Transcrition profiling of shoots from related model and cultivated Lotus plant species following salt acclimation
ABSTRACT: Many plant researchers have applied genomic tools to model species to identify abiotic stress responsive genes that might be useful for improving stress tolerance in crops. However, it is unclear whether this translational approach will be successful given the complexity of abiotic stress tolerance. We carried out a functional genomic (ionomic, transcriptomic and metabolomic) comparison of three model and three forage species of the genus Lotus with varying tolerance to salinity. Transcriptome analysis showed that about 60 % of expressed genes were responsive to salt treatment in one or more of the six species tested, but less than 1 % was responsive in all genotypes. Therefore, genotype-specific responses overshadowed conserved transcriptional responses to salinity and represent an impediment to translational genomics. Fortunately, 'triangulation' from multiple species enabled the identification of a core set of conserved and tolerant-specific responses that could provide durable tolerance across genotypes.
One of the objectives of plant translational genomics is to use knowledge and genes discovered in model species to improve crops. However, the value of translational genomics to plant breeding, especially for complex traits like abiotic stress tolerance, remains uncertain. Using comparative genomics (ionomics, transcriptomics and metabolomics) we analyzed the responses to salinity of three model and three cultivated species of the legume genus Lotus. At physiological and ionomic levels, models r ...[more]
Project description:L. japonicus (Regel) Larsen cv, Gifu were initially obtained from Prof. Jens Stougaard<br>(University Aarhus, Denmark) and then self-propagated at the University of Seville.<br>Seeds were scarified and surface-sterilized,<br>germinated in 1% agar Petri dishes, and transferred to pots using a 1:1 (v/v) mixture<br>of vermiculite and sand as solid support.<br>Five seedlings were planted in each pot and grown<br>during 35 days in a growth chamber under 16/8 hours<br>day/night, 20/18ï¿½C, with a photosynthetic photon flux<br>density of 250 ï¿½mol/m2ï¿½s and a constant humidity of 70%.<br> Plants were watered with Hornum nutrient solution.<br>Drought was applied withholding irrigation for the reported period<br>of time and sample plants or leaves were harvested for further analysis.
Project description:Model legume Lotus japonicus was subjected to non-lethal long-term salinity and profiled at the transcriptomic level. Three independent experiments were performed, testing two experimental designs: a traditional gradual acclimation following a step-wise increase of salt concentration and an initial acclimation approach (ia).
Project description:L. japonicus (Regel) Larsen cv, Gifu were initially obtained from Prof. Jens Stougaard <br>(University Aarhus, Denmark) and then self-propagated at the University of Seville.<br> Ljgln2-2 mutant was isolated from photorespiratory mutant screening as described <br>previously (Orea et al., 2002; Mï¿½rquez et al., 2005; Betti et al., 2006). <br>The mutant progeny of two consecutive back-crosses with WT was used<br> for the present work. WT and mutant seeds were scarified and surface-sterilized,<br> germinated in 1% agar Petri dishes, and transferred to pots using a 1:1 (v/v) mixture<br> of vermiculite and sand as solid support. <br>Five seedlings were planted in each pot and grown <br>during 35 days in a growth chamber under 16/8 hours<br> day/night, 20/18ï¿½C, with a photosynthetic photon flux <br>density of 250 ï¿½mol/m2ï¿½s and a constant humidity of 70%.<br> CO2 was automatically injected to a final concentration of 0.7% (v/v),<br> to allow for normal growth of Ljgln2-2 mutant in a photorespiration <br>suppressed atmosphere. Plants were watered with Hornum nutrient solution <br>(Handberg & Stougaard, 1992).<br> Drought was applied withholding irrigation for the reported period <br>of time and sample plants or leaves were harvested for further analysis.
Project description:Transcriptomic profiling was carried out for leaves of Lotus japonicus plants grown with different mineral nitrogen sources (NO3-, NH4+ or NH4NO3) or under conditions of biological nitrogen fixation (Nod). Nodulated plants were inoculated with Mesorhizobium loti and watered with nitrogen-free “Hornum” medium supplemented with 3 mM KCl. Plants under different nitrogen nutritions were watered with “Hornum” nutrient solution containing 10 mM KNO3 (NO3- plants) or with 10 mM NH4Cl supplemented with 3 mM KCl (NH4+ plants) or with 5 mM NH4NO3 supplemented with 3 mM KNO3 (NH4NO3 plants). After all the plants reached the size of 7 trifoils, leaf tissue was harvested. Every harvest involved at least three independent biological replicates for each treatment.
Project description:Wildtype and mutant plants lacking the plastidic isoform of glutamine synthetase were grown under CO2-enriched atmosphere and then transferred to low CO2 conditions. Transcriptomic profiling was carried out for plants under CO2-enriched atmosphere and plants after 2 days of transfer to low CO2 conditions.
Project description:Exponentially growing Sulfolobus acidocaldarius were treated with NaAc to generate replication runout and arrest in G2 phase. The cells were then resuspended in fresh acetate-free media which generates a synchronous population. Samples for investigation of gene expression change were taken during the synchronised populations progress through the cell cycle.
Project description:In order to study the physiological consequences of a high-copper diet on hepatic gene expression, 6 mM CuCl2 was added to the drinking water for a period of 1 month. After this period, livers of seven control mice and eight copper-treated mice were isolated and were subjected to microarray analysis and copper measurements. The hepatic gene expression profile of copper-treated mice was compared to non-treated mice using a pooled reference.
Project description:Nine time points for microarray analysis were chosen to study early and late transcriptional responses in copper metabolism upon copper overload in HepG2 cells. Samples of copper-treated cells were hybridized using non-treated samples as a reference.