Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions

Water availability is undoubtedly one of the most important environmental factors affecting crop production. Drought causes a gradual deprivation of water in the soil from top to deep layers and can occur at diverse stages of plant development. Roots are the first organs that perceive water deficit in soil and their adaptive development contributes to drought adaptation. Domestication has contributed to a bottleneck in genetic diversity. Wild species or landraces represent a pool of genetic diversity that has not been exploited yet in breeding program. In this study, we used a collection of 230 two-row spring barley landraces to detect phenotypic variation in root system plasticity in response to drought and to identify new quantitative trait loci (QTL) involved in root system architecture under diverse growth conditions. For this purpose, young seedlings grown for 21 days in pouches under control and osmotic-stress conditions were phenotyped and genotyped using the barley 50k iSelect SNP array, and genome-wide association studies (GWAS) were conducted using three different GWAS methods (MLM GAPIT, FarmCPU, and BLINK) to detect genotype/phenotype associations. In total, 276 significant marker-trait associations (MTAs; p-value (FDR)< 0.05) were identified for root (14 and 12 traits under osmotic-stress and control conditions, respectively) and for three shoot traits under both conditions. In total, 52 QTL (multi-trait or identified by at least two different GWAS approaches) were investigated to identify genes representing promising candidates with a role in root development and adaptation to drought stress.

A Novel Image-Based Screening Method to Study Water-Deficit Response and Recovery of Barley Populations Using Canopy Dynamics Phenotyping and Simple Metabolite Profiling

Plant phenotyping platforms offer automated, fast scoring of traits that simplify the selection of varieties that are more competitive under stress conditions. However, indoor phenotyping methods are frequently based on the analysis of plant growth in individual pots. We present a reproducible indoor phenotyping method for screening young barley populations under water stress conditions and after subsequent rewatering. The method is based on a simple read-out of data using RGB imaging, projected canopy height, as a useful feature for indirectly following the kinetics of growth and water loss in a population of barley. A total of 47 variables including 15 traits and 32 biochemical metabolites measured (morphometric parameters, chlorophyll fluorescence imaging, quantification of stress-related metabolites; amino acids and polyamines, and enzymatic activities) were used to validate the method. The study allowed the identification of metabolites related to water stress response and recovery. Specifically, we found that cadaverine (Cad), 1,3-aminopropane (DAP), tryptamine (Tryp), and tyramine (Tyra) were the major contributors to the water stress response, whereas Cad, DAP, and Tyra, but not Tryp, remained at higher levels in the stressed plants even after rewatering. In this work, we designed, optimized and validated a non-invasive image-based method for automated screening of potential water stress tolerance genotypes in barley populations. We demonstrated the applicability of the method using transgenic barley lines with different sensitivity to drought stress showing that combining canopy height and the metabolite profile we can discriminate tolerant from sensitive genotypes. We showed that the projected canopy height a sensitive trait that truly reflects other invasively studied morphological, physiological, and metabolic traits and that our presented methodological setup can be easily applicable for large-scale screenings in low-cost systems equipped with a simple RGB camera. We believe that our approach will contribute to accelerate the study and understanding of the plant water stress response and recovery capacity in crops, such as barley.

Blue light suppression alters cytokinin homeostasis in wheat leaves senescing under shading stress

Blue light (BL) suppression accelerates the senescence rate of wheat (Triticum aestivum L.) leaves exposed to shading. In order to study whether this effect involves the alteration of different cytokinin (CK) metabolites, CK-degradation, as well as the expression profile of genes responsible of CK-perception, -inactivation, -reactivation and/or -turnover, leaf segments of 30 day-old plants were placed in boxes containing bi-distilled water and covered with blue (B) or green (G) light filters, which supplied a similar irradiance but differed in the percentage of BL transmitted (G << B). A neutral (N) filter was used as control. When appropriate, different CK metabolites or an inhibitor of CK-degradation were added in order to alter the endogenous CK levels. A rapid decrement of trans-zeatin (tZ) and cis-zeatin (cZ) content was observed after leaf excision, which progressed at a higher rate in treatment G than in the control and B treatments. Senescence progression correlated with an accumulation of glycosylated forms (particularly cZ-derivatives), and an increment of CK-degradation, both of which were slowed in the presence of BL. On the contrary, CK-reactivation (analyzed through TaGLU1-3 expression) was delayed in the absence of BL. When different CK were exogenously supplied, tZ was the only natural free base capable to emulate the senescence-retarding effect of BL. Even though the signaling components involved in the regulation of senescence rate and CK-homeostasis by BL remain elusive, our data suggest that changes in the expression profile and/or functioning of the transcription factor HY5 might play an important role.

Whole transcriptome analysis of transgenic barley with altered cytokinin homeostasis and increased tolerance to drought stress

Cytokinin plant hormones have been shown to play an important role in plant response to abiotic stresses. Herein, we expand upon the findings of Pospíšilová et al. [30] regarding preparation of novel transgenic barley lines overexpressing cytokinin dehydrogenase 1 gene from Arabidopsis under the control of mild root-specific promotor of maize β-glycosidase. These lines showed drought-tolerant phenotype mainly due to alteration of root architecture and stronger lignification of root tissue. A detailed transcriptomic analysis of roots of transgenic plants subjected to revitalization after drought stress revealed attenuated response through the HvHK3 cytokinin receptor and up-regulation of two transcription factors implicated in stress responses and abscisic acid sensitivity. Increased expression of several genes involved in the phenylpropanoid pathway as well as of genes encoding arogenate dehydratase/lyase participating in phenylalanine synthesis was found in roots during revitalization. Although more precursors of lignin synthesis were present in roots after drought stress, final lignin accumulation did not change compared to that in plants grown under optimal conditions. Changes in transcriptome indicated a higher auxin turnover in transgenic roots. The same analysis in leaves revealed that genes encoding putative enzymes responsible for production of jasmonates and other volatile compounds were up-regulated. Although transgenic barley leaves showed lower chlorophyll content and down-regulation of genes encoding proteins involved in photosynthesis than did wild-type plants when cultivated under optimal conditions, they did show a tendency to return to initial photochemical activities faster than did wild-type leaves when re-watered after severe drought stress. In contrast to optimal conditions, comparative transcriptomic analysis of revitalized leaves displayed up-regulation of genes encoding enzymes and proteins involved in photosynthesis, and especially those encoded by the chloroplast genome. Taken together, our results indicate that the partial cytokinin insensitivity induced in barley overexpressing cytokinin dehydrogenase contributes to tolerance to drought stress.

The control of root growth by reactive oxygen species in Salix nigra Marsh. seedlings

The production of reactive oxygen species (ROS) in specific regions of Salix seedlings roots seems essential for the normal growth of this organ. We examined the role of different ROS in the control of root development in Salix nigra seedlings, and explored possible mechanisms involved in the regulation of ROS generation and action. Root growth was not significantly affected by OH quenchers, while it was either partially or completely inhibited in the presence of H₂O₂ or O₂·⁻ scavengers, respectively. O₂·⁻ production was elevated in the root apex, particularly in the subapical meristem and protodermal zones. Apical O₂·⁻ generation activity was correlated to a high level of either Cu/Zn superoxide dismutase protein as well as carbonylated proteins. While NADPH-oxidase (NOX) was probably the main source of O₂·⁻ generation, the existence of other sources should not be discarded. O₂·⁻ production was also high in root hairs during budding, but it markedly decreased when the hair began to actively elongate. Root hair formation increased in the presence of H₂O₂ scavengers, and was suppressed when H₂O₂ or peroxidase inhibitors were supplied. The negative effect of H₂O₂ was partially counteracted by a MAPKK inhibitor. Possible mechanisms of action of the different ROS in comparison with other plant model systems are discussed.