treatments on Medicago Role of the root hair in water and nutrient uptake and the establishment of the nitrogen-fixing symbiotic interaction with rhizobia. Overall design: The RNA was extracted from root hairs of Medicago: control vs treated by nod factors (2 biological replicates) INRA - CNRS – UEVE 3
transcriptome profile of plant roots treated with Nod factors This experiment was part of a larger study to elucidate the early effects of Nod factor treatment on the Medicago truncatula phosphoproteome, transcriptome and metabolome in wildtype and two mutant strains. In this experiment, RNA-Seq was used to measure transcriptional changes in plant roots treated +/- Nod factors for 1 hr. RNA was extracted and sequenced from three biological replicates of each treatment condition in wildtype as well as mutants in nfp and dmi3, two genes known to be involved ......[More] University of Wisconsin-Madison 6
Hormone treatment RNA-seq libraries were obtained from roots of Medicago truncatula A17 plants three days post germination. The seedlings were immersed in water (pH 6.8) containing the hormones at different concentrations; 1 uM IAA (Auxin), 100 nM BAP (Cytokinin) and an equal volume of the solvent control (DMSO). The seedlings were placed in the dark for 3 hours after which the root tips were removed and 40-60 roots per replicate were used. Sonali Roy (sroy@noble.org) or Ivone Torres-Jerez (itjerez@noble.org) 3
Symbiotic Interactions and Root Development In order to better understand the commonalities and differences in lateral root and nodule development, we compared their organogenesis and correlated this with changes in gene expression. To initiate lateral roots in Medicago truncatula we turned 2-day-old seedlings 135°, before returning them to their original axis of growth, while for nodule initiation we applied droplets of Sinorhizobium meliloti on the susceptibility zone of the root. Overall design: Medicago truncatula mRNA samples from ro......[More] Tak Lee (tak.lee@slcu.cam.ac.uk) 59
Macronutrient Deficiencies 1 RNA-seq libraries were prepared from roots and shoots of plants grown under sulfur (S), potassium (K), nitrogen (N) and phosphorus depleted conditions. The response to persistent deficiency was tested by growing the plants for 3 weeks under full nutrition (FN) or under deficiency of N, P, K or S. Additional samples were collected from plants re-supplied with FN for 6 h following the nutrient-deficiency treatment. Thomas de Bang (tdb@plen.ku.dk) 24
Macronutrient Deficiencies 2 RNA-seq libraries were prepared from roots and shoots of plants grown under full nutrition, and with no nitrogen or phosphorus collected after 22 days of germination. Pooja Pandey-Pant (pppant@noble.org) 6
Nodule Development 1 RNA-seq libraries were obtained from roots and nodules at varying developmental stages of nodulation with Sinorhizobium meliloti. The stages were: pre-inoculated root; root at 4 dpi, harboring the initial nodule bump during initiation; nodule at 10 dpi (expanding nodule); nodule at 14 dpi (actively-fixing nodule), and 28 dpi (senescing nodule). Additional samples were collected from nodules that were re-supplied with nitrogen at 14 dpi, to suppress nitrogen fixation. Rebecca Dickstein (Rebecca.Dickstein@unt.edu) or Vijay Veerappan (veerappanv@easternct.edu) 7
Plant Organs RNA-seq libraries were prepared from different plant organs: root, leaf, leaf bud, pod, flower, petiole, and bare stalk collected at different stages. Ivone Torres-Jerez (itjerez@noble.org)
Transcriptomic changes in Medicago truncatula root nodules during drought stress RNA was obtained from Medicago truncatula non-inoculated roots (R) and root nodules (inoculated with Sinorhizobium meliloti) either subjected to drought for two (T2) or four (T4) days, or well-watered control (T0). Two biological replicates for each sample was obtained. Each biological replicate consisted of roots or nodules harvested from 10-12 plants. RNA obtained from root nodules contained both plant and bacterial RNA. Weronika Czarnocka (weronika_czarnocka@sggw.pl) 4
Salt Stress RNA-seq libraries were prepared from roots and shoots of plants grown under salt treatment (NaCl) collected after 25 days. Yun Kang (ykang@noble.org)
Symbiotic Interactions 1 Publicly available RNA-seq dataset from LIPM-INRA-CNRS was collected from P-starved root tissue treated with sulfated or non-sulfated Myc-LCOs for three hours. LIPM-INRA-CNRS (weblipm@toulouse.inra.fr) 3
Symbiotic Interactions 2 M. truncatula plants (wild type and SUNN mutant) were inoculated or not with the arbuscular mycorrhizal fungus Rhizophagus irregularis. RNA-seq libraries were prepared from root and shoot tissues. Thomas de Bang (tdb@plen.ku.dk) 8
Nodule Development 2 RNA-seq datasets from LIPM-INRA-CNRS were collected from root nodules at 15 dpi after inoculation with S. meliloti. LIPM-INRA-CNRS (weblipm@toulouse.inra.fr) 5
The U-box family genes in Medicago truncatula: key elements in response to salt, cold, and drought stresses The ubiquitination pathway regulates growth, development, and stress responses in plants, and the U-box protein family of ubiquitin ligases has important roles in this pathway. Here, 64 putative U-box proteins were identified in the Medicago truncatula genome. In addition to the conserved U-box motif, other functional domains, such as the ARM, kinase, KAP, and WD40 domains, were also detected. Phylogenetic analysis of the M. truncatula U-box proteins grouped them into six subfamilies, and chromo......[More] Jiang Xi Agricultural University 12