Effects of Drought-Stress on Fusarium Crown Rot Development in Barley

The G143S mutation in cytochrome b confers high resistance to pyraclostrobin in Fusarium pseudograminearum

BACKGROUND

Wheat crown rot (WCR), primarily caused by Fusarium pseudograminearum has become more and more prevalent in winter wheat areas in China. However, limited fungicides have been registered for the control of WCR in China so far. Pyraclostrobin is a representative quinone outside inhibitor (QoI) with excellent activity against Fusarium spp. There is currently limited research on the resistance risk and resistance mechanism of F. pseudograminearum to pyraclostrobin.

RESULTS

Here, we determined the activity of pyraclostrobin against F. pseudograminearum. The EC50 values ranged from 0.022 to 0.172 μg mL-1 with an average EC50 value of 0.071 ± 0.030 μg mL-1. Four highly pyraclostrobin-resistant mutants were obtained from two sensitive strains by ultraviolet (UV) mutagenesis in the laboratory. The mutants showed decreased mycelial growth rate and virulence as compared with the corresponding wild-type strains, indicating that pyraclostrobin resistance suffered a fitness penalty in F. pseudograminearum. It was found that the high resistance of four mutants was caused by the G143S mutation in Cytb. Molecular docking analysis also further confirms that the G143S mutation in Cytb decreased the binding affinity between pyraclostrobin and Cytb.

CONCLUSION

The resistance risk of F. pseudograminearum to pyraclostrobin could be low to medium. Although a mutation at the G143S position of Cytb could potentially occur, this mutation decreases the fitness of the mutant, which may reduce its survival in the environment. Therefore, the negative consequences of a possible mutation are lower. This makes pyraclostrobin a good candidate for controlling crown rot in wheat. © 2024 Society of Chemical Industry.

Drought: A context-dependent damper and aggravator of plant diseases

Drought dynamically influences the interactions between plants and pathogens, thereby affecting disease outbreaks. Understanding the intricate mechanistic aspects of the multiscale interactions among plants, pathogens, and the environment-known as the disease triangle-is paramount for enhancing the climate resilience of crop plants. In this review, we systematically compile and comprehensively analyse current knowledge on the influence of drought on the severity of plant diseases. We emphasise that studying these stresses in isolation is not sufficient to predict how plants respond to combined stress from both drought and pathogens. The impact of drought and pathogens on plants is complex and multifaceted, encompassing the activation of antagonistic signalling cascades in response to stress factors. The nature, intensity, and temporality of drought and pathogen stress occurrence significantly influence the outcome of diseases. We delineate the drought-sensitive nodes of plant immunity and highlight the emerging points of crosstalk between drought and defence signalling under combined stress. The limited mechanistic understanding of these interactions is acknowledged as a key research gap in this area. The information synthesised herein will be crucial for crafting strategies for the accurate prediction and mitigation of future crop disease risks, particularly in the context of a changing climate.

Transcriptomic insights into shared responses to Fusarium crown rot infection and drought stresses in bread wheat (Triticum aestivum L.)

KEY MESSAGE

Shared changes in transcriptomes caused by Fusarium crown rot infection and drought stress were investigated based on a single pair of near-isogenic lines developed for a major locus conferring tolerance to both stresses. Fusarium crown rot (FCR) is a devastating disease in many areas of cereal production worldwide. It is well-known that drought stress enhances FCR severity but possible molecular relationship between these two stresses remains unclear. To investigate their relationships, we generated several pairs of near isogenic lines (NILs) targeting a locus conferring FCR resistance on chromosome 2D in bread wheat. One pair of these NILs showing significant differences between the two isolines for both FCR resistance and drought tolerance was used to investigate transcriptomic changes in responsive to these two stresses. Our results showed that the two isolines likely deployed different strategies in dealing with the stresses, and significant differences in expressed gene networks exist between the two time points of drought stresses evaluated in this study. Nevertheless, results from analysing Gene Ontology terms and transcription factors revealed that similar regulatory frameworks were activated in coping with these two stresses. Based on the position of the targeted locus, changes in expression following FCR infection and drought stresses, and the presence of non-synonymous variants between the two isolines, several candidate genes conferring resistance or tolerance to these two types of stresses were identified. The NILs generated, the large number of DEGs with single-nucleotide polymorphisms detected between the two isolines, and the candidate genes identified would be invaluable in fine mapping and cloning the gene(s) underlying the targeted locus.

Resistant risk and resistance-related point mutation in SdhC1 of pydiflumetofen in Fusarium pseudograminearum

BACKGROUND

Fusarium pseudograminearum is one of the dominant pathogens of Fusarium crown rot (FCR) worldwide. Unfortunately, no fungicides have yet been registered for the control of FCR in wheat in China. Pydiflumetofen, a new-generation succinate dehydrogenase inhibitor, exhibits excellent inhibitory activity to Fusarium spp. A resistance risk assessment of F. pseudograminearum to pydiflumetofen and the resistance mechanism involved have not yet been investigated.

RESULTS

The median effective concentration (EC50 ) value of 103 F. pseudograminearum isolates to pydiflumetofen was 0.0162 μg mL-1 , and the sensitivity exhibited a unimodal distribution. Four resistant mutants were generated by fungicide adaption, which possessed similar or impaired fitness compared to corresponding parental isolates based on the results of mycelial growth, conidiation, conidium germination rate, and virulence determination. Pydiflumetofen showed strong positive cross-resistance with cyclobutrifluram and fluopyram but no cross-resistance with carbendazim, phenamacril, tebuconazole, fludioxonil, or pyraclostrobin. Sequence alignment revealed that pydiflumetofen-resistant F. pseudograminearum mutants had two single-point mutations of A83V or R86K in FpSdhC1 . Molecular docking further confirmed that point mutation of A83V or R86K in FpSdhC1 could confer resistance of F. pseudograminearum to pydiflumetofen.

CONCLUSION

Fusarium pseudograminearum shows an overall moderate risk of developing resistance to pydiflumetofen, and point mutation FpSdhC1 A83V or FpSdhC1 R86K could confer pydiflumetofen resistance in F. pseudograminearum. This study provided vital data for monitoring the emergence of resistance and developing resistance management strategies for pydiflumetofen. © 2023 Society of Chemical Industry.

Fine mapping of a Fusarium crown rot resistant locus on chromosome arm 6HL in barley by exploiting near isogenic lines, transcriptome profiling, and a large near isogenic line-derived population

KEY MESSAGE

This study reported validation and fine mapping of a Fusarium crown rot resistant locus on chromosome arm 6HL in barley using near isogenic lines, transcriptome sequences, and a large near isogenic line-derived population. Fusarium crown rot (FCR), caused by Fusarium pseudograminearum, is a chronic and serious disease affecting cereal production in semi-arid regions globally. The increasing prevalence of this disease in recent years is attributed to the widespread adoption of minimum tillage and stubble retention practices. In the study reported here, we generated eight pairs of near isogenic lines (NILs) targeting a putative QTL (Qcrs.caf-6H) conferring FCR resistance in barley. Assessing the NILs confirmed the large effect of this locus. Aimed to develop markers that can be reliably used in incorporating this resistant allele into breeding programs and identify candidate genes, transcriptomic analyses were conducted against three of the NIL pairs and a large NIL-derived population consisting of 1085 F7 recombinant inbred lines generated. By analyzing the transcriptomic data and the fine mapping population, Qcrs.caf-6H was delineated into an interval of 0.9 cM covering a physical distance of ~ 547 kb. Six markers co-segregating with this locus were developed. Based on differential gene expression and SNP variations between the two isolines among the three NIL pairs, candidate genes underlying the resistance at this locus were detected. These results would improve the efficiency of incorporating the targeted locus into barley breeding programs and facilitate the cloning of causal gene(s) responsible for the resistance.

Resistance Risk and Resistance-Related Point Mutation in SdhB and SdhC1 of Cyclobutrifluram in Fusarium pseudograminearum

Cyclobutrifluram is a novel succinate dehydrogenase inhibitor (SDHI) developed by Syngenta and helps to inhibit Fusarium pseudograminearum. Here, the potential for cyclobutrifluram resistance in F. pseudograminearum and the resistance mechanism involved were evaluated. Baseline sensitivity of F. pseudograminearum to cyclobutrifluram was determined with a mean EC₅₀ value of 0.0248 μg/mL. Fungicide adaption generated five resistant mutants, which possess a comparable or a slightly impaired fitness compared to corresponding parental isolates. This indicates that the resistance risk of F. pseudograminearum to cyclobutrifluram might be moderate. Cyclobutrifluram-resistant isolates also demonstrated resistance to pydiflumetofen but sensitivity to carbendazim, phenamacril, tebuconazole, fludioxonil, or pyraclostrobin. Additionally, point mutations H248Y in FpSdhB and A83V or R86K in FpSdhC₁ were found in cyclobutrifluram-resistant F. pseudograminearum mutants. Molecular docking and overexpression transformation assay revealed that FpSdhB^H248Y and FpSdhC₁^A83V or FpSdhC₁^R86K confer the resistance of F. pseudograminearum to cyclobutrifluram.

Pest categorisation of Fusarium pseudograminearum

The EFSA Plant Health Panel performed a pest categorisation of Fusarium pseudograminearum O'Donnell & T. Aoki. F. pseudograminearum is a soil-borne fungal pathogen, able to cause a disease known as Fusarium crown rot (FCR, also known as foot and root rot) and occasionally Fusarium head blight on small grain cereals, particularly Triticum aestivum L., Triticum turgidum L. spp. durum (Dest.), Hordeum vulgare L. and triticale (xTriticosecale). In addition, F. pseudograminearum has been isolated from soybean (Glycine max L.) and from some grass genera, such as Phalaris, Agropyron and Bromus, which represent potentially important inoculum reservoirs. This pathogen has been reported in arid and semi-arid cropping regions in Australia, New Zealand, North and South America, northern Africa and South Africa, the Middle East and Asia. In the EU, it has been reported in Italy since 1994 and later in Spain on field-grown durum wheat, but uncertainty remains regarding the actual distribution of the pathogen in the EU. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. Seeds of host plants and soil and other substrates are the main pathways for the entry and spread of the pathogen into the EU. There are no reports of interceptions of F. pseudograminearum in the EU. Host availability and climate suitability occurring in the EU favour establishment of the pathogen and allow it to establish in areas from which it has not been reported. Phytosanitary measures are available to prevent the introduction of the pathogen into the EU, and additional measures are available to mitigate the risk of spread. In the non-EU areas of its present distribution, the pathogen has a direct impact on cultivated hosts (e.g. wheat, barley, triticale and soybean) that are also relevant for the EU. However, no crop losses have been reported so far in the EU. The Panel concludes that F. pseudograminearum satisfies all the criteria to be regarded as a potential Union quarantine pest.

The use of biological selenium nanoparticles to suppress Triticum aestivum L. crown and root rot diseases induced by Fusarium species and improve yield under drought and heat stress

Fusarium species threaten wheat crops around the world and cause global losses. The global trend is toward using biological materials such as selenium (Se) in nano form to control these fungi. Bulk selenium is toxic and harmful at high doses; however, selenium nanoparticles are safe; therefore, the aim of this study to employ the biological selenium nanoparticles (BioSeNPs) synthesized by Lactobacillus acidophilus ML14 in controlling wheat crown and root rot diseases (CRDs) induced by Fusarium spp., especially Fusarium culmorum and Fusarium graminearum, and their reflection on the growth and productivity of wheat. The ability of BioSeNPs to suppress the development and propagation of F. culmorum and F. graminearum and the CRDs incidence were also investigated. The obtained BioSeNPs were spherical with a size of 46 nm and a net charge of -23.48. The BioSeNPs significantly scavenged 88 and 92% of DPPḢ and ABTṠ radicals and successfully inhibited the fungal growth in the range of 20-40 µg/mL; these biological activities were related to the small size of BioSeNPs and the phenolic content in their suspension. Under greenhouse conditions, the wheat supplemented with BioSeNPs (100 µg/mL) was significantly reduced the incidence of CRDs by 75% and considerably enhanced plant growth, grain quantity and quality by 5-40%. Also, photosynthetic pigments and gas exchange parameters were significantly increased as compared to chemical selenium nanoparticles (Che-SeNPs) and control. This study results could be recommended the use of BioSeNPs (100 µg/mL) in reducing CRDs incidence and severity in wheat plants, enhancing their tolerance with drought and heat stress, and increasing their growth and productivity as compared to control and Che-SeNPs.

Evaluation of heavy metals effects on morpho-anatomical alterations of wheat (Triticum aestivum L.) seedlings

The present study aimed to evaluate the effects of Cd and Cr as separate and in combinations in hydroponically grown seedlings of FA-08 and SH-13 cultivars of wheat (Triticum aestivum L.). The concentrations of heavy metals were higher in the root as compared to shoot and were more pronounced in SH-13 than FA-08 cultivar. The decrease in the seedling length and biomass was observed when the metals were applied in combined form (Cd-Cr 80-120, Cd-Cr 100-120, Cr-Cd 140-80, and Cr-Cd 140-100). There were more declines in root length in the cultivar SH-13 as compared to the shoot length, as the concentration of HMs increased. The root at level Cr-140 and shoot at level Cd-100 showed more reduction in SH-13 than FA-08. The high concentration of Cd and Cr affected the root epidermis, the cortical cells, and the xylem vessel. The size and number of stomata, length of long cells and short cells, and trichome were reduced at the concentration Cd-100 and Cr-140. The present study showed that the higher concentration of Cd and Cr affects the morpho-anatomical features of both selected wheat cultivar moderately.

Comparing transcriptional responses to Fusarium crown rot in wheat and barley identified an important relationship between disease resistance and drought tolerance

BACKGROUND

Fusarium crown rot (FCR) is a chronic disease in cereal production worldwide. The impact of this disease is highly environmentally dependant and significant yield losses occur mainly in drought-affected crops.

RESULTS

In the study reported here, we evaluated possible relationships between genes conferring FCR resistance and drought tolerance using two approaches. The first approach studied FCR induced differentially expressed genes (DEGs) targeting two barley and one wheat loci against a panel of genes curated from the literature based on known functions in drought tolerance. Of the 149 curated genes, 61.0% were responsive to FCR infection across the three loci. The second approach was a comparison of the global DEGs induced by FCR infection with the global transcriptomic responses under drought in wheat. This analysis found that approximately 48.0% of the DEGs detected one week following drought treatment and 74.4% of the DEGs detected three weeks following drought treatment were also differentially expressed between the susceptible and resistant isolines under FCR infection at one or more timepoints. As for the results from the first approach, the vast majority of common DEGs were downregulated under drought and expressed more highly in the resistant isoline than the sensitive isoline under FCR infection.

CONCLUSIONS

Results from this study suggest that the resistant isoline in wheat was experiencing less drought stress, which could contribute to the stronger defence response than the sensitive isoline. However, most of the genes induced by drought stress in barley were more highly expressed in the susceptible isolines than the resistant isolines under infection, indicating that genes conferring drought tolerance and FCR resistance may interact differently between these two crop species. Nevertheless, the strong relationship between FCR resistance and drought responsiveness provides further evidence indicating the possibility to enhance FCR resistance by manipulating genes conferring drought tolerance.

A Two-Year Occurrence of Fusarium T-2 and HT-2 Toxin in Croatian Cereals Relative of the Regional Weather

To investigate into the T-2 and HT-2 toxin occurrence, 240 samples of unprocessed cereals (maize, wheat, barley, and oats) were sampled from different fields located in three Croatian regions during 2017-2018. In all samples, sum concentrations of T-2/HT-2 toxin were determined using the ELISA method, while the LC-MS/MS was used as a confirmatory method for both mycotoxins in positive samples (>LOD) and the establishment of T-2 over HT-2 toxin ratios. The results showed oats to be the most contaminated cereal, with T-2/HT-2 toxins detected in 70.0% of samples, followed by barley (40.9%), maize (26.8%) and wheat (19.2%), with the mean T-2/HT-2 ratio ranging from 1:2.7 in maize to 1:4.4 in oats. Sum T-2/HT-2 concentrations in two maize samples were higher than the indicative level recommended by the European Commission, necessitating subsequent investigations into the conditions under which these poorly investigated mycotoxins are produced. Statistically significantly (p < 0.05) higher concentrations of T-2/HT-2 toxin were determined in oats throughout study regions as compared to those found in wheat, but not maize and barley, while the concentrations of these mycotoxins were related to the regional weather in Croatia.

Application of Endophytic Bacillus subtilis and Salicylic Acid to Improve Wheat Growth and Tolerance under Combined Drought and Fusarium Root Rot Stresses

In nature, plants are constantly exposed to a varied abiotic and biotic stresses or their combinations, limiting the productivity of major crops, including wheat. Combinations of drought and soil-borne Fusarium-instigated diseases are the most common combinations of stresses, significantly reducing wheat yield around the world. Here, were analyzed the potential of application of endophytic bacteria Bacillus subtilis (strain 10–4) together with the natural signal molecule salicylic acid (SA) to improve growth and tolerance of Triticum aestivum L. (wheat) plants under combined drought and Fusarium culmorum-instigated root rot (FRR) stresses. It was revealed that pre-sowing treatment with B. subtilis 10–4, SA, and B. subtilis 10–4 + SA, both under normal and combined drought conditions, notably reduced (by 50–80% or more) the incidence of FRR development in wheat plants, with the most notable effect for B. subtilis 10–4 + SA (wherein disease symptoms were almost absent). Moreover, B. subtilis 10–4, SA, and especially B. subtilis 10–4 + SA increased plant growth (root and shoot length, fresh and dry biomass) under normal (up to 20–50%), drought (up to 15–40%), FRR (up to 15–30%), and combined drought + FRR stresses (up to 20%), with the maximum effect for B. subtilis 10–4 + SA. Additionally, B. subtilis 10–4, SA, and B. subtilis 10–4 + SA decreased stress (drought, FRR, and combined drought + FRR)-instigated lipid peroxidation and osmotic damages of plant cells. The findings indicate that endophytic bacteria B. subtilis 10–4 alone and in a mixture with SA may be used as an effective eco-friendly agent to improve wheat growth and tolerance under the influence of drought, FRR, and combinations of these stresses.

Adaptive Traits to Improve Durum Wheat Yield in Drought and Crown Rot Environments

Durum wheat (Triticum turgidum L. ssp. durum) production can experience significant yield losses due to crown rot (CR) disease. Losses are usually exacerbated when disease infection coincides with terminal drought. Durum wheat is very susceptible to CR, and resistant germplasm is not currently available in elite breeding pools. We hypothesize that deploying physiological traits for drought adaptation, such as optimal root system architecture to reduce water stress, might minimize losses due to CR infection. This study evaluated a subset of lines from a nested association mapping population for stay-green traits, CR incidence and yield in field experiments as well as root traits under controlled conditions. Weekly measurements of normalized difference vegetative index (NDVI) in the field were used to model canopy senescence and to determine stay-green traits for each genotype. Genome-wide association studies using DArTseq molecular markers identified quantitative trait loci (QTLs) on chromosome 6B (qCR-6B) associated with CR tolerance and stay-green. We explored the value of qCR-6B and a major QTL for root angle QTL qSRA-6A using yield datasets from six rainfed environments, including two environments with high CR disease pressure. In the absence of CR, the favorable allele for qSRA-6A provided an average yield advantage of 0.57 t·ha⁻¹, whereas in the presence of CR, the combination of favorable alleles for both qSRA-6A and qCR-6B resulted in a yield advantage of 0.90 t·ha⁻¹. Results of this study highlight the value of combining above- and belowground physiological traits to enhance yield potential. We anticipate that these insights will assist breeders to design improved durum varieties that mitigate production losses due to water deficit and CR.

Fusarium Crown Rot of Winter Wheat Influenced by Resource Competition Near a Tree Windbreak

Fusarium crown rot becomes most severe when wheat is stressed for water near the time of anthesis. This research examined the potential to study crown rot in the gradient of resource competition near a tree windbreak. Winter wheat was planted for 2 years into a field infested by Fusarium pseudograminearum and bordered by 17-m-high Austrian pines. Crown rot, plant growth and yield, and soil water content were evaluated at six distances (5 to 46 m) perpendicular to the tree line in strip plots inoculated or not inoculated with the pathogen. Crown rot was minor (<5% whiteheads) in noninoculated strips and greater in inoculated strips (26 to 35%) in a 21-m zone from 9 to 30 m from the tree line (0.5-1.8 times the tree height; 0.5-1.8H). At 46 m (2.7H), crown rot was similar in noninoculated and inoculated strips (2 to 5% whiteheads). Whiteheads and culm browning were roughly the reverse of soil water depletion by tree roots. Grain yield at 23 m compared with 46 m was reduced by 33 to 35% in noninoculated plots and by 43 to 49% in inoculated plots. It is possible to study associations between water stress and Fusarium crown rot in the zone of resource competition near windbreaks.

Fusarium Crown Rot Whitehead Symptom as Influenced by Wheat Crop Management and Sampling Date

Symptoms of Fusarium crown rot of wheat include premature death of inflorescens (whiteheads), lesions on subcrown internodes, and rotting of crown tissue and lower stem internodes. Each symptom type is influenced by a different set of environmental conditions. Whiteheads are the easiest symptom to quantify and are frequently reported in the Pacific Northwest U.S.A. The objective of this research was to examine factors associated with whitehead expression and relationships with wheat yield and test weight. Incidence of whiteheads differed for inoculations with different isolates of F. pseudograminearum and F. culmorum, and over years due to weather factors. Whiteheads became less as planting dates for winter wheat were delayed until after September, and incidence was increased with increasing nitrogen application rate. Dates of initial and greatest expression of whiteheads differed among cultivars, which was associated in part with the cultivar heading date. Whiteheads were not correlated with subcrown internode lesions or browning of crown tissue. Whiteheads were also not correlated with grain test weight. Whiteheads were sometimes negatively associated with grain yield, but that relationship was variable and could not be considered a reliable, recurrent, or accurate measure of crown rot severity. These results indicate the need for caution in reporting whiteheads as a sole indicator of cultivar susceptibility to Fusarium crown rot.

Validation and delineation of a locus conferring Fusarium crown rot resistance on 1HL in barley by analysing transcriptomes from multiple pairs of near isogenic lines

BACKGROUND

Fusarium crown rot (FCR) is a chronic and severe disease in cereal production in semi-arid regions worldwide. A putative quantitative trait locus conferring FCR resistance, Qcrs.cpi-1H, had previously been mapped on the long arm of chromosome 1H in barley.

RESULTS

In this study, five pairs of near-isogenic lines (NILs) targeting the 1HL locus were developed. Analysing the NILs found that the resistant allele at Qcrs.cpi-1H significantly reduced FCR severity. Transcriptomic analysis was then conducted against three of the NIL pairs, which placed the Qcrs.cpi-1H locus in an interval spanning about 11 Mbp. A total of 56 expressed genes bearing single nucleotide polymorphisms (SNPs) were detected in this interval. Five of them contain non-synonymous SNPs. These results would facilitate detailed mapping as well as cloning gene(s) underlying the resistance locus.

CONCLUSION

NILs developed in this study and the transcriptomic sequences obtained from them did not only allow the validation of the resistance locus Qcrs.cpi-1H and the identification of candidate genes underlying its resistance, they also allowed the delineation of the resistance locus and the development of SNPs markers which formed a solid base for detailed mapping as well as cloning gene(s) underlying the locus.

Characterization of Fusarium and Neocosmospora Species Associated With Crown Rot and Stem Canker of Pistachio Rootstocks in California

California produces 99.1% of pistachios grown in the United States, and diseases affecting pistachio rootstocks represent a constant challenge to the industry. Field surveys of fungi associated with pistachio rootstocks with symptoms of crown rot and stem canker in three central California counties followed by phylogenetic analyses of translation elongation factor 1-α and second largest subunit of RNA polymerase II gene fragments identified three Fusarium species (Fusarium equiseti, Fusarium oxysporum, and Fusarium proliferatum) and two Neocosmospora species (Neocosmospora falciformis and Neocosmospora solani). F. oxysporum and N. falciformis were the fungal species most frequently recovered from symptomatic pistachio trees. Inoculations of detached twigs of cultivar Kerman pistachio Pioneer Gold I and clonal University of California, Berkeley I (UCBI) rootstocks showed that all five species could colonize pistachio wood and cause vascular discolorations. Pathogenicity tests in potted pistachio trees completed Koch's postulates and confirmed that F. oxysporum, F. proliferatum, N. falciformis, and N. solani were capable of producing rot and discoloration in stems of clonal UCBI rootstocks, the most widely planted pistachio rootstock in California. To our knowledge, this study is the first to present insights into the biodiversity and biology of Fusarium and Neocosmospora species associated with pistachio trees in California.

Development of tightly linked markers and identification of candidate genes for Fusarium crown rot resistance in barley by exploiting a near-isogenic line-derived population

This study demonstrates the feasibility of developing co-segregating markers and identifying candidate genes for Fusarium crown rot resistance in barley based on the generation and exploitation of a near-isogenic line-derived large population. Fusarium crown rot (FCR) is a chronic and severe disease in cereals in semi-arid regions worldwide. Previous studies showed that FCR assessment could be affected by many factors including plant height, growth rate as well as drought stress. Thus, accurate assessment, which is essential for detailed mapping of any locus conferring FCR resistance, is difficult. Targeting one of the resistance loci reported earlier, we developed a near-isogenic line-derived population consisting of 1820 F9 lines. By analysing this population, the Qcrs.cpi-4H locus was mapped to an interval of 0.09 cM covering a physical distance of about 637 kb and 13 markers co-segregating with the targeted locus were developed. Candidate genes underlying the resistance locus were identified by analysing the expression and sequence variation of genes in the targeted interval. The accurate localization and the development of co-segregating markers should facilitate the incorporation of this large-effect QTL into breeding programmes as well as the cloning of gene(s) underlying the locus.

The ratio of trichomes to stomata is associated with water use efficiency in Solanum lycopersicum (tomato)

Trichomes are specialised structures that originate from the aerial epidermis of plants, and play key roles in the interaction between the plant and the environment. In this study we investigated the trichome phenotypes of four lines selected from the Solanum lycopersicum × Solanum pennellii introgression line (IL) population for differences in trichome density, and their impact on plant performance under water-deficit conditions. We performed comparative analyses at morphological and photosynthetic levels of plants grown under well-watered (WW) and also under water-deficit (WD) conditions in the field. Under WD conditions, we observed higher trichome density in ILs 11-3 and 4-1, and lower stomatal size in IL 4-1 compared with plants grown under WW conditions. The intrinsic water use efficiency (WUEi ) was higher under WD conditions in IL 11-3, and the plant-level water use efficiency (WUEb ) was also higher in IL 11-3 and in M82 for WD plants. The ratio of trichomes to stomata (T/S) was positively correlated with WUEi and WUEb , indicating an important role for both trichomes and stomata in drought tolerance in tomato, and offering a promising way to select for improved water use efficiency of major crops.

Integrating transcriptomic techniques and k-means clustering in metabolomics to identify markers of abiotic and biotic stress in Medicago truncatula

INTRODUCTION

Nitrogen-fixing legumes are invaluable crops, but are sensitive to physical and biological stresses. Whilst drought and infection from the soil-borne pathogen Fusarium oxysporum have been studied individually, their combined effects have not been widely investigated.

OBJECTIVES

We aimed to determine the effect of combined stress using methods usually associated with transcriptomics to detect metabolic differences between treatment groups that could not be identified by more traditional means, such as principal component analysis and partial least squares discriminant analysis.

METHODS

Liquid chromatography-high resolution mass spectrometry data from the root and leaves of model legume Medicago truncatula were analysed using Gaussian Process 2-Sample Test, k-means cluster analysis and temporal clustering by affinity propagation.

RESULTS

Metabolic differences were detected: we identified known stress markers, including changes in concentration for sucrose and citric acid, and showed that combined stress can exacerbate the effect of drought. Changes in roots were found to be smaller than those in leaves, but differences due to Fusarium infection were identified. The transfer of sucrose from leaves to roots can be seen in the time series using transcriptomic techniques with the metabolomics time series. Other metabolite concentrations that change as a result of treatment include phosphoric acid, malic acid and tetrahydroxychalcone.

CONCLUSIONS

Probing metabolomic data with transcriptomic tools provides new insights and could help to identify resilient plant varieties, thereby increasing future crop yield and improving food security.