Measurement of plant growth in view of an integrative analysis of regulatory networks

As the regulatory networks of growth at the cellular level are elucidated at a fast pace, their complexity is not reduced; on the contrary, the tissue, organ and even whole-plant level affect cell proliferation and expansion by means of development-induced and environment-induced signaling events in growth regulatory processes. Measurement of growth across different levels aids in gaining a mechanistic understanding of growth, and in defining the spatial and temporal resolution of sampling strategies for molecular analyses in the model Arabidopsis thaliana and increasingly also in crop species. The latter claim their place at the forefront of plant research, since global issues and future needs drive the translation from laboratory model-acquired knowledge of growth processes to improvements in crop productivity in field conditions

To respond or not to respond? Natural variation of root architectural responses to nutrient signals

The amino acid glutamate (Glu) acts as a fast excitatory neurotransmitter in mammals. Its importance in plant signalling was recognized with the discovery of channel proteins similar to mammalian Glu receptors, as well as distinct changes in root-system architecture in response to very small amounts of soil Glu. Based on natural genetic variation within Arabidopsis, Walch-Liu et al. (2017) have now identified a major locus underpinning this root response, as well as several loci controlling it through gene by environment interactions with nitrate and temperature. It is a significant step towards unraveling crosstalk between signalling pathways that enable plants to adjust their growth and development to multiple environmental stimuli

Evolutionary processes from the perspective of flowering time diversity.

Although it is well appreciated that genetic studies of flowering time regulation have led to fundamental advances in the fields of molecular and developmental biology, the ways in which genetic studies of flowering time diversity have enriched the field of evolutionary biology have received less attention despite often being equally profound. Because flowering time is a complex, environmentally responsive trait that has critical impacts on plant fitness, crop yield, and reproductive isolation, research into the genetic architecture and molecular basis of its evolution continues to yield novel insights into our understanding of domestication, adaptation, and speciation. For instance, recent studies of flowering time variation have reconstructed how, when, and where polygenic evolution of phenotypic plasticity proceeded from standing variation and de novo mutations; shown how antagonistic pleiotropy and temporally varying selection maintain polymorphisms in natural populations; and provided important case studies of how assortative mating can evolve and facilitate speciation with gene flow. In addition, functional studies have built detailed regulatory networks for this trait in diverse taxa, leading to new knowledge about how and why developmental pathways are rewired and elaborated through evolutionary time

Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis

The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions

Acclimation responses of Arabidopsis thaliana to sustained phosphite treatments

Phosphite () induces a range of physiological and developmental responses in plants by disturbing the homeostasis of the macronutrient phosphate. Because of its close structural resemblance to phosphate, phosphite impairs the sensing, membrane transport, and subcellular compartmentation of phosphate. In addition, phosphite induces plant defence responses by an as yet unknown mode of action. In this study, the acclimation of Arabidopsis thaliana plants to a sustained phosphite supply in the growth medium was investigated and compared with plants growing under varying phosphate supplies. Unlike phosphate, phosphite did not suppress the formation of lateral roots in several Arabidopsis accessions. In addition, the expression of well-documented phosphate-starvation-induced genes, such as miRNA399d and At4, was not repressed by phosphite accumulation, whilst the induction of PHT1;1 and PAP1 was accentuated. Thus, a mimicking of phosphate by phosphite was not observed for these classical phosphate-starvation responses. Metabolomic analysis of phosphite-treated plants showed changes in several metabolite pools, most prominently those of aspartate, asparagine, glutamate, and serine. These alterations in amino acid pools provide novel insights for the understanding of phosphite-induced pathogen resistance

Systems Evolutionary Biology of Waddington’s Canalization and Genetic Assimilation

In recent years, there has been growing interest in computer modeling of the evolution of gene and cell regulatory networks, in general, and in computational studies of the classic ideas of Baldwin, Schmalhausen, Waddington, and followers, in particular. Two related aspects of Waddington’s evolutionary theories are the concepts of canalization and of genetic assimilation. Canalization is associated with the robust development of an individual to diverse perturbations and noise, though, when fluctuations in developmental factors exceed a particular limit, the normal developmental trajectory can be “thrown out” of the robust canal, resulting in an altered phenotype. If selective pressure favors the new phenotype, an initial individual loss of canalization can lead to phenotypic changes in the population (with canalization then becoming established for the new phenotype). Genetic assimilation is the subsequent genetic fixing of the new trait in the population. Recent experimental and theoretical works have established a quantitative basis for these classic concepts of Waddington; this chapter will review these new developments in systems evolutionary biology

Aerobic power, huddling and the efficiency of torpor in the South American marsupial, Dromiciops gliroides.

During periods of cold, small endotherms depend on a continuous supply of food and energy to maintain euthermic body temperature (T(b)), which can be challenging if food is limited. In these conditions, energy-saving strategies are critical to reduce the energetic requirements for survival. Mammals from temperate regions show a wide arrange of such strategies, including torpor and huddling. Here we provide a quantitative description of thermoregulatory capacities and energy-saving strategies in Dromiciops gliroides, a Microbiotherid marsupial inhabiting temperate rain forests. Unlike many mammals from temperate regions, preliminary studies have suggested that this species has low capacity for control and regulation of body temperature, but there is still an incomplete picture of its bioenergetics. In order to more fully understand the physiological capacities of this "living fossil", we measured its scope of aerobic power and the interaction between huddling and torpor. Specifically, we evaluated: (1) the relation between basal (BMR) and maximum metabolic rate (MMR), and (2) the role of huddling on the characteristics of torpor at different temperatures. We found that BMR and MMR were above the expected values for marsupials and the factorial aerobic scope (from [Formula: see text]CO(2)) was 6.0±0.45 (using [Formula: see text]CO(2)) and 6.2±0.23 (using [Formula: see text]O(2)), an unusually low value for mammals. Also, repeatability of physiological variables was non-significant, as in previous studies, suggesting poor time-consistency of energy metabolism. Comparisons of energy expenditure and body temperature (using attached data-loggers) between grouped and isolated individuals showed that at 20°C both average resting metabolic rate and body temperature were higher in groups, essentially because animals remained non-torpid. At 10°C, however, all individuals became torpid and no differences were observed between grouped and isolated individuals. In summary, our study suggests that the main response of Dromiciops gliroides to low ambient temperature is reduced body temperature and torpor, irrespective of huddling. Low aerobic power and low time-consistency of most thermoregulatory traits of Dromiciops gliroides support the idea of poor thermoregulatory abilities in this species

In silico identification of novel genetic factors associated with longevity in Drosophila

To determine genetic factors causing variation in survival into old age, several genome-wide association studies (GWAS) have been carried out on panels of long-lived individuals. The findings from a number of these GWAS studies were somewhat inconclusive, owing to the small sample sizes investigated. It is for this reason that model organisms such as Drosophila melanogaster have become increasingly important in identifying genetic factors underlying longevity. In this study we hypothesised that co-location of novel genes/genomic regions with genes, known to be associated with longevity, that share biological function with co-located genes, make them good candidates for novel genomic regions, linked to longevity. We further hypothesised that single nucleotide polymorphisms (SNPs) residing within these co-located regions may influence longevity either individually (when a SNP in one of these genes causes a particular phenotype) or collectively (when one or several SNPs in these regions occur in the same individual thus causing the phenotype). Summary statistics of datasets of SNPs generated by two GWAS (Burke et al., 2013; Ivanov et al., 2015) which include position of each SNP and a corresponding statistic (D or P- value) showing the strength of association with longevity were used in this study to guide the initial choice of genes/loci strongly associated with longevity. First, a network approach was applied to predict novel genes/genomic regions/SNPs, playing a role in longevity, which integrated three-dimensional (3D) chromosome conformation data (Hi-C) and two GWAS datasets. Networks were created using genes/genomic regions, known to associate with longevity, as original nodes with additional nodes (regions) later added to these networks if they strongly interacted (i.e. came into close proximity as measured by the Hi-C data) with the original nodes. Various network measures were calculated, in order to identify important previously unknown regions. These previously unknown regions were further explored and longevity associated genes were found including Rim and Tpi with a 'long-lived' phenotype, and some newly found regions were observed to be common between both GWAS datasets. A human ortholog search of genes found in this analysis resulted in matches to human genes with functions related to lifespan. Subnetworks of these GWAS-based networks were sought for enrichment in GO terms and several genes with no previous association with longevity but enriched in longevity-related terms were identified. Second, SNPs residing in non-coding regions, e.g. within transcription factor binding sites (TFBSs) recognised by transcription factors (TF) and borders between Topologically Associated Domains (TADs) were analysed. Each TF typically recognises a collection of often dissimilar DNA motifs. Here we hypothesised that TFs may recognise a certain structure, e.g. non-B DNA structures, rather than sequence motifs. Structures such as slipped, cruciform, triplexes and tetraplexes, formed on direct, inverted and mirrored repeats and G-quartets were considered and SNPs residing within these structures were analysed. For the study of SNPs in TAD borders we hypothesised that SNPs residing in these border regions may cause a severe disruption to the way in which regulation usually occurs within these TADs. We found that a significant proportion (~2%) of non-coding SNPs, reported in the DGRP GWAS dataset, resided in TAD border regions on the Drosophila genome, when compared to a match control dataset (