Combining growth-promoting genes leads to positive epistasis in Arabidopsis thaliana

Several genes have been described to positively influence final leaf size in Arabidopsis when mutated or overexpressed. However, the connections between these growth regulating genes are still poorly understood. Clearly such knowledge would significantly contribute to understand the biological processes driving leaf growth. In this study, we performed a combinatorial screen with thirteen transgenic Arabidopsis lines with an increased leaf size. Surprisingly, we found that from 61 analyzed combinations, 39% showed an additional increase in leaf size and most of these resulted from a positive epistasis on growth. Similar to what is found in other organisms in which such an epistasis assay was performed, only few genes were highly connected in synergistic combinations. We also observed a positive epistasis in the majority of the combinations with samba, BR11(OE) or SAUR19(OE), suggesting that these growth regulators are more prone to lead to synergistic effects in binary combinations. Furthermore, positive epistasis was not only found with combinations of genes with a similar mode of action, but also with genes which affect distinct processes, such as cell proliferation and cell expansion

Leaf responses to mild drought stress in natural variants of Arabidopsis

Although the response of plants exposed to severe drought stress has been studied extensively, little is known about how plants adapt their growth under mild drought stress conditions. Here, we analyzed the leaf and rosette growth response of six Arabidopsis (Arabidopsis thaliana) accessions originating from different geographic regions when exposed to mild drought stress. The automated phenotyping platform WIWAM was used to impose stress early during leaf development, when the third leaf emerges from the shoot apical meristem. Analysis of growth-related phenotypes showed differences in leaf development between the accessions. In all six accessions, mild drought stress reduced both leaf pavement cell area and number without affecting the stomatal index. Genome-wide transcriptome analysis (using RNA sequencing) of early developing leaf tissue identified 354 genes differentially expressed under mild drought stress in the six accessions. Our results indicate the existence of a robust response over different genetic backgrounds to mild drought stress in developing leaves. The processes involved in the overall mild drought stress response comprised abscisic acid signaling, proline metabolism, and cell wall adjustments. In addition to these known severe drought-related responses, 87 genes were found to be specific for the response of young developing leaves to mild drought stress

High-resolution time-resolved imaging of in vitro Arabidopsis rosette growth

Although quantitative characterization of growth phenotypes is of key importance for the understanding of essential networks driving plant growth, the majority of growth-related genes are still being identified based on qualitative visual observations and/or single-endpoint quantitative measurements. We developed an in vitro growth imaging system (IGIS) to perform time-resolved analysis of rosette growth. In this system, Arabidopsis plants are grown in Petri dishes mounted on a rotating disk, and images of each plate are taken on an hourly basis. Automated image analysis was developed in order to obtain several growth-related parameters, such as projected rosette area, rosette relative growth rate, compactness and stockiness, over time. To illustrate the use of the platform and the resulting data, we present the results for the growth response of Col-0 plants subjected to three mild stress conditions. Although the reduction in rosette area was relatively similar at 19days after stratification, the time-lapse analysis demonstrated that plants react differently to salt, osmotic and oxidative stress. The rosette area was altered at various time points during development, and leaf movement and shape parameters were also affected differently. We also used the IGIS to analyze in detail the growth behavior of mutants with enhanced leaf size. Analysis of several growth-related parameters over time in these mutants revealed several specificities in growth behavior, underlining the high complexity of leaf growth coordination. These results demonstrate that time-resolved imaging of in vitro rosette growth generates a better understanding of growth phenotypes than endpoint measurements

Leaf Growth Response to Mild Drought: Natural Variation in Arabidopsis Sheds Light on Trait Architecture.

Plant growth and crop yield are negatively affected by a reduction in water availability. However, a clear understanding of how growth is regulated under nonlethal drought conditions is lacking. Recent advances in genomics, phenomics, and transcriptomics allow in-depth analysis of natural variation. In this study, we conducted a detailed screening of leaf growth responses to mild drought in a worldwide collection of Arabidopsis thaliana accessions. The genetic architecture of the growth responses upon mild drought was investigated by subjecting the different leaf growth phenotypes to genome-wide association mapping and by characterizing the transcriptome of young developing leaves. Although no major effect locus was found to be associated with growth in mild drought, the transcriptome analysis delivered further insight into the natural variation of transcriptional responses to mild drought in a specific tissue. Coexpression analysis indicated the presence of gene clusters that co-vary over different genetic backgrounds, among others a cluster of genes with important regulatory functions in the growth response to osmotic stress. It was found that the occurrence of a mild drought stress response in leaves can be inferred with high accuracy across accessions based on the expression profile of 283 genes. A genome-wide association study on the expression data revealed that trans regulation seems to be more important than cis regulation in the transcriptional response to environmental perturbations

Increased Leaf Size: Different Means to an End: Increased Leaf Size: Different Means to an End

Increased Leaf Size: Different Means to an End. Increased Leaf Size: Different Means to an En

Soil phosphorus tests compared on established European long-term trials: which test is the winner?

A variety of tests for available soil phosphorus (P) is used worldwide, each with a historical and local background. The test ranging from intensity based ones, indicating P solubility to quantity based ones, i.e. near complete total soil P extraction. A study was set up to identify the most suitable soil P test in a fully comparative way by using the same set of soils of contrasting fields on a set of soil P tests. The requirement for this is to find P response trials in which various fertilizer responses are only related to varying P doses. Soil samples (n=254) were collected from the plough layer of 12 fields complying to these conditions. The soils were collected from the field or from archived soil collection and were gathered in Belgium (2), France (3), Germany (1), United Kingdom (5) and Sweden (1). In all these fields different P fertilisation doses during several years (3-123 years) resulted in differences in soil P status and a significant P response in all 12 fields, sometimes for different crops per field. The relative response, i.e. the crop yield relative to that in highest P rate, ranged between 6.5 and 107.1%. Soil P availability was measured in the 254 gathered soil samples by different methods: (1) extraction with ammonium lactate and acetate at pH 3.75 (Egnér et al., 1960); (2) extraction with 0.5 M NaHCO3 (Olsen et al., 1954); (3) extraction with 0.01 M CaCl2 (Houba et al., 2000); (4) extraction with ammonium oxalate (Schwertmann, 1964), with possibility to calculate the phosphate saturation degree (5) diffusive gradient in thin film technique (DGT) (Degryse et al., 2009). For each method, the relative yield, i.e. the obtained yield divided by the maximum yield observed on the same field, was plotted versus the measured soil P availability. A Mitscherlich curve was fitted on all data and on the data of every field separately. The “critical soil P availability” was defined as that concentration related to 95% relative yield. The best soil P test was determined based on several indices: R² of the Mitscherlich curve, coefficient of variance (CV) of the field specific critical values, CV of the crop type specific critical value, the amount of fault positive or fault negative results included, ... The performances of the tests are approximately equal and differences between the soil P tests are minimal. A more detailed statistical analysis still need to be done, and the results of this analysis will be presented during the conference

The Mitochondrial DNA (mtDNA)-Associated Protein SWIB5 Influences mtDNA Architecture and Homologous Recombination

In addition to the nucleus, mitochondria and chloroplasts in plant cells also contain genomes. Efficient DNA repair pathways are crucial in these organelles to fix damage resulting from endogenous and exogenous factors. Plant organellar genomes are complex compared to their animal counterparts and although several plant-specific mediators of organelle DNA repair have been reported, many regulators remain to be identified. Here, we show that a mitochondrial SWI/SNF (nucleosome remodeling) complex B protein, SWIB5, is capable of associating with mitochondrial DNA (mtDNA) in Arabidopsis thaliana. Gain- and loss-of-function mutants provided evidence for a role of SWIB5 in influencing mtDNA architecture and homologous recombination at specific intermediate-sized repeats both under normal and genotoxic conditions. SWIB5 interacts with other mitochondrial SWIB proteins. Gene expression and mutant phenotypic analysis of SWIB5 and SWIB family members suggests a link between organellar genome maintenance and cell proliferation. Taken together, our work presents a protein family that influences mtDNA architecture and homologous recombination in plants and suggests a link between organelle functioning and plant development