Plant Biology最新文献

Plant development in many species including Arabidopsis relies on the accurate balance between growth and defence. A high degree of plant immunity is often accompanied by reduced growth. On the one hand, this growth-defence trade-off depends on the redistribution of metabolic power to either growth or defence. On the other hand, its regulation requires distinct molecular signalling pathways. Reduced growth of the Arabidopsis autoimmune mutant chs3-2D, which shows strong resistance to pathogens, has been rescued by the addition of the low molecular weight compound Ro 8-4304. The application of Ro 8-4304, however, also resulted in a decrease of immune responses to wild-type levels. We applied chemical modification of Ro 8-4304 to identify a derivative that rescues growth of the autoimmune mutant chs3-2D without compromising it immune capacity. In a screening of Ro 8-4304 derivatives, removal of a fluorine atom resulted in the derivative Ro-A03 that rescued growth, but did not affect the increased immune gene expression in chs3-2D. In the presence of Ro-A03 chs3-2D seedlings showed wild-type-like growth, but were more resistant to bacterial pathogens than wild-type seedlings, in line with salicylic acid levels that were higher than in the absence of Ro-A03. We generated a compound by chemical modification that can efficiently rescue growth without decreasing the immune response of the chs3-2D autoimmune mutant.

Rice plays a pivotal role as a vital food source for human consumption. Identifying gene-phenotype associations (GPAs) can significantly enhance the tolerance of rice to environmental stress and its overall yield. Nevertheless, the experimental process of discovering GPAs is not only consume a lot of resources but also time-consuming. The computational screening for GPAs has emerged as an essential tool to complement and expedite biological experiments. In this study, we tackle the prediction of GPAs by framing it as a node classification task, and introduce RGPA-GCN, an innovative computational approach leveraging graph convolutional networks. RGPA-GCN constructs a topology graph through the application of the k-nearest neighbor method for effective information aggregation. The nodes within this graph encapsulate both gene functional similarity and phenotype semantic similarity, enhancing the accuracy of our predictions. Notably, the RGPA-GCN approach demonstrates its ability to predict both unknown GPAs and previously unseen genes or phenotypes. Leveraging 5-fold cross-validation, RGPA-GCN exhibits commendable performance, outperforming six classical machine learning methods, and three state-of-the-art models. Additionally, the ablation studies on the sampler and the case studies involving five different phenotypes yields promising results, underscoring the effectiveness of this approach.

Discerning the genes, regulatory networks and environmental cues involved in plant development represents a major goal in the plant sciences. However, genes and regulatory networks have not evolved in controlled environmental conditions but in natural environments. Hence, conducting experiments in natural settings is of paramount importance to dissect the underlying mechanisms of plant development realistically. We undertook common garden experiments in a natural environment in two contrasting years to quantify whole-genome gene expression patterns over diurnal, seasonal and annual timescales across the life-cycle phenology of Arabidopsis thaliana. Natural accessions were locally adapted to their environments by adjusting key life-history traits across an altitudinal gradient in southern Spain. We found that accession, seasonal (across developmental stages) and diurnal (morning and afternoon) comparisons chiefly structured whole-genome gene expression. We detected most of the differentially expressed genes from various biological functions and flowering-related regulatory pathways as shared among all natural accessions. Nevertheless, accessions more similar in early flowering time also exhibited more similar gene expression patterns. We also detected several flowering time genes from all known regulatory pathways across timescales, particularly from the photoperiod and circadian clock pathways. Overall, our results stressed the remarkable plasticity in both life-cycle phenology and whole-genome gene expression patterns in natural A. thaliana accessions, showed that local adaptation in fitness-related life-history traits can also be detected at the whole-genome gene expression level and highlighted the value of natural accessions with respect to laboratory strains for in natura gene expression experiments.

As one of the three major food crops, rice (Oryza sativa L.) originated in temperate and tropical regions. Its geographical and production distribution is restricted by low temperatures. This study aimed to elucidate the effects of OsLTSD2 (Low-temperature Stress Regulated DUF829 protein) overexpression (OE) on rice under low-temperature (LT) stress. This study investigated the survival rates, agronomic traits and stress-related physiological-biochemical indices of wild-type and OsLTSD2 OE plants under LT stress to validate the impact of OsLTSD2 OE on cold tolerance. Abscisic acid (ABA) phenotype experiments and transcriptome data were further analysed to elucidate the molecular mechanisms underlying OsLTSD2-mediated cold-stress regulation in rice. OsLTSD2 is located in the cell membrane and its expression can be affected by temperature stress. OE of OsLTSD2 negatively regulated cold tolerance and reducing sensitivity to exogenous ABA. Meanwhile, it resulted in more severe damage of cell membranes in rice under LT, and the reactive oxygen species-scavenging system also exhibited similarly impaired performance. Transcriptome analysis identified that the expression of genes involved in DNA replication, cell cycle and stress response was significantly downregulated in OE lines. Our findings indicate that OsLTSD2 negatively regulates cold tolerance in rice through impairing cell membrane stability, reducing sensitivity to exogenous ABA and modulating cell cycle stability.

Fusarium wilt is a major problem in agriculture. It significantly affects the growth and development of chickpea and its management mainly relies on heavy use of chemical fertilizers. The negative impacts posed by the excessive use of chemical pesticides necessitate the investigation into microbial antagonism. Currently, root-associated single microorganisms form the basis for microbe-based biological control. Recent studies have highlighted the synergistic interaction among microbes for management of biotic stresses. The present study focussed on the development of an effective microbial consortium for enhanced plant growth and health. The biocontrol agents, Paenibacillus lentimorbus (NBRI-CHM12), Bacillus amyloliquefaciens (NBRI-SN13) and Trichoderma harzianum (NBRI-Fx), were combined with P solubilizer Pseudomonas putida (NBRI-RA) based on their compatibility, plant growth-promoting traits (PGP) and antagonism against Fusarium oxysporum. The best selected consortium of NBRI-CHM12 and RA was inspected for disease management against F. oxysporum f. sp. ciceris on sensitive (JG-62) and resistant (K-850) chickpea cultivars. The NBRI-CHM12+RA consortium led to increased productivity (dry weight) in both JG-62 (81.48%) and K-850 (20.5%) cultivars. Modulation in pectin- and cellulose-degrading enzymes (PCDEs), reactive oxygen species (ROS), antioxidants and phenylpropanoid activity in plant justifies enhanced induced systemic resistance in the presence of consortium. The consortium also showed a reduction in Fusarium population compared to individual treatments, positively correlating with enhanced soil microbial enzymatic activities. The use of microbial consortia is best suited to fulfil the dual purpose of plant growth promotion and disease suppression.

General metabolism and responses to internal or external signals are tightly regulated in plants. We hypothesise that a network of intermediate regulatory proteins including transcription factors, kinases, and E3 ligases connect input signals like light, temperature, circadian clock, and ontogenetic pathways to output pathways. We therefore investigate the transcriptional dynamics of these regulators. RNA sequencing was performed on 3-week-old Arabidopsis thaliana Col-0 rosettes grown under 12 h/12 h light/dark conditions sampled every 2 h over 24 h to match publicly available single-cell data of same age plants. Both were analysed to identify the abundance of intermediate regulators in time and space. Intermediate regulators are of significantly lower abundance compared with other transcripts in the Arabidopsis transcriptome. More than half of expressed kinases, E3 ligases and transcriptions factors vary in either time, space or both in mature leaves. Dynamic expression patterns of regulators allow plants to maintain tightly regulated metabolism while providing sufficient room for specific stress responses. High plasticity of the Arabidopsis transcriptome highlights the importance of considering sampling time-of-day and cellular resolution for experiments.

This study investigates the reproductive and vegetative development of Bryum argenteum in two contrasting tropical environments: the Seasonal Tropical Dry Forest (SDTF) and the Brazilian Atlantic Forest (BAF). By comparing ecotypes from these regions, we aimed to understand how environmental variation influences sex-specific traits, reproductive strategies and potential trade-offs between sexual and asexual reproduction. We conducted temporal analyses of protonema growth, shoot production, sex expression, bulbil formation and gametangia development in laboratory-grown samples representing male and female ecotypes from both environments. Significant differences were found between ecotypes and sexes. Male BAF ecotypes showed lower protonema growth and delayed shoot production compared to other groups. SDTF males exhibited the highest sex expression at Week 8. A negative relationship between sex expression and bulbil production was detected only in SDTF males. Gametangia development also varied, with male BAF ecotypes requiring more time to initiate sexual expression and mature phases revealing further distinctions. The observed differences across ecotypes and sexes reflect adaptive strategies shaped by the ecological conditions of each habitat. In particular, the delayed or reduced reproductive investment in male BAF ecotypes and the trade-offs in females suggest context-dependent allocation of resources. These patterns highlight the complex interplay between environment, sex and reproductive timing in tropical mosses.

Yoania is a rare achlorophyllous mycoheterotrophic orchid genus distributed across Japan, Taiwan, China, India and Vietnam, associating with wood-decomposing fungi. Studying mycoheterotrophic plants' mycorrhizal diversity is essential, as they depend entirely on fungi for carbon and nutrients. Here, we studied mycorrhizal interactions and nutrient strategies in three Yoania species from Taiwan and China. We hypothesize (H1) that Physisporinus associates with the Yoania species studied, and (H2) that when this symbiotic relationship alters nutritional patterns, this partnership will result in lower δ¹³C enrichment than in other fully mycoheterotrophic, wood-decaying-fungus-associated orchids. High-throughput DNA sequencing was used to investigate the mycorrhizal fungal communities of three Yoania species. In addition, natural stable isotopes (δ¹³C and δ¹⁵N) were measured in two species, while δ²H and δ¹⁸O were measured in one of them to further evaluate nutrient acquisition strategies. In Taiwan, Yoania japonica and Yoania amagiensis var. squamipes, and in China, Yoania prainii, all associate with a single Physisporinus taxonomic unit, distinct from the Physisporinus taxonomic units associated with Yoania species in Japan. As a white-rot fungus, Physisporinus may preferentially decompose relatively ¹³C depleted lignin likely explaining the lower ¹³C enrichment of Yoania in comparison with other fully mycoheterotrophic orchids associated with wood-decomposing fungi. Our combined molecular and isotopic evidence suggests that the mycoheterotrophic orchid genus Yoania employs a nutritional strategy that is most likely linked to the use of lignin by its white-root fungal partner in forest ecosystems.

Temperature and humidity are key factors influencing seed germination, varying across vegetation types and in response to disturbances such as fire. This study investigated germination, recruitment, and seedling growth of the generalist tree Vochysia tucanorum Mart. (Vochysiaceae) in natural environments of southern Brazil, including savanna, savanna - forest transition, and forest vegetation. Three months after a fire event, we established 12 nurseries for treatment (four per vegetation type, each containing 15 seeds) and monitored environmental conditions and seedling development from December 2022 to July 2023. Data on temperature, humidity, germination, mortality, seedling height, and cotyledon thickness were compared between burn and unburn treatments. Average temperature differed among vegetation types but not between burned and unburned areas, while humidity increased by 28% in burned plots. The number of seeds that germinated was significantly higher in burned areas across all vegetation types. Seedlings in the savanna were smaller (mean 16 mm) than those in the transition (29.6 mm) and forest sites. Cotyledon thickness varied over time and between treatments but was not affected by vegetation type. Despite the wide ecological distribution of V. tucanorum, germination and recruitment were rare events. The limited germination in savanna vegetation indicates that microclimatic constraints, particularly reduced water availability, restrict seedling establishment. Once germinated, seedling growth depends largely on cotyledon reserves, which deplete more slowly in burned environments. These results improve our understanding of post-fire regeneration in a generalist wood species and demonstrate how fire and microclimatic conditions jointly influence recruitment dynamics in fire-prone environments.