Future prospects for ascochyta blight resistance breeding in cool season food legumes

Status of Phytotoxins Isolated from Necrotrophic Fungi Causing Diseases on Grain Legumes

Fungal phytotoxins can be defined as secondary metabolites toxic to host plants and are believed to be involved in the symptoms developed of a number of plant diseases by targeting host cellular machineries or interfering with host immune responses. As any crop, legumes can be affected by a number of fungal diseases, causing severe yield losses worldwide. In this review, we report and discuss the isolation, chemical, and biological characterization of fungal phytotoxins produced by the most important necrotrophic fungi involved in legume diseases. Their possible role in plant-pathogen interaction and structure-toxicity relationship studies have also been reported and discussed. Moreover, multidisciplinary studies on other prominent biological activity conducted on reviewed phytotoxins are described. Finally, we explore the challenges in the identification of new fungal metabolites and their possible applications in future experiments.

De Novo Long-Read Whole-Genome Assemblies and the Comparative Pan-Genome Analysis of Ascochyta Blight Pathogens Affecting Field Pea

Ascochyta Blight (AB) is a major disease of many cool-season legumes globally. In field pea, three fungal pathogens have been identified to be responsible for this disease in Australia, namely Peyronellaea pinodes, Peyronellaea pinodella and Phoma koolunga. Limited genomic resources for these pathogens have been generated, which has hampered the implementation of effective management strategies and breeding for resistant cultivars. Using Oxford Nanopore long-read sequencing, we report the first high-quality, fully annotated, near-chromosome-level nuclear and mitochondrial genome assemblies for 18 isolates from the Australian AB complex. Comparative genome analysis was performed to elucidate the differences and similarities between species and isolates using phylogenetic relationships and functional diversity. Our data indicated that P. pinodella and P. koolunga are heterothallic, while P. pinodes is homothallic. More homology and orthologous gene clusters are shared between P. pinodes and P. pinodella compared to P. koolunga. The analysis of the repetitive DNA content showed differences in the transposable repeat composition in the genomes and their expression in the transcriptomes. Significant repeat expansion in P. koolunga’s genome was seen, with strong repeat-induced point mutation (RIP) activity being evident. Phylogenetic analysis revealed that genetic diversity can be exploited for species marker development. This study provided the much-needed genetic resources and characterization of the AB species to further drive research in key areas such as disease epidemiology and host–pathogen interactions.

Conventional and molecular breeding for disease resistance in chickpea: status and strategies

Chickpea (Cicer arietinum L.) is an important grain legume at the global level. Among different biotic stresses, diseases are the most important factor limiting its production, causing yield losses up to 100% in severe condition. The major diseases that adversely affect yield of chickpea include Fusarium wilt, Ascochyta blight and Botrytis gray mold. However, dry root rot, collar rot, Sclerotinia stem rot, rust, stunt disease and phyllody have been noted as emerging biotic threats to chickpea production in many production regions. Identification and incorporation of different morphological and biochemical traits are required through breeding to enhance genetic gain for disease resistance. In recent years, remarkable progress has been made in the development of trait-specific breeding lines, genetic and genomic resources in chickpea. Advances in genomics technologies have opened up new avenues to introgress genes from secondary and tertiary gene pools for improving disease resistance in chickpea. In this review, we have discussed important diseases, constraints and improvement strategies for enhancing disease resistance in chickpea.

Harnessing the hidden allelic diversity of wild Cicer to accelerate genomics-assisted chickpea crop improvement

Chickpea, commonly called Bengal gram or Garbanzo bean, faces a productivity crisis around the globe due to numerous biotic and abiotic stresses. The eroded genetic base of the cultivated Cicer gene pool is becoming a significant bottleneck in developing stress-resilient chickpea cultivars. In this scenario, the crop wild relatives (CWR) of chickpea, with the useful genomic wealth of their wild adaptation, give a ray of hope to improve the genetic background of the cultivated Cicer gene pool. To extrapolate these unearthed genomic diversities of wild, we require a thorough understanding of the pre-historic domestication episodes that are changing their shape with the expansion of the available scientific evidence. Keeping aforesaid in view, the current review article provides a glimpsed overview on several efforts done so far to reveal the mysterious origin and evolution of the Cicer gene pool, along with the constraints in their utilization for chickpea crop improvement. It encapsulates various stress-resilient CWR of chickpea and their use in several pre-breeding programs to develop numerous breeding populations for crop genetic enhancement. Further, this review will recapitulate the significant contributions of structural, functional and comparative genomics, pan-genomics and diverse genomics-assisted breeding strategy in dissecting the untapped trait-specific allelic/gene diversity and domestication pattern behind the CWR of chickpea, along with their potential and promises. We expect the newly explored genetic variations may be used in the breeding programs for re-wilding the cultigens' genomic background to open a new avenue for genetic gain and crop improvement capacity of chickpea.

Interactive Gene Expression Patterns of Susceptible and Resistant Lens ervoides Recombinant Inbred Lines and the Necrotroph Ascochyta lentis

Ascochyta lentis is a foliar pathogen of Lens species and is of worldwide importance in cultivated lentil production. High levels of resistance were identified in the wild species Lens ervoides. This resistance was explored through histopathology, qPCR estimation of fungal biomass and transcriptome sequencing in a susceptible and a resistant recombinant inbred line (RIL) of L. ervoides infected with an aggressive isolate of A. lentis. Necrotrophic growth was delayed in the resistant RIL compared to accelerated necrotrophy of A. lentis in the susceptible RIL. Analysis of the fungal secretome indicated that the early activation of cell wall-degrading enzymes contributed to increased virulence of A. lentis. On the host side, gene co-expression analysis revealed that the invasion by A. lentis caused mRNA, DNA and protein decay in infected plants regardless of the level of resistance in the host. The resistant RIL exhibited a stronger gene co-expression in lipid localization and sulfur processes, and cellular responses to nutrients and stimuli than the susceptible RIL. In addition, differential gene analysis revealed that the repression of both, gibberellin signaling and cell death associated with the hypersensitive response (HR), were associated with enhanced A. lentis resistance.

Phytotoxic Metabolites Produced by Legume-Associated Ascochyta and Its Related Genera in the Dothideomycetes

Phytotoxins, secondary metabolites toxic to plants and produced by fungi, are believed to play an important role in disease development by targeting host cellular machineries and/or interfering with host immune responses. The Ascochyta blight diseases on different legume plants are caused by Ascochyta and related taxa, such as Phoma. The causal agents of the Ascochyta blight are often associated with specific legume plants, showing a relatively narrow host range. The legume-associated Ascochyta and Phoma are known to produce a diverse array of polyketide-derived secondary metabolites, many of which exhibited significant phytotoxicity and have been claimed as virulence or pathogenicity factors. In this article, we reviewed the current state of knowledge on the diversity and biological activities of the phytotoxic compounds produced by Ascochyta and Phoma species. Also, we touched on the secondary metabolite biosynthesis gene clusters identified thus far and discussed the role of metabolites in the fungal biology.

Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses

Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.

Lentiquinones A, B, and C, Phytotoxic Anthraquinone Derivatives Isolated from Ascochyta lentis, a Pathogen of Lentil

A strain of the pathogenic fungus Ascochyta lentis isolated from lentil ( Lens culinaris) was studied to ascertain its capability to produce bioactive metabolites. From the culture filtrates were found three new anthraquinone derivatives, named lentiquinones A (1), B (2), and C (3), and the known lentisone. From the mycelium, four known analogues were identified, namely pachybasin (in larger amount), ω-hydroxypachybasin, 1,7-dihydroxy-3-methylanthracene-9,10-dione, and phomarin. Lentiquinones A-C were characterized by spectroscopic methods as 3,4,6-trihydroxy-8-methyl-2 H-benzo[ g]chromene-5,10-dione, 2,3,4,5,10-pentahydroxy-7-methyl-3,4,4a,10-tetrahydroanthracen-9(2 H)-one, and its 2-epimer, respectively, and the relative configuration of the two latter compounds was deduced by X-ray diffraction data analysis. The absolute configuration of lentiquinones B and C was determined as (2 R,3 S,4 S,4a S,10 R) and (2 S,3 S,4 S,4a S,10 R), respectively, by electronic circular dichroism (ECD) in solution and solid state, and TDDFT calculations. When tested by using different bioassays, the novel compounds showed interesting activities. In particular, applied to punctured leaves of host and nonhost plants, the three new compounds and lentisone caused severe necrosis, with lentiquinone A being the most active among the new metabolites. On cress ( Lepidium sativum), this latter compound proved to be particularly active in inhibiting root elongation. On Lemna minor all the compounds reduced the content of chlorophyll, with 1,7-dihyroxy-3-methylanthracene-9,10-dione being the most active. The new compounds, together with lentisone, proved to have antibiotic properties.

Lathyroxins A and B, Phytotoxic Monosubstituted Phenols Isolated from Ascochyta lentis var. lathyri, a Fungal Pathogen of Grass Pea ( Lathyrus sativus)

Ascochyta lentis var. lathyri has recently been reported to be the causal agent of Ascochyta blight of grass pea ( Lathyrus sativus), a disease characterized by the appearance of necrotic lesions of leaves and stems. Considering the novelty of the pathogen and the possible involvement of secondary metabolites in symptom appearance, a study was carried out to ascertain the capability of this fungus to produce bioactive metabolites. Some phytotoxic phenols were isolated from the culture filtrates of the fungus. In particular, two new phytotoxic metabolites, named lathyroxins A and B, were characterized by spectroscopic methods as 4-(2-hydroxy-3,3-dimethoxypropyl)phenol and 3-(4-hydroxyphenyl)propane-1,2-diol, respectively, and the R absolute configuration of C-2 of their 2-dimethoxy- and 2,3-diol-propyl side chain was assigned. Moreover, other well-known fungal metabolites, namely, p-hydroxybenzaldehyde, p-methoxyphenol, and tyrosol, were also identified. Lathyroxins A and B showed interesting phytotoxic properties, being able to cause necrosis on leaves and to inhibit seed germination and rootlet elongation. Moreover, both of the new metabolites had no effect against bacteria, arthropods, and nematodes.

Effects of Temperature Stresses on the Resistance of Chickpea Genotypes and Aggressiveness of Didymella rabiei Isolates

Chickpea (Cicer arietinum L.) is an important food and rotation crop in many parts of the world. Cold (freezing and chilling temperatures) and Ascochyta blight (Didymella rabiei) are the major constraints in chickpea production. The effects of temperature stresses on chickpea susceptibility and pathogen aggressiveness are not well documented in the Cicer-Didymella pathosystem. Two experiments were conducted under controlled conditions using chickpea genotypes and pathogen isolates in 2011 and 2012. In Experiment 1, four isolates of D. rabiei (AR-01, AR-02, AR-03 and AR-04), six chickpea genotypes (Ghab-1, Ghab-2, Ghab-3, Ghab-4, Ghab-5 and ICC-12004) and four temperature regimes (10, 15, 20, and 25°C) were studied using 10 day-old seedlings. In Experiment 2, three chickpea genotypes (Ghab-1, Ghab-2, and ICC-12004) were exposed to 5 and 10 days of chilling temperature exposure at 5°C and non-exposed seedlings were used as controls. Seedlings of the three chickpea genotypes were inoculated with the four pathogen isolates used in Experiment 1. Three disease parameters (incubation period, latent period and disease severity) were measured to evaluate treatment effects. In Experiment 1, highly significant interactions between genotypes and isolates; genotypes and temperature; and isolate and temperature were observed for incubation and latent periods. Genotype x isolate and temperature x isolate interactions also significantly affected disease severity. The resistant genotype ICC-12004 showed long incubation and latent periods and low disease severity at all temperatures. The highly aggressive isolate AR-04 caused symptoms, produced pycnidia in short duration as well as high disease severity across temperature regimes, which indicated it is adapted to a wide range of temperatures. Short incubation and latent periods and high disease severity were observed on genotypes exposed to chilling temperature. Our findings showed that the significant interactions of genotypes and isolates with temperature did not cause changes in the rank orders of the resistance of chickpea genotypes and aggressiveness of pathogen isolates. Moreover, chilling temperature predisposed chickpea genotypes to D. rabiei infection; developing multiple stress resistance is thus a pre-requisite for the expansion of winter-sown chickpea in West Asia and North Africa.

Fine Mapping of QTLs for Ascochyta Blight Resistance in Pea Using Heterogeneous Inbred Families

Ascochyta blight (AB) is an important disease of pea which can cause severe grain yield loss under wet conditions. In our previous study, we identified two quantitative trait loci (QTLs) abIII-1 and abI-IV-2 for AB resistance and these QTLs were consistent across locations and/or years in an inter-specific pea population (PR-19) developed from a cross between Alfetta (Pisum sativum) and P651 (P. fulvum). The objectives of this study were to fine map the abIII-1 and abI-IV-2 QTLs using a high density single nucleotide polymorphism (SNP)-based genetic linkage map and analyze identified markers in heterogeneous inbred family (HIF) populations. Selective genotyping of 51 PR-19 recombinant inbred lines was performed using genotyping-by-sequencing (GBS) and the resulting high density genetic linkage map was used to identify eight new SNP markers within the abI-IV-2 QTL, whereas no additional SNPs were identified within the abIII-1 QTL. Two HIF populations HIF-224 (143 lines) and HIF-173 (126 lines) were developed from F6 RILs PR-19-224 and PR-19-173, respectively. The HIF populations evaluated under field conditions in 2015 and 2016 showed a wide range of variation for reaction to AB resistance. Lodging score had significant positive (P < 0.001) correlation with AB scores. HIFs were genotyped using SNP markers within targeted QTLs. The genotypic and phenotypic data of the HIFs were used to identify two new QTLs, abI-IV-2.1 and abI-IV-2.2 for AB resistance within the abI-IV-2 QTL. These QTLs individually explained 5.5 to 14% of the total phenotypic variation. Resistance to lodging was also associated with these two QTLs. Identified SNP markers will be useful in marker assisted selection for development of pea cultivars with improved AB resistance.

mlo-Based Resistance: An Apparently Universal "Weapon" to Defeat Powdery Mildew Disease

Loss-of-function mutations of one or more of the appropriate Mildew resistance locus o (Mlo) genes are an apparently reliable "weapon" to protect plants from infection by powdery mildew fungi, as they confer durable broad-spectrum resistance. Originally detected as a natural mutation in an Ethiopian barley landrace, this so-called mlo-based resistance has been successfully employed in European barley agriculture for nearly four decades. More recently, mlo-mediated resistance was discovered to be inducible in virtually every plant species of economic or scientific relevance. By now, mlo resistance has been found (as natural mutants) or generated (by induced mutagenesis, gene silencing, and targeted or nontargeted gene knock-out) in a broad range of monocotyledonous and dicotyledonous plant species. Here, we review features of mlo resistance in barley, discuss approaches to identify the appropriate Mlo gene targets to induce mlo-based resistance, and consider the issue of pleiotropic effects often associated with mlo-mediated immunity, which can harm plant yield and quality. We portray mlo-based resistance as an apparently universal and effective weapon to defeat powdery mildew disease in a multitude of plant species.

Clarification on Host Range of Didymella pinodes the Causal Agent of Pea Ascochyta Blight

Didymella pinodes is the principal causal agent of ascochyta blight, one of the most important fungal diseases of pea (Pisum sativum) worldwide. Understanding its host specificity has crucial implications in epidemiology and management; however, this has not been clearly delineated yet. In this study we attempt to clarify the host range of D. pinodes and to compare it with that of other close Didymella spp. D. pinodes was very virulent on pea accessions, although differences in virulence were identified among isolates. On the contrary, studied isolates of D. fabae, D. rabiei, and D. lentil showed a reduced ability to infect pea not causing macroscopically visible symptoms on any of the pea accessions tested. D. pinodes isolates were also infective to some extend on almost all species tested including species such as Hedysarum coronarium, Lathyrus sativus, Lupinus albus, Medicago spp., Trifolium spp., Trigonella foenum-graecum, and Vicia articulata which were not mentioned before as hosts of D. pinodes. On the contrary, D. lentil and D. rabiei were more specific, infecting only lentil and chickpea, respectively. D. fabae was intermediate, infecting mainly faba bean, but also slightly other species such as Glycine max, Phaseolus vulgaris, Trifolium spp., Vicia sativa, and V. articulata. DNA sequence analysis of the nuclear ribosomal internal transcribed spacer region (ITS) was performed to confirm identity of the isolates studies and to determine phylogenetic relationship among the Didymella species, revealing the presence of two clearly distinct clades. Clade one was represented by two supported subclusters including D. fabae isolates as well as D. rabiei with D. lentil isolates. Clade two was the largest and included all the D. pinodes isolates as well as Phoma medicaginis var. pinodella. Genetic distance between D. pinodes and the other Didymella spp. isolates was not correlated with overall differences in pathogenicity. Based on evidences presented here, D. pinodes is not specialized on pea and its host range is larger than that of D. fabae, D. lentil, and D. rabiei. This has relevant implications in epidemiology and control as these species might act as alternative hosts for D. pinodes.

In planta Identification of Putative Pathogenicity Factors from the Chickpea Pathogen Ascochyta rabiei by De novo Transcriptome Sequencing Using RNA-Seq and Massive Analysis of cDNA Ends

The most important foliar diseases in legumes worldwide are ascochyta blights. Up to now, in the Ascochyta-legume pathosystem most studies focused on the identification of resistance genes in the host, while very little is known about the pathogenicity factors of the fungal pathogen. Moreover, available data were often obtained from fungi growing under artificial conditions. Therefore, in this study we aimed at the identification of the pathogenicity factors of Ascochyta rabiei, causing ascochyta blight in chickpea. To identify potential fungal pathogenicity factors, we employed RNA-seq and Massive Analysis of cDNA Ends (MACE) to produce comprehensive expression profiles of A. rabiei genes isolated either from the fungus growing in absence of its host or from fungi infecting chickpea leaves. We further provide a comprehensive de novo assembly of the A. rabiei transcriptome comprising 22,725 contigs with an average length of 1178 bp. Since pathogenicity factors are usually secreted, we predicted the A. rabiei secretome, yielding 550 putatively secreted proteins. MACE identified 596 transcripts that were up-regulated during infection. An analysis of these genes identified a collection of candidate pathogenicity factors and unraveled the pathogen's strategy for infecting its host.

Lathyrus sativus transcriptome resistance response to Ascochyta lathyri investigated by deepSuperSAGE analysis

Lathyrus sativus (grass pea) is a temperate grain legume crop with a great potential for expansion in dry areas or zones that are becoming more drought-prone. It is also recognized as a potential source of resistance to several important diseases in legumes, such as ascochyta blight. Nevertheless, the lack of detailed genomic and/or transcriptomic information hampers further exploitation of grass pea resistance-related genes in precision breeding. To elucidate the pathways differentially regulated during ascochyta-grass pea interaction and to identify resistance candidate genes, we compared the early response of the leaf gene expression profile of a resistant L. sativus genotype to Ascochyta lathyri infection with a non-inoculated control sample from the same genotype employing deepSuperSAGE. This analysis generated 14.387 UniTags of which 95.7% mapped to a reference grass pea/rust interaction transcriptome. From the total mapped UniTags, 738 were significantly differentially expressed between control and inoculated leaves. The results indicate that several gene classes acting in different phases of the plant/pathogen interaction are involved in the L. sativus response to A. lathyri infection. Most notably a clear up-regulation of defense-related genes involved in and/or regulated by the ethylene pathway was observed. There was also evidence of alterations in cell wall metabolism indicated by overexpression of cellulose synthase and lignin biosynthesis genes. This first genome-wide overview of the gene expression profile of the L. sativus response to ascochyta infection delivered a valuable set of candidate resistance genes for future use in precision breeding.

Identification of quantitative trait loci and candidate genes for specific cellular resistance responses against Didymella pinodes in pea

KEY MESSAGE

Phenotyping of specific cellular resistance responses and improvement of previous genetic map allowed the identification of novel genomic regions controlling cellular mechanisms involved in pea resistance to ascochyta blight and provided candidate genes suitable for MAS. Didymella pinodes, causing ascochyta blight, is a major pathogen of the pea crop and is responsible for serious damage and yield losses. Resistance is inherited polygenically and several quantitative trait loci (QTLs) have been already identified. However, the position of these QTLs should be further refined to identify molecular markers more closely linked to the resistance genes. In previous works, resistance was scored visually estimating the final disease symptoms; in this study, we have conducted a more precise phenotyping of resistance evaluating specific cellular resistance responses at the histological level to perform a more accurate QTL analysis. In addition, P665 × Messire genetic map used to identify the QTLs was improved by adding 117 SNP markers located in genes. This combined approach has allowed the identification, for the first time, of genomic regions controlling cellular mechanisms directly involved in pea resistance to ascochyta blight. Furthermore, the inclusion of the gene-based SNP markers has allowed the identification of candidate genes co-located with QTLs and has provided robust markers for marker-assisted selection.

Lentisone, a new phytotoxic anthraquinone produced by Ascochyta lentis, the causal agent of Ascochyta blight in Lens culinaris

An aggressive isolate of Ascochyta lentis obtained from lentil (Lens culinaris L.) produced various metabolites in vitro. The metabolites were isolated from the culture filtrates and characterized by spectroscopic, chemical, and optical methods. A new phytotoxic anthraquinone, named lentisone, was isolated and characterized as (1S*,2S*,3S*)-1,2,3,8-tetrahydroxy-1,2,3,4-tetrahydro-6-methylanthraquinone together with the well-known pachybasin (1-hydroxy-3-methylanthraquinone), tyrosol, and pseurotin A. Lentisone, tyrosol, and pseurotin A were phytotoxic to lentil, with lentisone the most toxic of all. The toxicity of these compounds is light-dependent. Finally, lentisone was also found to be phytotoxic to chickpea, pea, and faba bean, with toxicity in the latter higher than in any other tested legume, including lentil.

Pinolide, a new nonenolide produced by Didymella pinodes , the causal agent of ascochyta blight on Pisum sativum

An aggressive isolate of Didymella pinodes isolated from pea ( Pisum sativum ) produced four different metabolites in vitro. The metabolites isolated from the culture filtrates were characterized by spectroscopic and optical methods. A new nonenolide, named pinolide, was isolated and characterized as (2S*,7R*,8S*,5E,9R*)-2,7,8-trihydroxy-9-propyl-5-nonen-9-olide. Pinolidoxin, the main toxin produced by D. pinodes, was also isolated together with two other closely related nonenolides, identified as herbarumin II and 2-epi-herbarumin II. Herbarumin II and 2-epi-herbarumin II have been previously isolated from the fungi Phoma herbarum and Paraphaeosphaeria recurvifoliae , respectively, but described here to be isolated for the first time from D. pinodes. When tested on leaves of the host plant and other legumes and weeds, pinolidoxin was phytotoxic in all of the plant species, whereas the other three nonenolides did not produce any symptoms. The importance of the stereochemistry of the hydroxy group at C-7 on phytotoxicity also is discussed.