Pine genes regulated by the necrotrophic pathogen Fusarium circinatum

Identification and Characterization of Neocosmospora silvicola Causing Canker Disease on Pinus armandii in China

Chinese white pine, Pinus armandii, is a source of high-quality timber and an afforestation tree in China, which plays an important ecological and social role in water and soil conservation. Recently, a new canker disease has been reported in Longnan City, Gansu Province, where P. armandii is mainly distributed. In this study, the causal agent was isolated from diseased samples and identified as a fungal pathogen, Neocosmospora silvicola, based on morphological characteristics and molecular analyses (internal transcribed spacer, large subunit, RNA polymerase II, and translation elongation factor-1α). Pathogenicity tests on P. armandii revealed that N. silvicola isolates caused a 60% average mortality rate in artificially inoculated 2-year-old seedlings. The pathogenicity of these isolates was also observed on the branches of 10-year-old P. armandii trees with a 100% mortality rate. These results agree with the isolation of N. silvicola from diseased plants, suggesting the possible role of this fungus in the decline of P. armandii plants. Mycelial growth of N. silvicola was fastest on potato dextrose agar medium, and growth occurred at pH values ranging from 4.0 to 11.0 with temperatures between 5 and 40°C. The fungus also grew rapidly in complete darkness compared with other light conditions. Of the eight carbon and seven nitrogen sources tested, starch and sodium nitrate, respectively, were highly efficient in supporting the mycelial growth of N. silvicola. The ability of N. silvicola to grow at low temperatures (5°C) may explain its occurrence in the Longnan area of Gansu Province. This article is the first report of N. silvicola as an important fungal pathogen causing branch and stem cankers on Pinus tree species, which remains a threat to the forests.

Multispecies comparison of host responses to Fusarium circinatum challenge in tropical pines show consistency in resistance mechanisms

Fusarium circinatum poses a threat to both commercial and natural pine forests. Large variation in host resistance exists between species, with many economically important species being susceptible. Development of resistant genotypes could be expedited and optimised by investigating the molecular mechanisms underlying host resistance and susceptibility as well as increasing the available genetic resources. RNA-seq data, from F. circinatum inoculated and mock-inoculated ca. 6-month-old shoot tissue at 3- and 7-days postinoculation, was generated for three commercially important tropical pines, Pinus oocarpa, Pinus maximinoi and Pinus greggii. De novo transcriptomes were assembled and used to investigate the NLR and PR gene content within available pine references. Host responses to F. circinatum challenge were investigated in P. oocarpa (resistant) and P. greggii (susceptible), in comparison to previously generated expression profiles from Pinus tecunumanii (resistant) and Pinus patula (susceptible). Expression results indicated crosstalk between induced salicylate, jasmonate and ethylene signalling is involved in host resistance and compromised in susceptible hosts. Additionally, higher constitutive expression of sulfur metabolism and flavonoid biosynthesis in resistant hosts suggest involvement of these metabolites in resistance.

Studying tree response to biotic stress using a multi-disciplinary approach: The pine pitch canker case study

In an era of climate change and global trade, forests sustainability is endangered by several biotic threats. Pine pitch canker (PPC), caused by Fusarium circinatum, is one of the most important disease affecting conifers worldwide. To date, no effective control measures have been found for this disease. Earlier studies on PPC were mainly focused on the pathogen itself or on determining the levels of susceptibility of different hosts to F. circinatum infection. However, over the last years, plenty of information on the mechanisms that may explain the susceptibility or resistance to PPC has been published. This data are useful to better understand tree response to biotic stress and, most importantly, to aid the development of innovative and scientific-based disease control measures. This review gathers and discusses the main advances on PPC knowledge, especially focusing on multi-disciplinary studies investigating the response of pines with different levels of susceptibility to PPC upon infection. After an overview of the general knowledge of the disease, the importance of integrating information from physiological and Omics studies to unveil the mechanisms behind PPC susceptibility/resistance and to develop control strategies is explored. An extensive review of the main host responses to PPC was performed, including changes in water relations, signalling (ROS and hormones), primary metabolism, and defence (resin, phenolics, and PR proteins). A general picture of pine response to PPC is suggested according to the host susceptibility level and the next steps and gaps on PPC research are pointed out.

Comparative proteomics of Pinus-Fusarium circinatum interactions reveal metabolic clues to biotic stress resistance

Fusarium circinatum, causing pine pitch canker (PPC), affects conifers productivity and health worldwide. Selection and breeding for resistance arises as the most promising approach to fight PPC. Therefore, it is crucial to explore the response of hosts with varying levels of susceptibility to PPC to unveil the genes/pathways behind these phenotypes. We evaluated the dynamics of the needle proteome of a susceptible (Pinus radiata) and a relatively resistant (Pinus pinea) species upon F. circinatum inoculation by GeLC-MS/MS. Integration with physiological data and validation of key genes by qPCR allowed to identify core pathways regulating these contrasting responses. In P. radiata, the pathogen may target both the secondary metabolism to negatively regulate immune response and chloroplast redox proteins to increase energy-producing pathways for amino acid production in its favour. In contrast, chloroplast redox regulation may assure redox homeostasis in P. pinea, as well as nonenzymatic antioxidants. The presence of membrane trafficking-related proteins exclusively in P. pinea likely explains its defence response against F. circinatum. A crosstalk between abscisic acid and epigenetic regulation of gene expression is also proposed in PPC response. These results are useful to support breeding programs aiming to achieve PPC resistance.

Co-Infections by Fusarium circinatum and Phytophthora spp. on Pinus radiata: Complex Phenotypic and Molecular Interactions

This study investigated the complex phenotypic and genetic response of Monterey pine (Pinus radiata) seedlings to co-infections by F. circinatum, the causal agent of pine pitch canker disease, and the oomycetes Phytophthora xcambivora and P. parvispora. Monterey pine seedlings were wound-inoculated with each single pathogen and with the combinations F. circinatum/P. xcambivora and F. circinatum/P. parvispora. Initially, seedlings inoculated only with F. circinatum showed less severe symptoms than seedlings co-inoculated or inoculated only with P. xcambivora or P. parvispora. However, 30 days post-inoculation (dpi), all inoculated seedlings, including those inoculated only with F. circinatum, showed severe symptoms with no significant differences among treatments. The transcriptomic profiles of three genes encoding pathogenesis-related proteins, i.e., chitinase (PR3), thaumatin-like protein (PR5), phenylalanine ammonia-lyase (PAL), and the pyruvate decarboxylase (PDC)-encoding gene were analyzed at various time intervals after inoculation. In seedlings inoculated with single pathogens, F. circinatum stimulated the up-regulation of all genes, while between the two oomycetes, only P. xcambivora induced significant up-regulations. In seedlings co-inoculated with F. circinatum and P.xcambivora or P. parvispora none of the genes showed a significant over-expression 4 dpi. In contrast, at 11 dpi, significant up-regulation was observed for PR5 in the combination F. circinatum/P.xcambivora and PDC in the combination F. circinatum/P. parvispora, thus suggesting a possible synergism of multiple infections in triggering this plant defense mechanism.

Dual RNA-Sequencing Analysis of Resistant (Pinus pinea) and Susceptible (Pinus radiata) Hosts during Fusarium circinatum Challenge

Fusarium circinatum causes one of the most important diseases of conifers worldwide, the pine pitch canker (PPC). However, no effective field intervention measures aiming to control or eradicate PPC are available. Due to the variation in host genetic resistance, the development of resistant varieties is postulated as a viable and promising strategy. By using an integrated approach, this study aimed to identify differences in the molecular responses and physiological traits of the highly susceptible Pinus radiata and the highly resistant Pinus pinea to F. circinatum at an early stage of infection. Dual RNA-Seq analysis also allowed to evaluate pathogen behavior when infecting each pine species. No significant changes in the physiological analysis were found upon pathogen infection, although transcriptional reprogramming was observed mainly in the resistant species. The transcriptome profiling of P. pinea revealed an early perception of the pathogen infection together with a strong and coordinated defense activation through the reinforcement and lignification of the cell wall, the antioxidant activity, the induction of PR genes, and the biosynthesis of defense hormones. On the contrary, P. radiata had a weaker response, possibly due to impaired perception of the fungal infection that led to a reduced downstream defense signaling. Fusarium circinatum showed a different transcriptomic profile depending on the pine species being infected. While in P. pinea, the pathogen focused on the degradation of plant cell walls, active uptake of the plant nutrients was showed in P. radiata. These findings present useful knowledge for the development of breeding programs to manage PPC.

Compost Tea Reduces the Susceptibility of Pinus radiata to Fusarium circinatum in Nursery Production

Nutrition is one of the factors that most limits forestry plant growth; thus, current production in nurseries is based on conventional fertilization focused on enhancing vigor. However, an excessive intake of mineral nitrogen can cause morphological imbalances and the formation of more succulent tissues which, consequently, increase susceptibility to plant pathogens. Fusarium circinatum is the causal agent of pitch canker in plants of the Pinus genus, with Pinus radiata being the species most susceptible to this disease. This study compares the response of P. radiata seedlings to infection by F. circinatum as influenced by two fertilizers-conventional and aerated compost tea (ACT)-applied during the nursery phase. The potential of ACT against F. circinatum was first tested in vitro, where it was found to inhibit the pathogen's mycelial growth and conidial germination. In the greenhouse, infected plants fertilized with ACT exhibited less severe internal and external symptoms of pitch canker and lower levels of pathogen colonization of both stems and needles than with conventional fertilizer. An analysis of the hormone content and defense-related gene expression shows greater salicylic acid production and phenylalanine ammonium-lyase and chalcone synthase expression in ACT-fertilized pine. All of the parameters assessed are consistent in showing that biofertilization with ACT reduces the susceptibility of pine seedlings to the disease compared with conventional fertilization.

Pinus Susceptibility to Pitch Canker Triggers Specific Physiological Responses in Symptomatic Plants: An Integrated Approach

Fusarium circinatum, the causal agent of pine pitch canker (PPC), is an emergent and still understudied risk that threatens Pinus forests worldwide, with potential production and sustainability losses. In order to explore the response of pine species with distinct levels of susceptibility to PPC, we investigated changes in physiology, hormones, specific gene transcripts, and primary metabolism occurring in symptomatic Pinus pinea, Pinus pinaster, and Pinus radiata upon inoculation with F. circinatum. Pinus radiata and P. pinaster exhibiting high and intermediate susceptibility to PPC, respectively, suffered changes in plant water status and photosynthetic impairment. This was associated with sink metabolism induction, a general accumulation of amino acids and overexpression of pathogenesis-related genes. On the other hand, P. pinea exhibited the greatest resistance to PPC and stomatal opening, transpiration increase, and glycerol accumulation were observed in inoculated plants. A stronger induction of pyruvate decarboxylase transcripts and differential hormones regulation were also found for inoculated P. pinea in comparison with the susceptible Pinus species studied. The specific physiological changes reported herein are the first steps to understand the complex Pinus-Fusarium interaction and create tools for the selection of resistant genotypes thus contributing to disease mitigation.

Evolution of disease response genes in loblolly pine: insights from candidate genes

Background

Host-pathogen interactions that may lead to a competitive co-evolution of virulence and resistance mechanisms present an attractive system to study molecular evolution because strong, recent (or even current) selective pressure is expected at many genomic loci. However, it is unclear whether these selective forces would act to preserve existing diversity, promote novel diversity, or reduce linked neutral diversity during rapid fixation of advantageous alleles. In plants, the lack of adaptive immunity places a larger burden on genetic diversity to ensure survival of plant populations. This burden is even greater if the generation time of the plant is much longer than the generation time of the pathogen.

Methodology/Principal Findings

Here, we present nucleotide polymorphism and substitution data for 41 candidate genes from the long-lived forest tree loblolly pine, selected primarily for their prospective influences on host-pathogen interactions. This dataset is analyzed together with 15 drought-tolerance and 13 wood-quality genes from previous studies. A wide range of neutrality tests were performed and tested against expectations from realistic demographic models.

Conclusions/Significance

Collectively, our analyses found that axr (auxin response factor), caf1 (chromatin assembly factor) and gatabp1 (gata binding protein 1) candidate genes carry patterns consistent with directional selection and erd3 (early response to drought 3) displays patterns suggestive of a selective sweep, both of which are consistent with the arm-race model of disease response evolution. Furthermore, we have identified patterns consistent with diversifying selection at erf1-like (ethylene responsive factor 1), ccoaoemt (caffeoyl-CoA-O-methyltransferase), cyp450-like (cytochrome p450-like) and pr4.3 (pathogen response 4.3), expected under the trench-warfare evolution model. Finally, a drought-tolerance candidate related to the plant cell wall, lp5, displayed patterns consistent with balancing selection. In conclusion, both arms-race and trench-warfare models seem compatible with patterns of polymorphism found in different disease-response candidate genes, indicating a mixed strategy of disease tolerance evolution for loblolly pine, a major tree crop in southeastern United States.

Association mapping of quantitative disease resistance in a natural population of loblolly pine (Pinus taeda L.)

Genetic resistance to disease incited by necrotrophic pathogens is not well understood in plants. Whereas resistance is often quantitative, there is limited information on the genes that underpin quantitative variation in disease resistance. We used a population genomic approach to identify genes in loblolly pine (Pinus taeda) that are associated with resistance to pitch canker, a disease incited by the necrotrophic pathogen Fusarium circinatum. A set of 498 largely unrelated, clonally propagated genotypes were inoculated with F. circinatum microconidia and lesion length, a measure of disease resistance, data were collected 4, 8, and 12 weeks after inoculation. Best linear unbiased prediction was used to adjust for imbalance in number of observations and to identify highly susceptible and highly resistant genotypes ("tails"). The tails were reinoculated to validate the results of the full population screen. Significant associations were detected in 10 single nucleotide polymorphisms (SNPs) (out of 3938 tested). As hypothesized for genes involved in quantitative resistance, the 10 SNPs had small effects and proposed roles in basal resistance, direct defense, and signal transduction. We also discovered associated genes with unknown function, which would have remained undetected in a candidate gene approach constrained by annotation for disease resistance or stress response.

Anatomical and chemical defenses of conifer bark against bark beetles and other pests

Conifers are long-lived organisms, and part of their success is due to their potent defense mechanisms. This review focuses on bark defenses, a front line against organisms trying to reach the nutrient-rich phloem. A major breach of the bark can lead to tree death, as evidenced by the millions of trees killed every year by specialized bark-invading insects. Different defense strategies have arisen in conifer lineages, but the general strategy is one of overlapping constitutive mechanical and chemical defenses overlaid with the capacity to up-regulate additional defenses. The defense strategy incorporates a graded response from 'repel', through 'defend' and 'kill', to 'compartmentalize', depending upon the advance of the invading organism. Using a combination of toxic and polymer chemistry, anatomical structures and their placement, and inducible defenses, conifers have evolved bark defense mechanisms that work against a variety of pests. However, these can be overcome by strategies including aggregation pheromones of bark beetles and introduction of virulent phytopathogens. The defense structures and chemicals in conifer bark are reviewed and questions about their coevolution with bark beetles are discussed.

Genetic dissection of fusiform rust and pitch canker disease traits in loblolly pine

Loblolly pine (Pinus taeda L.) exhibits genetic resistance to fusiform rust disease (incited by the biotrophic fungus, Cronartium quercuum f. sp. fusiforme) and pitch canker disease (incited by the necrotrophic fungus, Fusarium circinatum). In this study, a total of 14,015 loblolly pine cuttings from 1,065 clones were screened in controlled greenhouse conditions to identify phenotypes of clones, families, and parents that guide a genetic dissection of disease traits associated with pitch canker and fusiform rust. A total of 23,373 phenotypic data points were collected for lesion length (pitch canker) and gall score, gall length, and gall width (fusiform rust). We verified heritable fusiform rust and pitch canker traits and calculated parental, clonal, and full-sib family rankings for both diseases. Genetic correlations revealed that traits associated with fusiform rust are genetically distinct from one another, and that the genetic mechanisms underlying pitch canker and fusiform rust resistance are independent. The disease phenotyping described here is a critical step towards identifying specific loci and alleles associated with fusiform rust and pitch canker resistance.