Low temperature induced defence gene expression in winter wheat in relation to resistance to snow moulds and other wheat diseases

When two negatives make a positive: the favorable impact of the combination of abiotic stress and pathogen infection on plants

Combined abiotic and biotic stresses modify plant defense signaling, leading to either the activation or suppression of defense responses. Although the majority of combined abiotic and biotic stresses reduce plant fitness, certain abiotic stresses reduce the severity of pathogen infection in plants. Remarkably, certain pathogens also improve the tolerance of some plants to a few abiotic stresses. While considerable research focuses on the detrimental impact of combined stresses on plants, the upside of combined stress remains hidden. This review succinctly discusses the interactions between abiotic stresses and pathogen infection that benefit plant fitness. Various factors that govern the positive influence of combined abiotic stress and pathogen infection on plant performance are also discussed. In addition, we provide a brief overview of the role of pathogens, mainly viruses, in improving plant responses to abiotic stresses. We further highlight the critical nodes in defense signaling that guide plant responses during abiotic stress towards enhanced resistance to pathogens. Studies on antagonistic interactions between abiotic and biotic stressors can uncover candidates in host plant defense that may shield plants from combined stresses.

Boosting Immunity and Management against Wheat Fusarium Diseases by a Sustainable, Circular Nanostructured Delivery Platform

Fusarium head blight (FHB) and Fusarium crown rot (FCR) are managed by the application of imidazole fungicides, which will be strictly limited by 2030, as stated by the European Green Deal. Here, a novel and eco-sustainable nanostructured particle formulation (NPF) is presented by following the principles of the circular economy. Cellulose nanocrystals (CNC) and resistant starch were obtained from the bran of a high amylose (HA) bread wheat and employed as carrier and excipient, while chitosan and gallic acid were functionalized as antifungal and elicitor active principles. The NPF inhibited conidia germination and mycelium growth, and mechanically interacted with conidia. The NPF optimally reduced FHB and FCR symptoms in susceptible bread wheat genotypes while being biocompatible on plants. The expression level of 21 genes involved in the induction of innate immunity was investigated in Sumai3 (FHB resistant) Cadenza (susceptible) and Cadenza SBEIIa (a mutant characterized by high-amylose starch content) and most of them were up-regulated in Cadenza SBEIIa spikes treated with the NPF, indicating that this genotype may possess an interesting genomic background particularly responsive to elicitor-like molecules. Quantification of fungal biomass revealed that the NPF controlled FHB spread, while Cadenza SBEIIa was resistant to FCR fungal spread. The present research work highlights that the NPF is a powerful weapon for FHB sustainable management, while the genome of Cadenza SBEIIa should be investigated deeply as particularly responsive to elicitor-like molecules and resistant to FCR fungal spread.

A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material

Diploid plant genomes typically contain ~35,000 genes, almost all belonging to highly conserved gene families. Only a small fraction are lineage-specific, which are found in only one or few closely related species. Little is known about how genes arise de novo in plant genomes and how often this occurs; however, they are believed to be important for plants diversification and adaptation. We developed a pipeline to identify lineage-specific genes in Triticeae, using newly available genome assemblies of wheat, barley, and rye. Applying a set of stringent criteria, we identified 5942 candidate Triticeae-specific genes (TSGs), of which 2337 were validated as protein-coding genes in wheat. Differential gene expression analyses revealed that stress-induced wheat TSGs are strongly enriched in putative secreted proteins. Some were previously described to be involved in Triticeae non-host resistance and cold response. Additionally, we show that 1079 TSGs have sequence homology to transposable elements (TEs), ~68% of them deriving from regulatory non-coding regions of Gypsy retrotransposons. Most importantly, we demonstrate that these TSGs are enriched in transmembrane domains and are among the most highly expressed wheat genes overall. To summarize, we conclude that de novo gene formation is relatively rare and that Triticeae probably possess ~779 lineage-specific genes per haploid genome. TSGs, which respond to pathogen and environmental stresses, may be interesting candidates for future targeted resistance breeding in Triticeae. Finally, we propose that non-coding regions of TEs might provide important genetic raw material for the functional innovation of TM domains and the evolution of novel secreted proteins.

Cold-modulated leaf compounds in winter triticale DH lines tolerant to freezing and Microdochium nivale infection: LC-MS and Raman study

Tolerance to freezing and seedling diseases caused by Microdochium spp. is an essential trait for the wintering of triticale (×Triticosecale Wittmack) and other cereals. Preceding multi-year studies indicate that after long-term exposure to the low temperature, cereal seedlings acquire a genotype-dependent cross-tolerance to other subsequent stresses. This paper presents the first non-gel protein profiling performed via high performance liquid chromatography coupled with Mass Spectrometry as well as Fourier Transform-Raman spectroscopy measurements performed directly on leaves of triticale seedlings growing under different conditions. The research used doubled haploid lines selected from the mapping population, with extreme tolerance/susceptibility to freezing and M. nivale infection. These non-targeted methods led to the detection of twenty two proteins cold-accumulated in the most tolerant seedlings in relation to susceptible ones, classified as involved in protein biosynthesis, response to different stimuli, energy balancing, oxidative stress response, protein modification, membrane structure and anthocyanin synthesis. Additionally, in seedlings of the most freezing- and M. nivale -tolerant line, cold-hardening caused decrease of the carotenoid and chlorophyll content. Moreover, a decrease in the band intensity typical for carbohydrates as well as an increase in the band intensity characteristic for protein compounds were detected. Both studied lines revealed a different answer to stress in the characteristics of phenolic components.

Alterations in the Transcriptome of Rye Plants following the Microdochium nivale Infection: Identification of Resistance/Susceptibility-Related Reactions Based on RNA-Seq Analysis

Microdochium nivale is a progressive and devastating phytopathogen that causes different types of cereal crop and grass diseases that are poorly characterized at the molecular level. Although rye (Secale cereale L.) is one of the most resistant crops to most of the phytopathogens, it is severely damaged by M. nivale. The recent high-quality chromosome-scale assembly of rye genome has improved whole-genome studies of this crop. In the present work, the first transcriptome study of the M. nivale-infected crop plant (rye) with the detailed functional gene classification was carried out, along with the physiological verification of the RNA-Seq data. The results revealed plant reactions that contributed to their resistance or susceptibility to M. nivale. Phytohormone abscisic acid was shown to promote plant tolerance to M. nivale. Flavonoids were proposed to contribute to plant resistance to this pathogen. The upregulation of plant lipase encoding genes and the induction of lipase activity in M. nivale-infected plants revealed in our study were presumed to play an important role in plant susceptibility to the studied phytopathogen. Our work disclosed important aspects of plant-M. nivale interactions, outlined the directions for future studies on poorly characterized plant diseases caused by this phytopathogen, and provided new opportunities to improve cereals breeding and food security strategies.

Quantitative Trait Loci and Candidate Genes Associated with Cold-Acclimation and Microdochium nivale Tolerance/Susceptibility in Winter Triticale (x Triticosecale)

Tolerance to pink snow mold caused by Microdochium nivale appears after a cold-hardening period and it is an essential, genotype-dependent, complex quantitative trait for the wintering of triticale (x Triticosecale) and other cereals. Despite long-term studies, a marker for the selection of the tolerant genotypes is still insufficiently recognized. Chlorophyll fluorescence has been reported as a sensitive indicator of stress effects on photosynthesis and can be used to predict plant tolerance. In this study, the genomic regions (QTLs) associated with the level of winter triticale seedlings damage caused by M. nivale infection as well as photosynthesis quantum efficiency and chlorophyll a fluorescence parameters were identified in seedlings of mapping population of 89 doubled haploids lines (DHs) derived from F₁ hybrid of cv. 'Hewo' and cv. 'Magnat' accompanied with the genetic map consisting of 20 linkage groups with a total map length 4997.4 cm. Independent experiments performed in controlled conditions revealed 13 regions identified by a composite interval mapping, located on 7A, 1B, 2B, 6B, 7B, 3R, 5R, and 6R linkage groups and related to the PI, PI_ABS, TR_o/CS, ABS/CS, ABS/CS_m, ABS/RC, and Qy values as well as M. nivale tolerance T and susceptibility level P expressed by the seedling damage index. Additionally, candidate genes were in silico identified with the sequence position on wheat (2B and 7B) and rye (5R) chromosomes, where relevant QTL regions were found. The most important candidate genes indicated for M. nivale tolerance of cold-hardened triticale seedlings include those coding: sterol 3-beta-glucosyltransferase UGT80A2-like, transcription factor NAI1-like, and flavonol3-sulfotransferase-like proteins on chromosomes 2B and 5R.

Conducting Field Trials for Frost Tolerance Breeding in Cereals

Cereal species can be damaged by frost either during winter or at flowering stage. Frost tolerance per se is only a part of the mechanisms that allow plants to survive during winter, while winter-hardiness also considers other biotic or physical stresses that challenge the plants during the winter season, limiting their survival rate. While frost tolerance can also be tested in controlled environments, winter-hardiness can only be determined with field evaluations. Post-heading frost damage occurs from radiation frost events in spring during the reproductive stages. A reliable evaluation of winter-hardiness or of post heading frost damage should be carried out with field trials replicated across years and locations to overcome the irregular occurrence of natural conditions which satisfactorily differentiate genotypes. The evaluation of post-heading frost damage requires a specific attention to plant phenology. The extent of frost damage is traditionally determined with a visual score at the end of the winter, although, recently an image-based phenotyping coupled with unmanned aerial vehicles (UAVs) has been proposed.

Snow mold of winter cereals: a complex disease and a challenge for resistance breeding

Snow mold resistance is a complex quantitative trait highly affected by environmental conditions during winter that must be addressed by resistance breeding. Snow mold resistance in winter cereals is an important trait for many countries in the Northern Hemisphere. The disease is caused by at least four complexes of soilborne fungi and oomycetes of which Microdochium nivale and M. majus are among the most common pathogens. They have a broad host range covering all winter and spring cereals and can basically affect all plant growth stages and organs. Their attack leads to a low germination rate, and/or pre- and post-emergence death of seedlings after winter and, depending on largely unknown environmental conditions, also to foot rot, leaf blight, and head blight. Resistance in winter wheat and triticale is governed by a multitude of quantitative trait loci (QTL) with mainly additive effects highly affected by genotype × environment interaction. Snow mold resistance interacts with winter hardiness in a complex way leading to a co-localization of resistance QTLs with QTLs/genes for freezing tolerance. In practical breeding, a multistep procedure is necessary with (1) freezing tolerance tests, (2) climate chamber tests for snow mold resistance, and (3) field tests in locations with and without regularly occurring snow cover. In the future, resistance sources should be genetically characterized also in rye by QTL mapping or genome-wide association studies. The development of genomic selection procedures should be prioritized in breeding research.

Analysis of MAPK and MAPKK gene families in wheat and related Triticeae species

Background

The mitogen-activated protein kinase (MAPK) family is involved in signal transduction networks that underpin many different biological processes in plants, ranging from development to biotic and abiotic stress responses. To date this class of enzymes has received little attention in Triticeae species, which include important cereal crops (wheat, barley, rye and triticale) that represent over 20% of the total protein food-source worldwide.

Results

The work presented here focuses on two subfamilies of Triticeae MAPKs, the MAP kinases (MPKs), and the MAPK kinases (MKKs) whose members phosphorylate the MPKs. In silico analysis of multiple Triticeae sequence databases led to the identification of 152 MAPKs belonging to these two sub-families. Some previously identified MAPKs were renamed to reflect the literature consensus on MAPK nomenclature. Two novel MPKs, MPK24 and MPK25, have been identified, including the first example of a plant MPK carrying the TGY activation loop sequence common to mammalian p38 MPKs. An EF-hand calcium-binding domain was found in members of the Triticeae MPK17 clade, a feature that appears to be specific to Triticeae species. New insights into the novel MEY activation loop identified in MPK11s are offered. When the exon-intron patterns for some MPKs and MKKs of wheat, barley and ancestors of wheat were assembled based on transcript data in GenBank, they showed deviations from the same sequence predicted in Ensembl. The functional relevance of MAPKs as derived from patterns of gene expression, MPK activation and MKK-MPK interaction is discussed.

Conclusions

A comprehensive resource of accurately annotated and curated Triticeae MPK and MKK sequences has been created for wheat, barley, rye, triticale, and two ancestral wheat species, goat grass and red wild einkorn. The work we present here offers a central information resource that will resolve existing confusion in the literature and sustain expansion of MAPK research in the crucial Triticeae grains.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4545-9) contains supplementary material, which is available to authorized users.

Dissection of resistance to Microdochium nivale in Lolium multiflorum/Festuca arundinacea introgression forms

The potential of resistance to Microdochium nivale is still not recognized for numerous plant species. The forage grasses of Lolium-Festuca complex are important for grass-biomass production in the temperate regions. Lolium multiflorum is a grass with a high forage quality and productivity but also a relatively low resistance to M. nivale. On the contrary, F. arundinacea has a higher potential of resistance but simultaneously a significantly lower forage quality. These two species cross with each other and the intergeneric hybrids possess complementary characters of both genera. Herein, for the first time, we perform the research on L. multiflorum/F. arundinacea introgression forms to decipher mechanisms of resistance to M. nivale in that group of plants. Two forms with distinct levels of resistance were used as models in cytogenetic and biochemical studies. The resistant plant was shown to be a tetraploid with 28 L. multiflorum chromosomes, including one with three F. arundinacea introgressions. The susceptible introgression form revealed the unbalanced genomic structure and only 25 chromosomes. Twenty four chromosomes were shown to be L. multiflorum chromosomes, including one chromosome with F. arundinacea segment. One Festuca chromosome with additional two interstitial F. arundinacea segments, was also revealed in the susceptible form. The selected introgression forms differed in the accumulation profiles of total soluble carbohydrates, phytohormones, and phenolics in the leaf and crown tissue under the control and infection conditions. The higher amount of carbohydrates and salicylic acid in the leaves and crowns as well as a lower amount of abscisic acid in both studied organs and jasmonic acid in the crowns, were shown to be crucial for the expression of resistance to M. nivale in the analyzed hybrids.

Genomic Regions Associated with Tolerance to Freezing Stress and Snow Mold in Winter Wheat

Plants grown through the winter are subject to selective pressures that vary with each year's unique conditions, necessitating tolerance of numerous abiotic and biotic stress factors. The objective of this study was to identify molecular markers in winter wheat (Triticum aestivum L.) associated with tolerance of two of these stresses, freezing temperatures and snow mold-a fungal disease complex active under snow cover. A population of 155 F2:5 recombinant inbred lines from a cross between soft white wheat cultivars "Finch" and "Eltan" was evaluated for snow mold tolerance in the field, and for freezing tolerance under controlled conditions. A total of 663 molecular markers was used to construct a genetic linkage map and identify marker-trait associations. One quantitative trait locus (QTL) associated with both freezing and snow mold tolerance was identified on chromosome 5A. A second, distinct, QTL associated with freezing tolerance also was found on 5A, and a third on 4B. A second QTL associated with snow mold tolerance was identified on chromosome 6B. The QTL on 5A associated with both traits was closely linked with the Fr-A2 (Frost-Resistance A2) locus; its significant association with both traits may have resulted from pleiotropic effects, or from greater low temperature tolerance enabling the plants to better defend against snow mold pathogens. The QTL on 4B associated with freezing tolerance, and the QTL on 6B associated with snow mold tolerance have not been reported previously, and may be useful in the identification of sources of tolerance for these traits.

Global transcriptome changes in perennial ryegrass during early infection by pink snow mould

Lack of resistance to pink snow mould (Microdochium nivale) is a major constraint for adaptation of perennial ryegrass (Lolium perenne L.) to continental regions with long-lasting snow cover at higher latitudes. Almost all investigations of genetic variation in resistance have been performed using cold acclimated plants. However, there may be variation in resistance mechanisms that are functioning independently of cold acclimation. In this study our aim was to identify candidate genes involved in such resistance mechanisms. We first characterized variation in resistance to M. nivale among non-acclimated genotypes from the Norwegian cultivar 'Fagerlin' based on relative regrowth and fungal quantification by real-time qPCR. One resistant and one susceptible genotype were selected for transcriptome analysis using paired-end sequencing by Illumina Hiseq 2000. Transcriptome profiles, GO enrichment and KEGG pathway analysis indicate that defense response related genes are differentially expressed between the resistant and the susceptible genotype. A significant up-regulation of defense related genes, as well as genes involved in cell wall cellulose metabolic processes and aryl-alcohol dehydrogenase (NADP+) activity, was observed in the resistant genotype. The candidate genes identified in this study might be potential molecular marker resources for breeding perennial ryegrass cultivars with improved resistance to pink snow mould.

A proteome analysis of freezing tolerance in red clover (Trifolium pratense L.)

BACKGROUND

Improvement of freezing tolerance of red clover (Trifolium pratense L.) would increase its persistence under cold climate. In this study, we assessed the freezing tolerance and compared the proteome composition of non-acclimated and cold-acclimated plants of two initial cultivars of red clover: Endure (E-TF0) and Christie (C-TF0) and of populations issued from these cultivars after three (TF3) and four (TF4) cycles of phenotypic recurrent selection for superior freezing tolerance. Through this approach, we wanted to identify proteins that are associated with the improvement of freezing tolerance in red clover.

RESULTS

Freezing tolerance expressed as the lethal temperature for 50 % of the plants (LT50) increased markedly from approximately -2 to -16 °C following cold acclimation. Recurrent selection allowed a significant 2 to 3 °C increase of the LT50 after four cycles of recurrent selection. Two-dimensional difference gel electrophoresis (2D-DIGE) was used to study variations in protein abundance. Principal component analysis based on 2D-DIGE revealed that the largest variability in the protein data set was attributable to the cold acclimation treatment and that the two genetic backgrounds had differential protein composition in the acclimated state only. Vegetative storage proteins (VSP), which are essential nitrogen reserves for plant regrowth, and dehydrins were among the most striking changes in proteome composition of cold acclimated crowns of red clovers. A subset of proteins varied in abundance in response to selection including a dehydrin that increased in abundance in TF3 and TF4 populations as compared to TF0 in the Endure background.

CONCLUSION

Recurrent selection performed indoor is an effective approach to improve the freezing tolerance of red clover. Significant improvement of freezing tolerance by recurrent selection was associated with differential accumulation of a small number of cold-regulated proteins that may play an important role in the determination of the level of freezing tolerance.

The link between flowering time and stress tolerance

Evolutionary success in plants is largely dependent on the successful transition from vegetative to reproductive growth. In the lifetime of a plant, flowering is not only an essential part of the reproductive process but also a critical developmental stage that can be vulnerable to environmental stresses. Exposure to stress during this period can cause substantial yield losses in seed-producing plants. However, it is becoming increasingly evident that altering flowering time is an evolutionary strategy adopted by plants to maximize the chances of reproduction under diverse stress conditions, ranging from pathogen infection to heat, salinity, and drought. Here, recent studies that have revealed new insights into how biotic and abiotic stress signals can be integrated into floral pathways are reviewed. A better understanding of how complex environmental variables affect plant phenology is important for future genetic manipulation of crops to increase productivity under the changing climate.

Photosynthesis-dependent physiological and genetic crosstalk between cold acclimation and cold-induced resistance to fungal pathogens in triticale (Triticosecale Wittm.)

The breeding for resistance against fungal pathogens in winter triticale (Triticosecale Wittm.) continues to be hindered by a complexity of the resistance mechanisms, strong interaction with environmental conditions, and dependence on the plant genotype. We showed, that temperature below 4 °C induced the plant genotype-dependent resistance against the fungal pathogen Microdochium nivale. The mechanism involved, at least, the adjustment of the reactions in the PSII proximity and photoprotection, followed by an improvement of the growth and development. The genotypes capable to develop the cold-induced resistance, showed a higher maximum quantum yield of PSII and a more efficient integration of the primary photochemistry of light reactions with the dark reactions. Moreover, induction of the photoprotective mechanism, involving at least the peroxidases scavenging hydrogen peroxide, was observed for such genotypes. Adjustment of the photosynthesis and stress acclimation has enabled fast plant growth and avoidance of the developmental stages sensitive to fungal infection. The same mechanisms allowed the quick regrow of plants during the post-disease period. In contrast, genotypes that were unable to develop resistance despite cold hardening had less flexible balancing of the photoprotection and photoinhibition processes. Traits related to: photosynthesis-dependent cold-acclimation and cold-induced resistance; biomass accumulation and growth; as well as protection system involving peroxidases; were integrated also at a genetic level. Analysing 95 lines of the mapping population SaKa3006×Modus we determined region on chromosomes 5B and 7R shared within all tested traits. Moreover, similar expression pattern of a set of the genes related to PSII was determined with the metaanalysis of the multiple microarray experiments. Comparable results for peroxidases, involving APXs and GPXs and followed by PRXs, indicated a similar function during cold acclimation and defense responses. These data provide a new insight into the cross talk between cold acclimation and cold-induced resistance in triticale, indicating a key role of photosynthesis-related processes.

Conducting field trials for frost tolerance breeding in cereals

Cereal species can be damaged by frost either during winter or at flowering stage. Frost tolerance per se is only a part of the mechanisms that allow the plants to survive during winter; winterhardiness also considers other biotic or physical stresses that challenge the plants during the winter season limiting their survival rate. While frost tolerance can also be tested in controlled environments, winterhardiness can be determined only with field evaluations. Post-heading frost damage occurs from radiation frost events in spring during the reproductive stages. A reliable evaluation of winterhardiness or of post-heading frost damage should be carried out with field trials replicated across years and locations to overcome the irregular occurrence of natural conditions which satisfactorily differentiate genotypes. The evaluation of post-heading frost damage requires a specific attention to plant phenology. The extent of frost damage is usually determined with a visual score at the end of the winter.

Controlling crop diseases using induced resistance: challenges for the future

A number of different types of induced resistance have been defined based on differences in signalling pathways and spectra of effectiveness, including systemic acquired resistance and induced systemic resistance. Such resistance can be induced in plants by application of a variety of biotic and abiotic agents. The resulting resistance tends to be broad-spectrum and can be long-lasting, but is rarely complete, with most inducing agents reducing disease by between 20 and 85%. Since induced resistance is a host response, its expression under field conditions is likely to be influenced by a number of factors, including the environment, genotype, crop nutrition and the extent to which plants are already induced. Although research in this area has increased over the last few years, our understanding of the impact of these influences on the expression of induced resistance is still poor. There have also been a number of studies in recent years aimed at understanding of how best to use induced resistance in practical crop protection. However, such studies are relatively rare and further research geared towards incorporating induced resistance into disease management programmes, if appropriate, is required.

Complex phytohormone responses during the cold acclimation of two wheat cultivars differing in cold tolerance, winter Samanta and spring Sandra

Hormonal changes accompanying the cold stress (4°C) response that are related to the level of frost tolerance (FT; measured as LT50) and the content of the most abundant dehydrin, WCS120, were compared in the leaves and crowns of the winter wheat (Triticum aestivum L.) cv. Samanta and the spring wheat cv. Sandra. The characteristic feature of the alarm phase (1 day) response was a rapid elevation of abscisic acid (ABA) and an increase of protective proteins (dehydrin WCS120). This response was faster and stronger in winter wheat, where it coincided with the downregulation of bioactive cytokinins and auxin as well as enhanced deactivation of gibberellins, indicating rapid suppression of growth. Next, the ethylene precursor aminocyclopropane carboxylic acid was quickly upregulated. After 3-7 days of cold exposure, plant adaptation to the low temperature was correlated with a decrease in ABA and elevation of growth-promoting hormones (cytokinins, auxin and gibberellins). The content of other stress hormones, i.e., salicylic acid and jasmonic acid, also began to increase. After prolonged cold exposure (21 days), a resistance phase occurred. The winter cultivar exhibited substantially enhanced FT, which was associated with a decline in bioactive cytokinins and auxin. The inability of the spring cultivar to further increase its FT was correlated with maintenance of a relatively higher cytokinin and auxin content, which was achieved during the acclimation period.