First Report of Phoma herbarum on Field Pea (Pisum sativum) in Australia

Ascochyta blight in North Dakota field pea: the pathogen complex and its fungicide sensitivity

Worldwide, Ascochyta blight is caused by a complex of host-specific fungal pathogens, including Ascochyta pisi, Didymella pinodes, and Didymella pinodella. The application of foliar fungicides is often necessary for disease management, but a better understanding of pathogen prevalence, aggressiveness, and fungicide sensitivity is needed to optimize control. Leaf and stem samples were obtained from 56 field pea production fields in 14 counties in North Dakota from 2017 to 2020 and isolates were collected from lesions characteristic of Ascochyta blight. Based on fungal characteristics and sequencing the ITS1-5.8S-ITS2 region, 73% of isolates were confirmed to be D. pinodes (n = 177) and 27% were A. pisi (n = 65). Across pathogens, aggressiveness was similar among some isolates in greenhouse assays. The in vitro pyraclostrobin sensitivity of all D. pinodes isolates collected from 2017 to 2020 was lower than that of the three baseline isolates. Sensitivity of 91% of A. pisi isolates collected in 2019 and 2020 was lower than the sensitivity of two known sensitive isolates. Resistance factors (Rf) from mean EC50 values of pyraclostrobin baseline/known sensitive isolates to isolates collected from 2017 to 2020 ranged from 2 to 1,429 for D. pinodes and 1 to 209 for A. pisi. In vitro prothioconazole sensitivity of 91% of D. pinodes isolates collected from 2017 to 2020 was lower than the sensitivity of the baseline isolates and 98% of A. pisi isolates collected from 2019 to 2020 was lower than the sensitivity of the known sensitive isolates. Prothioconazole Rf ranged from 1 to 338 for D. pinodes and 1 to 127 for A. pisi. Based on in vitro results, 92% of D. pinodes and 98% of A. pisi isolates collected displayed reduced-sensitivity/resistance to both fungicides when compared to baseline/known sensitive isolates. Disease control under greenhouse conditions of both pathogens provided by both fungicides was significantly lower in isolates determined to be reduced-sensitive or resistant in in vitro assays when compared to sensitive. Results reported here reinforce growers desperate need of alternative fungicides and/or management tools to fight Ascochyta blight in North Dakota and neighboring regions.

Genome and Transcriptome Analysis of Ascochyta pisi Provides Insights into the Pathogenesis of Ascochyta Blight of Pea

Ascochyta blight caused by Ascochyta pisi is a major constraint to pea (Pisum sativum L.) production worldwide. Deciphering the pathogenic mechanism of A. pisi on peas will help in breeding resistant pea varieties and developing effective approaches for disease management. However, little is known about the genomic features and pathogenic factors of A. pisi. In this study, we first report that A. pisi is one of the causal agents of ascochyta blight disease of pea in China. The genome of the representative isolate A. pisi HNA23 was sequenced using PacBio and Illumina sequencing technologies. The HNA23 genome assembly is almost 41.5 Mb in size and harbors 10,796 putative protein-encoding genes. We predicted 555 carbohydrate-active enzymes (CAZymes), 1,008 secreted proteins, 74 small secreted cysteine-rich proteins (SSCPs), and 26 secondary metabolite biosynthetic gene clusters (SMGCs). A comparison of A. pisi genome features with the features of 6 other available genomes of Ascochyta species showed that CAZymes, the secretome, and SMGCs of this genus are considerably conserved. Importantly, the transcriptomes of HNA23 during infection of peas at three stages were further analyzed. We found that 245 CAZymes and 29 SSCPs were upregulated at all three tested infection stages. SMGCs were also trigged, but most of them were induced at only one stage of infection. Together, our results provide important genomic information on Ascochyta spp. and offer insights into the pathogenesis of A. pisi. IMPORTANCE Ascochyta blight is a major disease of legumes worldwide. Ascochyta pisi and other Ascochyta species have been identified as pathogens of ascochyta blight. Here, we first report that A. pisi causes ascochyta blight of pea in China, and we report the high-quality, fully annotated genome of A. pisi. Comparative genome analysis was performed to elucidate the differences and similarities among 7 Ascochyta species. We predict abundant CAZymes (569 per species), secreted proteins (851 per species), and prolific secondary metabolite gene clusters (29 per species) in these species. We identified a set of genes that may be responsible for fungal virulence based on transcriptomes in planta, including CAZymes, SSCPs, and secondary metabolites. The findings from the comparative genome analysis highlight the genetic diversity and help in understanding the evolutionary relationship of Ascochyta species. In planta transcriptome analysis provides reliable information for further investigation of the mechanism of the interaction between Ascochyta spp. and legumes.

Characterization of field pea (Pisum sativum) resistance against Peyronellaea pinodes and Didymella pinodella that cause ascochyta blight

Ascochyta blight is one of the most destructive diseases in field pea and is caused by either individual or combined infections by the necrotrophic pathogens Peyronellaea pinodes, Didymella pinodella, Ascochyta pisi and Ascochyta koolunga. Knowledge of disease epidemiology will help in understanding the resistance mechanisms, which, in turn, is beneficial in breeding for disease resistance. A pool of breeding lines and cultivars were inoculated with P. pinodes and D. pinodella to study the resistance responses and to characterize the underlying resistance reactions. In general, phenotypic analysis of controlled environment disease assays showed clear differential responses among genotypes against the two pathogens. The released variety PBA Wharton and the breeding line 11HP302-12HO-1 showed high levels of resistance against both pathogens whereas PBA Twilight and 10HP249-11HO-7 showed differential responses between the two pathogens, showing higher resistance against D. pinodella as compared to P. pinodes. OZP1604 had high infection levels against both pathogens. Histochemical analysis of leaves using diamino benzidine (DAB) showed the more resistant genotypes had lower accumulation of hydrogen peroxide compared to susceptible genotypes. The digital images of DAB staining were analyzed using ImageJ, an image analysis software. The image analysis results showed that quantification of leaf disease infection through image analysis is a useful tool in estimating the level of cell death in biotic stress studies. The qRT-PCR analysis of defense related genes showed that partially resistant genotypes had significantly higher expression of PsOXII and Pshmm6 in the P. pinodes treated plants, whereas expression of PsOXII, PsAPX1, PsCHS3 and PsOPR1 increased in partially resistant plants inoculated with D. pinodella. The differential timing and intensity of expression of a range of genes between resistant lines challenged with the same pathogen, or challenged with different pathogens, suggests that there are multiple pathways that restrict infection in this complex pathogen-host interaction. The combination of phenotypic, histochemical and molecular approaches provide a comprehensive picture of the infection process and resistance mechanism of pea plants against these pathogens.

Breeding and Genomics Interventions for Developing Ascochyta Blight Resistant Grain Legumes

Grain legumes are a key food source for ensuring global food security and sustaining agriculture. However, grain legume production is challenged by growing disease incidence due to global climate change. Ascochyta blight (AB) is a major disease, causing substantial yield losses in grain legumes worldwide. Harnessing the untapped reserve of global grain legume germplasm, landraces, and crop wild relatives (CWRs) could help minimize yield losses caused by AB infection in grain legumes. Several genetic determinants controlling AB resistance in various grain legumes have been identified following classical genetic and conventional breeding approaches. However, the advent of molecular markers, biparental quantitative trait loci (QTL) mapping, genome-wide association studies, genomic resources developed from various genome sequence assemblies, and whole-genome resequencing of global germplasm has revealed AB-resistant gene(s)/QTL/genomic regions/haplotypes on various linkage groups. These genomics resources allow plant breeders to embrace genomics-assisted selection for developing/transferring AB-resistant genomic regions to elite cultivars with great precision. Likewise, advances in functional genomics, especially transcriptomics and proteomics, have assisted in discovering possible candidate gene(s) and proteins and the underlying molecular mechanisms of AB resistance in various grain legumes. We discuss how emerging cutting-edge next-generation breeding tools, such as rapid generation advancement, field-based high-throughput phenotyping tools, genomic selection, and CRISPR/Cas9, could be used for fast-tracking AB-resistant grain legumes to meet the increasing demand for grain legume-based protein diets and thus ensuring global food security.

First Report of Phoma herbarum Causing Leaf Spot on Rhapis humilis in China

Rhapis humilis Blume is an ornamental plant for landscaping that is widely distributed in China. In February 2020, a leaf spot disease was observed on R. humilis in a nursery shed in Zhanjiang (21.17 N, 110.18 E), Guangdong, China. The disease incidence was more than 90%. The early symptom was small water-soaked lesions, which then turned into black necrotic spots. Eventually, the individual lesions coalesced into larger ones, leading to the death of diseased leaves. Ten diseased leaves were collected from the nursery. The diseased tissues were cut into 2 × 2 mm pieces, surface disinfected with 75% ethanol for 30 s and 2% sodium hypochlorite for 60 s, and then rinsed three times with sterile water before pathogen isolation. The tissues were plated on potato dextrose agar (PDA) medium and incubated at 28°C in the dark for 4 days. Pure cultures were produced by transferring hyphal tips to new PDA plates. Three isolates (RHPH-1, RHPH-2, and RHPH-3) were obtained. The colonies of the isolates were approximately 5 cm in diameter after 7 days. They were initially whitish and later became grayish white. The NaOH testing on MEA cultures was negative. No sporulation was detected after 30 days. The fertile structures of the specimens collected in the nursery were examined. Pycnidia were globose, measured 68 to 265 × 72 to 360 µm (n = 20), and mostly embedded. Conidia were aseptate, hyaline, and ellipsoid, measuring 3.6 to 6.5 × 2.2 to 2.7 µm (n = 30). Based on the morphological characteristics, the fungus was identified as in genus Phoma (Boerema et al. 2004). For molecular identification, the colony PCR method with MightyAmp DNA Polymerase (Takara-Bio, Dalian, China) (Lu et al. 2012) was used to amplify the internal transcribed spacer (ITS), partial RNA polymerase II largest subunit (RPB2), and beta-tubulin (β-tub) loci of three isolates using primer pairs ITS4/ITS5, RPB2-6F/RPB2-7R, and BT2a/BT2b, respectively (Chen et al, 2015; White et al, 1990). The sequences were deposited in GenBank (ITS, MZ419364-MZ419366; RPB2, MZ562293-MZ562295; and β-tub, MZ562296-MZ562298). Based on BLAST analysis, the sequences of the ITS, RPB2, and β-tub all showed 100% similarity to Phoma herbarum Westend. (CBS 377.92, accession nos. KT389536 for ITS; KT389663 for RPB2; and KT389837 for β-tub). Pathogenicity testing was performed in a greenhouse with 80% relative humidity at 25 to 30°C. Ten healthy plants of R. humilis were grown in pots, with one plant in each pot. The leaves were pinpricked with sterile needles before inoculation. They were inoculated with mycelial plugs of the isolates or sterile agar plugs (as control), with four plugs for each leaf. Five plants were used in each treatment. Disease symptoms similar to those in the nursery were observed on the inoculated plants 2 weeks after inoculation, whereas the control plants remained healthy. The fungus was reisolated from the symptomatic leaves and confirmed as P. herbarum by morphology and ITS analysis. P. herbarum was reported to cause leaf spot on Atractylodes lancea, Camellia sinensis, Elaeis guineensis, Lilium brownii, and Vetiveria zizanioides in China; Bituminaria bituminosa, Glycine max, Medicago sativa, and Pisum sativum in Australia; and Salvia nemorosa in Italy (Li et al. 2011; Li et al. 2012; Thangaraj et al. 2018). To our knowledge, the present study was the first to report P. herbarum causing leaf spot on R. humilis in China. P. herbarum seriously affects the supply of seedlings in R. humilis, and its epidemiology on R. humilis should be further studied.

Challenges With Managing Disease Complexes During Application of Different Measures Against Foliar Diseases of Field Pea

Studies were undertaken across five field locations in Western Australia to determine the relative changes in disease severity and subsequent field pea yield from up to four foliar pathogens associated with a field pea foliar disease complex (viz. genera Didymella, Phoma, Peronospora, and Septoria) across four different pea varieties sown at three different times and at three different densities. Delaying sowing of field pea significantly (P < 0.05) reduced the severity of Ascochyta blight (all five locations) and Septoria blight (one location), increased the severity of downy mildew (four locations), but had no effect on seed yield. In relation to Ascochyta blight severity at 80 days after sowing, at all locations the early time of sowing had significantly (P < 0.05) more severe Ascochyta blight than the mid and late times of sowing. Increasing actual plant density from 20 to 25 plants m-2 to 58 to 78 plants m-2 significantly (P < 0.05) increased the severity of the Ascochyta blight (four locations) and downy mildew (one location), and it increased seed yield at four locations irrespective of sowing date and three locations irrespective of variety. Compared with varieties Dundale, Wirrega, and Pennant, variety Alma showed significantly (P < 0.05) less severe Ascochyta blight, downy mildew, and Septoria blight (one location each). Grain yield was highest for the early time of sowing at three locations. Varieties Alma, Dundale, and Wirrega significantly (P < 0.05) outyielded Pennant at four locations. The percentage of isolations of individual Ascochyta blight pathogens at 80 days after the first time of sowing varied greatly, with genus Didymella ranging from 25 to 93% and genus Phoma ranging from 6 to 23% across the five field locations. This fluctuating nature of individual pathogen types and proportions within the Ascochyta blight complex, along with variation in the occurrence of pathogens Peronospora and Septoria, highlights the challenges to understand and manage the complexities of co-occurring different foliar pathogens of field pea. While the search for more effective host resistance continues, there is a need for and opportunities from further exploring and exploiting cultural management approaches focusing on crop sequence diversification, intercropping, manipulating time of sowing and stand density, and application of improved seed sanitation and residue/inoculum management practices. We discuss the constraints and opportunities toward overcoming the challenges associated with managing foliar disease complexes in field pea.

Development and Application of Real-Time and Conventional SSR-PCR Assays for Rapid and Sensitive Detection of Didymella pisi Associated with Ascochyta Blight of Dry Pea

Didymella pisi is the primary causal pathogen of Ascochyta blight (AB) of dry pea in Montana. Diagnosis of AB is challenging because there are six different species that cause AB worldwide and that can co-occur. Additionally, agar plate identification of D. pisi is challenging due to its slow growth rate. Currently, there are no PCR-based assays developed for specific detection of D. pisi or any fungal pathogen in the AB complex of dry pea. In this study, we evaluated simple sequence repeat (SSR) primer pairs for their specificity and sensitivity in real-time and conventional SSR-PCR both in vitro and in planta. The specificity of the assay was determined by testing DNA of 10 dry pea varieties, fungal species in the AB complex, and fungal species associated with dry pea. To avoid false-negative results, plant and fungal DNA markers were included as controls in a conventional multiplex SSR-PCR, to amplify any plant or fungal DNA in the absence of the D. pisi SSR target. SYBR Green SSR-quantitative PCR (qPCR) detection was conducted using the same primer pairs but in a uniplex format. D. pisi was specifically amplified, whereas other fungi and host DNA were not. Also, sensitivity experiments showed that the detection limit was 0.01 ng of DNA of D. pisi for both assays and 100 conidia in SSR-qPCR. These assays are valuable diagnostic tools for the detection of D. pisi.

First microsatellite markers developed and applied for the genetic diversity study and population structure of Didymella pisi associated with ascochyta blight of dry pea in Montana

Didymella pisi is the predominant causal pathogen of ascochyta blight of dry pea causing yield losses in Montana, where 415 000 acres were planted to dry pea in 2018. Thirty-three microsatellite markers were developed for dry pea pathogenic fungus, Didymella pisi, these markers were used to analyze genetic diversity and population structure of 205 isolates from four different geographical regions of Montana. These loci produced a total of 216 alleles with an average of 1.63 alleles per microsatellite marker. The polymorphic information content values ranged from 0.020 to 0.990 with an average of 0.323. The average observed heterozygosity across all loci varied from 0.000 to 0.018. The gene diversity among the loci ranged from 0.003 to 0.461. Unweighted Neighbor-joining and population structure analysis grouped these 205 isolates into two major sub-groups. The clusters did not match the geographic origin of the isolates. Analysis of molecular variance showed 85 % of the total variation within populations and only 15 % among populations. There was moderate genetic variation in the total populations (PhiPT = 0.153). Information obtained from this study could be useful as a base to design strategies for improved management such as breeding for resistance to ascochyta blight of dry pea in Montana.

Assessment of the Effect of Seed Infection with Ascochyta pisi on Pea in Western Canada

The role of seed infection with Ascochyta pisi using naturally infected seeds with an incidence from 0.5 to 14.5% was studied in field pea experiments in western Canada at locations with historically low inoculum pressure. A significant effect of A. pisi seed infection on the emergence of seedlings was observed in one experiment and when all data were pooled, but emergence was only reduced minimally, and symptoms of A. pisi on the aerial parts of the seedlings were rarely observed. The level of seed infection at planting had no impact on A. pisi disease severity on mature plants, on seed yield and size, or on the incidence of A. pisi infection of harvested seeds although A. pisi was the dominant species recovered from seeds. Results suggest that the disease did not progress significantly from seeds to seedlings, hence did not contribute to infection of aerial parts of the plants, and therefore infected seeds cannot be regarded as a source of inoculum in the epidemiology of this pathogen under western Canadian growing conditions. Assessing seed components of seeds with varying levels of A. pisi infection and seed staining revealed that the pathogen was present in all components of the seed, regardless of the severity of seed staining. This indicates that infected seeds may be an important way for the pathogen to survive in nature.

Studies on the Control of Ascochyta Blight in Field Peas (Pisum sativum L.) Caused by Ascochyta pinodes in Zhejiang Province, China

Ascochyta blight, an infection caused by a complex of Ascochyta pinodes, Ascochyta pinodella, Ascochyta pisi, and/or Phoma koolunga, is a destructive disease in many field peas (Pisum sativum L.)-growing regions, and it causes significant losses in grain yield. To understand the composition of fungi associated with this disease in Zhejiang Province, China, a total of 65 single-pycnidiospore fungal isolates were obtained from diseased pea samples collected from 5 locations in this region. These isolates were identified as Ascochyta pinodes by molecular techniques and their morphological and physiological characteristics. The mycelia of ZJ-1 could penetrate pea leaves across the stomas, and formed specific penetration structures and directly pierced leaves. The resistance level of 23 available pea cultivars was tested against their representative isolate A. pinodes ZJ-1 using the excised leaf-assay technique. The ZJ-1 mycelia could penetrate the leaves of all tested cultivars, and they developed typical symptoms, which suggested that all tested cultivars were susceptible to the fungus. Chemical fungicides and biological control agents were screened for management of this disease, and their efficacies were further determined. Most of the tested fungicides (11 out of 14) showed high activity toward ZJ-1 with EC50 < 5 μg/mL. Moreover, fungicides, including tebuconazole, boscalid, iprodione, carbendazim, and fludioxonil, displayed more than 80% disease control efficacy under the recorded conditions. Three biocontrol strains of Bacillus sp. and one of Pantoea agglomerans were isolated from pea-related niches and significantly reduced the severity of disease under greenhouse and field conditions. To our knowledge, this is the first study on ascochyta blight in field peas, and results presented here will be useful for controlling the disease in this area.

Synergisms between microbial pathogens in plant disease complexes: a growing trend

Plant diseases are often thought to be caused by one species or even by a specific strain. Microbes in nature, however, mostly occur as part of complex communities and this has been noted since the time of van Leeuwenhoek. Interestingly, most laboratory studies focus on single microbial strains grown in pure culture; we were therefore unaware of possible interspecies and/or inter-kingdom interactions of pathogenic microbes in the wild. In human and animal infections, it is now being recognized that many diseases are the result of multispecies synergistic interactions. This increases the complexity of the disease and has to be taken into consideration in the development of more effective control measures. On the other hand, there are only a few reports of synergistic pathogen-pathogen interactions in plant diseases and the mechanisms of interactions are currently unknown. Here we review some of these reports of synergism between different plant pathogens and their possible implications in crop health. Finally, we briefly highlight the recent technological advances in diagnostics as these are beginning to provide important insights into the microbial communities associated with complex plant diseases. These examples of synergistic interactions of plant pathogens that lead to disease complexes might prove to be more common than expected and understanding the underlying mechanisms might have important implications in plant disease epidemiology and management.

Relative Host Resistance to Black Spot Disease in Field Pea (Pisum sativum) is Determined by Individual Pathogens

Black spot, also known as Ascochyta blight, is the most important disease on field pea (Pisum sativum). It is caused by a complex of pathogens, the most important of which in Australia include Didymella pinodes, Phoma pinodella, and P. koolunga. The relative proportions of these and other component pathogens of the complex fluctuate widely across time and geographic locations in Australia, limiting the ability of breeders to develop varieties with effective resistance to black spot. To address this, 40 field pea genotypes were tested under controlled environment conditions for their individual stem and leaf responses against these three pathogens. Disease severity was calculated as area under disease progress curve (AUDPC), and subsequently converted to mean rank (MR). The overall rank (OR) for each pathogen was used to compare response of genotypes under inoculation with each pathogen. The expressions of host resistance across the field pea genotypes were largely dependent upon the individual test pathogen and whether the test was on stem or leaf. Overall, P. koolunga caused most severe stem disease; significantly more severe than either D. pinodes or P. pinodella. This is the first report of the host resistance identified in field pea to P. koolunga; the five genotypes showing highest resistance on stem, viz. 05P778-BSR-701, ATC 5338, ATC 5345, Dundale, and ATC 866, had AUDPC MR values <250.4, while the AUDPC MR values of the 19 genotypes showing the best resistance on leaf was less than 296.8. Two genotypes, ATC 866 and Dundale, showed resistance against P. koolunga on both stem and leaf. Against D. pinodes, the four and 16 most resistant genotypes on stem and leaf had AUDPC MR values <111.2 and <136.6, respectively, with four genotypes showing resistance on both stem and leaf including 05P770-BSR-705, Austrian Winter Pea, 06P822-(F5)-BSR-6, and 98107-62E. Against P. pinodella, four and eight genotypes showing the best resistance on stem and leaf had AUDPC MR values <81.3 and <221.9, respectively; three genotypes, viz. 98107-62E, Dundale, and Austrian Winter Pea showed combined resistance on stem and leaf. A few genotypes identified with resistance against two major pathogens of the complex will be of particular significance to breeding programs. These findings explain why field pea varieties arising from breeding programs in Australia fail to display the level or consistency of resistance required against black spot and why there needs to be a wider focus than D. pinodes in breeding programs.

Temporal and Spatial Changes in the Pea Black Spot Disease Complex in Western Australia

Black spot (also referred to as Ascochyta blight, Ascochyta foot rot and black stem, and Ascochyta leaf and pod spot) is a devastating disease of pea (Pisum sativum) caused by one or more pathogenic fungi, including Didymella pinodes, Ascochyta pisi, and Phoma pinodella. Surveys were conducted across pea-growing regions of Western Australia in 1984, 1987, 1989, 1996, 2010, and 2012. In total, 1,872 fungal isolates were collected in association with pea black spot disease symptoms. Internal transcribed spacer regions from representative isolates, chosen based on morphology, were sequenced to aid in identification. In most years and locations, D. pinodes was the predominant pathogen in the black spot complex. From 1984 to 2012, four new pathogens associated with black spot symptoms on leaves or stems (P. koolunga, P. herbarum, Boeremia exigua var. exigua, and P. glomerata) were confirmed. This study is the first to confirm P. koolunga in association with pea black spot symptoms in field pea in Western Australia and show that, by 2012, it was widely present in new regions. In 2012, P. koolunga was more prevalent than D. pinodes in Northam and P. pinodella in Esperance. P. herbarum and B. exigua var. exigua were only recorded in 2010. Although A. pisi was reported in Western Australia in 1912 and again in 1968 and is commonly associated with pea black spot in other states of Australia and elsewhere, it was not recorded in Western Australia from 1984 to 2012. It is clear that the pathogen population associated with the pea black spot complex in Western Australia has been dynamic across time and geographic location. This poses a particular challenge to development of effective resistance against the black spot complex, because breeding programs are focused almost exclusively on resistance to D. pinodes, largely ignoring other major pathogens in the disease complex. Furthermore, development and deployment of effective host resistance or fungicides against just one or two of the pathogens in the disease complex could radically shift the make-up of the population toward pathogen species that are least challenged by the host resistance or fungicides, creating an evolving black spot complex that remains ahead of breeding and other management efforts.