No abstract

Summary Plants are exposed to combinations of various biotic and abiotic stresses, but stress responses are usually investigated for single stresses only.Here, we investigated the genetic architecture underlying plant responses to 11 single stresses and several of their combinations by phenotyping 350 Arabidopsis thaliana accessions. A set of 214 000 single nucleotide polymorphisms (SNPs) was screened for marker‐trait associations in genome‐wide association (GWA) analyses using tailored multi‐trait mixed models.Stress responses that share phytohormonal signaling pathways also share genetic architecture underlying these responses. After removing the effects of general robustness, for the 30 most significant SNPs, average quantitative trait locus (QTL) effect sizes were larger for dual stresses than for single stresses.Plants appear to deploy broad‐spectrum defensive mechanisms influencing multiple traits in response to combined stresses. Association analyses identified QTLs with contrasting and with similar responses to biotic vs abiotic stresses, and below‐ground vs above‐ground stresses. Our approach allowed for an unprecedented comprehensive genetic analysis of how plants deal with a wide spectrum of stress conditions.

HighlightGrowth curve modelling and GWA mapping are combined to unravel the dynamic regulation of plant growth.

ORCID ID: 0000-0001-8918-0711 (J.J.B.K.)For crops that are grown for their fruits or seeds, elevated temperatures that occur during flowering and seed or fruit set have a stronger effect on yield than high temperatures during the vegetative stage. Even short-term exposure to heat can have a large impact on yield. In this study, we used Arabidopsis thaliana to study the effect of short-term heat exposure on flower and seed development. The impact of a single hot day (35°C) was determined in more than 250 natural accessions by measuring the lengths of the siliques along the main inflorescence. Two sensitive developmental stages were identified, one before anthesis, during male and female meiosis, and one after anthesis, during fertilization and early embryo development. In addition, we observed a correlation between flowering time and heat tolerance. Genome-wide association mapping revealed four quantitative trait loci (QTLs) strongly associated with the heat response. These QTLs were developmental stage specific, as different QTLs were detected before and after anthesis. For a number of QTLs, T-DNA insertion knockout lines could validate assigned candidate genes. Our findings show that the regulation of complex traits can be highly dependent on the developmental timing.

Large areas of arable land are often confronted with irregular rainfall resulting in limited water availability for part(s) of the growing seasons, which demands research for drought tolerance of plants. Natural variation was observed for biomass accumulation upon controlled moderate drought stress in 324 natural accessions of Arabidopsis. Improved performance under drought stress was correlated with early flowering and lack of vernalization requirement, indicating overlap in the regulatory networks of flowering time and drought response or correlated responses of these traits to natural selection. In addition, plant size was negatively correlated with relative water content (RWC) independent of the absolute water content (WC), indicating a prominent role for soluble compounds. Growth in control and drought conditions was determined over time and was modelled by an exponential function. Genome-wide association (GWA) mapping of temporal plant size data and of model parameters resulted in the detection of six time-dependent quantitative trait loci (QTLs) strongly associated with drought. Most QTLs would not have been identified if plant size was determined at a single time point. Analysis of earlier reported gene expression changes upon drought enabled us to identify for each QTL the most likely candidates.

Induction of anthocyanin accumulation by osmotic stress was assessed in 360 accessions of Arabidopsis thaliana. A wide range of natural variation, with phenotypes ranging from green to completely red/purple rosettes, was observed. A genome wide association (GWA) mapping approach revealed that sequence diversity in a small 15 kb region on chromosome 1 explained 40% of the variation observed. Sequence and expression analyses of alleles of the candidate gene MYB90 identified a causal polymorphism at amino acid (AA) position 210 of this transcription factor of the anthocyanin biosynthesis pathway. This amino acid discriminates the two most frequent alleles of MYB90. Both alleles are present in a substantial part of the population, suggesting balancing selection between these two alleles. Analysis of the geographical origin of the studied accessions suggests that the macro climate is not the driving force behind positive or negative selection for anthocyanin accumulation. An important role for local climatic conditions is, therefore, suggested. This study emphasizes that GWA mapping is a powerful approach to identify alleles that are under balancing selection pressure in nature.

Powdery mildew is a common disease affecting the commercial production of gerbera flowers (Gerbera hybrida, Asteraceae). Some varieties show a certain degree of resistance to it. Our objective was to identify biomarkers of resistance to powdery mildew using an 1H nuclear magnetic resonance spectroscopy and chemometrics approach in a complex, fully factorial experiment to suggest a target for selection and breeding. Resistant varieties were found to differ from those that were susceptible in the metabolites of the polyketide pathway, such as gerberin, parasorboside, and gerberinside. A new compound probably involved in resistance, 5-hydroxyhexanoic acid 3-O-β-D-glucoside, was described for the first time. A decision tree model was built to distinguish resistant varieties, with an accuracy of 57.7%, sensitivity of 72%, and specificity of 44.44% in an independent test. Our results suggest the mechanism of resistance to powdery mildew in gerbera and provide a potential tool for resistance screening in breeding programs.

Western flower thrips (WFT) are a major pest on many crops, including tomato. Thrips cause yield losses, not only through feeding damage, but also by the transmission of viruses of which the Tomato Spotted Wilt Virus is the most important one. In cultivated tomato, genetic diversity is extremely low, and all commercial lines are susceptible to WFT. Several wild relatives are WFT resistant and these resistances are based on glandular trichome-derived traits. Introgression of these traits in cultivated lines did not lead to WFT resistant commercial varieties so far. In this study, we investigated WFT resistance in cultivated tomato using a F2 population derived from a cross between a WFT susceptible and a WFT resistant cultivated tomato line. We discovered that this WFT resistance is independent of glandular trichome density or trichome-derived volatile profiles and is associated with three QTLs on chromosomes 4, 5 and 10. Foliar metabolic profiles of F3 families with low and high WFT feeding damage were clearly different. We identified α-tomatine and a phenolic compound as potential defensive compounds. Their causality and interaction need further investigation. Because this study is based on cultivated tomato lines, our findings can directly be used in nowadays breeding programs.