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Kowalski, A. M., Gooding, M., Ferrante, A., Slafer, G. A., Orford, S., Gasperini, D. & Griffiths, S. Agronomic assessment of the wheat semi-dwarfing gene Rht8 in contrasting nitrogen treatments and water regimes Field Crop Res 191, 150-160, (2016) DOI: 10.1016/j.fcr.2016.02.026

Reduced height 8 (Rht8) is the main alternative to the GA-insensitive Rht alleles in hot and dry environments where it reduces plant height without yield penalty. The potential of Rht8 in northern-European wheat breeding remains unclear, since the close linkage with the photoperiod-insensitive allele Ppd-D1a is unfavourable in the relatively cool summers. In the present study, two near-isogenic lines (NILs) contrasting for the Rht8/tall allele from Mara in a UK-adapted and photoperiod-sensitive wheat variety were evaluated in trials with varying nitrogen fertiliser (N) treatments and water regimes across sites in the UK and Spain.

The Rht8 introgression was associated with a robust height reduction of 11% regardless of N treatment and water regime and the Rht8 NIL was more resistant to root-lodging at agronomically-relevant N levels than the tall NIL. In the UK with reduced solar radiation over the growing season than the site in Spain, the Rht8 NIL showed a 10% yield penalty at standard agronomic N levels due to concomitant reduction in grain number and spike number whereas grain weight and harvest index were not significantly different to the tall NIL. The yield penalty associated with the Rht8 introgression was overcome at low N and in irrigated conditions in the UK, and in the high-temperature site in Spain. Decreased spike length and constant spikelet number in the Rht8 NIL resulted in spike compaction of 15%, independent of N and water regime. The genetic interval of Rht8 overlaps with the compactum gene on 2DS, raising the possibility of the same causative gene. Further genetic dissection of these loci is required.


    ANOVA, analysis of variance; Y, yield; HI, harvest index; GN, grain number (m−2); SS, spikelet number (spike−1); SN, spike number (m−2); HD, heading date; AN, anthesis; 12L, length of the second internode from the top; 13L, length of the third internode from the top; PAR, photosynthetically active radiation; R: FR, red: far-red light reflectance ratio; RCBD, randomised complete block design


Gasperini, D. & Acosta, I. F. and Farmer, E. E. Cotyledon Wounding of Arabidopsis Seedlings. Bio-protocol 6 (2), e1712, (2016)


Gasperini, D., Chauvin, A., Acosta, I.F., Kurenda, A., Stolz, S., Chétalat, A., Wolfender J.-L. & Farmer, E.E. Axial and Radial Oxylipin Transport. Plant Physiol. 169, 2244-2254, (2015) DOI: 10.1104/pp.15.01104


Gasperini, D., Chételat, A., Acosta, I.F., Goossens, J., Pauwels, L., Goossens, A., Dreos, R., Alonso, E. & Farmer, E.E. Multilayered Organization of Jasmonate Signalling in the Regulation of Root Growth PLoS Genet. 11 (6), e1005300, (2015) DOI: 10.1371/journal.pgen.1005300

Physical damage can strongly affect plant growth, reducing the biomass of developing organs situated at a distance from wounds. These effects, previously studied in leaves, require the activation of jasmonate (JA) signalling. Using a novel assay involving repetitive cotyledon wounding in Arabidopsis seedlings, we uncovered a function of JA in suppressing cell division and elongation in roots. Regulatory JA signalling components were then manipulated to delineate their relative impacts on root growth. The new transcription factor mutant myc2-322B was isolated. In vitro transcription assays and whole-plant approaches revealed that myc2-322B is a dosage-dependent gain-of-function mutant that can amplify JA growth responses. Moreover, myc2-322B displayed extreme hypersensitivity to JA that totally suppressed root elongation. The mutation weakly reduced root growth in undamaged plants but, when the upstream negative regulator NINJA was genetically removed, myc2-322B powerfully repressed root growth through its effects on cell division and cell elongation. Furthermore, in a JA-deficient mutant background, ninja1 myc2-322B still repressed root elongation, indicating that it is possible to generate JA-responses in the absence of JA. We show that NINJA forms a broadly expressed regulatory layer that is required to inhibit JA signalling in the apex of roots grown under basal conditions. By contrast, MYC2, MYC3 and MYC4 displayed cell layer-specific localisations and MYC3 and MYC4 were expressed in mutually exclusive regions. In nature, growing roots are likely subjected to constant mechanical stress during soil penetration that could lead to JA production and subsequent detrimental effects on growth. Our data reveal how distinct negative regulatory layers, including both NINJA-dependent and -independent mechanisms, restrain JA responses to allow normal root growth. Mechanistic insights from this work underline the importance of mapping JA signalling components to specific cell types in order to understand and potentially engineer the growth reduction that follows physical damage.


Raschke, A., Ibañez, C., Ullrich, K., Anwer, M., Becker, S., Glöckner, A., Trenner, J., Denk, K., Saal, B., Sun, X., Ni, M., Davis, S., Delker, C. & Quint, M. Natural variants of ELF3 affect thermomorphogenesis by transcriptionally modulating PIF4-dependent auxin response genes BMC Plant Biol. 15, 197, (2015) DOI: 10.1186/s12870-015-0566-6


Perception and transduction of temperature changes result in altered growth enabling plants to adapt to increased ambient temperature. While PHYTOCHROME-INTERACTING FACTOR4 (PIF4) has been identified as a major ambient temperature signaling hub, its upstream regulation seems complex and is poorly understood. Here, we exploited natural variation for thermo-responsive growth in Arabidopsis thaliana using quantitative trait locus (QTL) analysis.


We identified GIRAFFE2.1, a major QTL explaining ~18 % of the phenotypic variation for temperature-induced hypocotyl elongation in the Bay-0 x Sha recombinant inbred line population. Transgenic complementation demonstrated that allelic variation in the circadian clock regulator EARLY FLOWERING3 (ELF3) is underlying this QTL. The source of variation could be allocated to a single nucleotide polymorphism in the ELF3 coding region, resulting in differential expression of PIF4 and its target genes, likely causing the observed natural variation in thermo-responsive growth.

ConclusionsIn combination with other recent studies, this work establishes the role of ELF3 in the ambient temperature signaling network. Natural variation of ELF3-mediated gating of PIF4 expression during nightly growing periods seems to be affected by a coding sequence quantitative trait nucleotide that confers a selective advantage in certain environments. In addition, natural ELF3 alleles seem to differentially integrate temperature and photoperiod information to induce architectural changes. Thus, ELF3 emerges as an essential coordinator of growth and development in response to diverse environmental cues and implicates ELF3 as an important target of adaptation. 


Farmer, E.E., Gasperini, D. & Acosta, I.F. The squeeze cell hypothesis for the activation of jasmonate synthesis in response to wounding New Phytol. 204, 282-288, (2014) DOI: 10.1111/nph.12897


Acosta, I.F., Gasperini, D., Chételat, A., Stolz, S., Santuari, L. & Farmer, E.E. Role of NINJA in root jasmonate signaling. In: PNAS 110 (38), 15473-15478, (2013) DOI: 10.1073/pnas.1307910110


Poeschl, Y., Delker, C., Trenner, J., Ullrich, K. & Quint, M. & Grosse, I. Optimized probe masking for comparative transcriptomics of closely related species. PLOS ONE 8, e78497, (2013)

Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays are

restricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence,

transcriptomics approaches of non-model organisms as well as comparative transcriptomics studies among two or more

species often make use of cost-intensive RNAseq studies or, alternatively, by hybridizing transcripts of a query species to a

microarray of a closely related species. When analyzing these cross-species microarray expression data, differences in the

transcriptome of the query species can cause problems, such as the following: (i) lower hybridization accuracy of probes due

to mismatches or deletions, (ii) probes binding multiple transcripts of different genes, and (iii) probes binding transcripts of

non-orthologous genes. So far, methods for (i) exist, but these neglect (ii) and (iii). Here, we propose an approach for

comparative transcriptomics addressing problems (i) to (iii), which retains only transcript-specific probes binding transcripts

of orthologous genes. We apply this approach to an Arabidopsis lyrata expression data set measured on a microarray

designed for Arabidopsis thaliana, and compare it to two alternative approaches, a sequence-based approach and a genomic

DNA hybridization-based approach. We investigate the number of retained probe sets, and we validate the resulting

expression responses by qRT-PCR. We find that the proposed approach combines the benefit of sequence-based stringency

and accuracy while allowing the expression analysis of much more genes than the alternative sequence-based approach. As

an added benefit, the proposed approach requires probes to detect transcripts of orthologous genes only, which provides asuperior base for biological interpretation of the measured expression responses.


Gasperini, D., Greenland, A., Hedden, P., Dreos, R., Harwood, W. & Griffiths, S. Genetic and physiological analysis of Rht8 in bread wheat: an alternative source of semi-dwarfism with a reduced sensitivity to brassinosteroids.. In: J. Exp. Bot. 63, 4419-4436, (2012) DOI: 10.1093/jxb/ers138


Quint, M., Drost, H-G., Gabel, A., Ullrich, K., Bönner, M. & Grosse, I. A transcriptomic hourglass in plant embryogenesis Nature 490, 98-101, (2012)

Animal and plant development starts with a constituting phase called embryogenesis, which evolved independently in both lineages1. Comparative anatomy of vertebrate developmentbased on the Meckel-Serrès law2 and von Baers laws of embryology3 from the early nineteenth centuryshows that embryos from various taxa appear different in early stages, converge to a similar form during mid-embryogenesis, and again diverge in later stages. This morphogenetic series is known as the embryonic hourglass4, 5, and its bottleneck of high conservation in mid-embryogenesis is referred to as the phylotypic stage6. Recent analyses in zebrafish and Drosophila embryos provided convincing molecular support for the hourglass model, because during the phylotypic stage the transcriptome was dominated by ancient genes7 and global gene expression profiles were reported to be most conserved8. Although extensively explored in animals, an embryonic hourglass has not been reported in plants, which represent the second major kingdom in the tree of life that evolved embryogenesis. Here we provide phylotranscriptomic evidence for a molecular embryonic hourglass in Arabidopsis thaliana, using two complementary approaches. This is particularly significant because the possible absence of an hourglass based on morphological features in plants suggests that morphological and molecular patterns might be uncoupled. Together with the reported developmental hourglass patterns in animals, these findings indicate convergent evolution of the molecular hourglass and a conserved logic of embryogenesis across kingdoms.

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