Biology subjects

Scheible, W.-R.

Publications and source records attributed to Scheible, W.-R..

4 recordsLinked to original sources

bioRxiv2024

Comparative Transcriptomics of Arabidopsis, Medicago, Brachypodium and Setaria species during Phosphorus limitation

Translating biological knowledge from Arabidopsis to crop species is important to advance agriculture and secure food production in the face of dwindling fertilizer resources, biotic and abiotic stresses. However, it is often not trivial to identify functional homologs (orthologs) of Arabidopsis genes in crops. Combining sequence and expression data can improve the correct prediction of orthologs. Here, we conducted a large-scale RNA sequencing based transcriptomics study of Arabidopsis, Medicago, Brachypodium and Setaria grown side-by-side in Phosphorus (P)-sufficient and P-limited conditions to generate comparable transcriptomics datasets. Comparison of top 200 P-limitation induced genes in Arabidopsis revealed that [~]80% of these genes have identifiable close homologs in the other three species but only [~]50% retain their P-limitation response in the legume and grasses. Most of the hallmark genes of the P-starvation response were found conserved in all four species. This study reveals many known, novel, unannotated, conserved and species-specific regulations of the transcriptional P-starvation response. Identification and experimental verification of expressologs by independent RT-qPCR for P-limitation marker genes in Prunus showed the usefulness of comparative transcriptomics in pinpointing the functional orthologs in diverse crop species. This study provides an unprecedented resource for functional genomics and translational research to create P-efficient crops. HIGHLIGHTComparative transcriptomics reveals novel, known, conserved and specific transcriptome responding to Phosphorus limitation in Arabidopsis, Medicago, Brachypodium and Setaria to facilitate translational research in crops.

molecular biology↗

bioRxiv2024

A Multitrait Genome-Wide Association Study Reveals a Requirement for the Strigolactone Receptor DWARF14 in Optimal GOLVEN10 Signaling

GOLVEN/ROOT MERISTEM GROWTH FACTOR family of signaling peptides have been shown to control root lateral organ number, density and positioning in plants, although the signaling pathways involved remain obscure. A diverse set of 171 Medicago truncatula HapMap accessions with variation in responses to the GOLVEN 10 peptide, GLV10, were used to identify 74 significant loci controlling seven traits related to nodule formation and root architecture. Importantly, a single nucleotide polymorphism (SNP) in the upstream region of the MtGLV10 peptide-inducible strigolactone receptor gene, MtDWARF14 was significantly associated with insensitivity of nodule density to GLV10, suggesting a link between strigolactone signaling and GLV10 responsiveness. Three independent d14 mutants of the DWARF14 gene were found to hypernodulate, while overexpression of the gene led to reduction in nodule number, phenocopying GLV10. A null mutant, mtd14-1, remained sensitive to GLV10s effect on nodule density. However, at the transcriptional level, the mutant failed to effectively induce the expression of the GOLVEN marker genes, MtPLETHORA3 and MtPINLIKES2. Our study uncovers a hitherto unknown link between the strigolactone and GLV peptide signaling pathways using genotype x environment analysis of Medicago HapMap lines and provides a putative molecular mechanism for recovery from frost damage to fine roots.

plant biology↗

bioRxiv2022

The peptide GOLVEN10 controls nodule and lateral root organogenesis and positioning along the longitudinal root axis

O_LIGLV/RGF peptide encoding genes can be identified in genomes of all plants that can form roots or root-like structures suggesting they were essential for transition of plants to land. C_LIO_LIIn Medicago truncatula, five of fifteen GOLVEN(GLV)/ROOT MERISTEM GROWTH FACTOR (RGF) peptide coding genes were induced during nodule organogenesis and to a varying extent under nitrogen deficiency and auxin treatment. Expression of MtGLV9 and MtGLV10 at nodule initiation sites was dependent on the transcription factor NODULE INCEPTION. C_LIO_LIOverexpression of all five nodule-induced GLV genes in M. truncatula hairy roots as well as application of the corresponding synthetic peptides resulted in a 25-50% reduction in nodule number indicating GOLVENs are negative regulators of nodule organogenesis. C_LIO_LIThe peptide GOLVEN10 shifted the position of the first formed lateral root (rhizotaxis) as well as the first formed nodule along the longitudinal primary root axis, a phenomenon we term nodulotaxis, thereby reducing the absolute length of the zone of lateral organ formation on roots. C_LIO_LIApplication of synthetic GOLVEN10 peptide caused an increase in cell number but not cell length in each root cortical cell layer causing an increase in root length and a consequent spatiotemporal delay in formation of the first lateral organ. C_LI Plain Language SummaryNodule positioning is an understudied trait, yet it determines the length of the root that can support nodule formation and consequently the total number of functional nodules formed. We identify for the first time, genetic factors called GOLVEN peptides that alter nodule and lateral root positioning on the primary root along with several other traits including nodule organ initiation and root architecture.

plant biology↗

bioRxiv2021

Application of synthetic peptide CEP1 increases nutrient uptake rates along plant roots

The root system of a plant provides vital functions including resource uptake, storage, and anchorage in soil. Uptake from the soil of macro-nutrients like nitrogen (N), phosphorus (P), potassium (K), and sulphur (S) is critical for plant growth and development. Small signaling peptide (SSP) hormones are best known as potent regulators of plant growth and development with a few also known to have specialized roles in macronutrient utilization. Here we describe a high-throughput screen of SSP effects on root uptake of multiple nutrients. The SSP, MtCEP1 enhanced nitrate uptake rate per unit root length in Medicago truncatula plants deprived of N. MtCEP1 and AtCEP1 enhanced uptake not only of nitrate, but also phosphate and sulfate in both Medicago and Arabidopsis. Transcriptome analysis of Medicago roots treated with different MtCEP1 encoded peptide domains revealed that hundreds of genes respond to these peptides, including several nitrate transporters and a sulfate transporter that may mediate the uptake of these macronutrients downstream of CEP1 signaling. Likewise, several putative signaling pathway genes were induced in roots by CEP1 treatment. Thus, a scalable method has been developed for screening synthetic peptides of potential use in agriculture, with CEP1 shown to be one such peptide.

plant biology↗