Population structure of Cercospora kikuchii, the causal agent of Cercospora leaf blight and purple seed stain in soybean

Deciphering genetic factors contributing to enhanced resistance against Cercospora leaf blight in soybean (Glycine max L.) using GWAS analysis

Cercospora leaf blight (CLB), caused by Cercospora cf. flagellaris, C. kikuchii, and C. cf. sigesbeckiae, is a significant soybean [Glycine max (L.) Merr.] disease in regions with hot and humid conditions causing yield loss in the United States and Canada. There is limited information regarding resistant soybean cultivars, and there have been marginal efforts to identify the genomic regions underlying resistance to CLB. A Genome-Wide Association Study was conducted using a diverse panel of 460 soybean accessions from maturity groups III to VII to identify the genomic regions associated to the CLB disease. These accessions were evaluated for CLB in different regions of the southeastern United States over 3 years. In total, the study identified 99 Single Nucleotide Polymorphism (SNPs) associated with the disease severity and 85 SNPs associated with disease incidence. Across multiple environments, 47 disease severity SNPs and 23 incidence SNPs were common. Candidate genes within 10 kb of these SNPs were involved in biotic and abiotic stress pathways. This information will contribute to the development of resistant soybean germplasm. Further research is warranted to study the effect of pyramiding desirable genomic regions and investigate the role of identified genes in soybean CLB resistance.

Unravelling unexplored diversity of cercosporoid fungi (Mycosphaerellaceae, Mycosphaerellales, Ascomycota) in tropical Africa

Cercosporoid fungi (Mycosphaerellaceae, Mycosphaerellales, Ascomycota) are one of the largest and most diverse groups of hyphomycetes causing a wide range of diseases of economically important plants as well as of plants in the wild. Although more than 6000 species are known for this group, the documentation of this fungal group is far from complete. Especially in the tropics, the diversity of cercosporoid fungi is poorly known. The present study aims to identify and characterise cercosporoid fungi collected on host plants belonging to Fabaceae in Benin, West Africa. Information on their morphology, host species and DNA sequence data (18S rDNA, 28S rDNA, ITS and tef1) is provided. DNA sequence data were obtained by a simple and non-culture-based method for DNA isolation which has been applied for cercosporoid fungi for the first time in the context of the present study. Among the loci used for the phylogenetic analysis, tef1 provided the best resolution together with the multigene dataset. Species delimitation in many cases, however, was only possible by combining molecular sequence data with morphological characteristics. Based on forty specimens recently collected in Benin, 18 species are presented with morphological descriptions, illustrations and sequence data. Among these, six species in the genus Cercospora and two species in Pseudocercospora are proposed as species new to science. The newly described species are Cercospora (C.) beninensis on Crotalariamacrocalyx, C.parakouensis on Desmodiumtortuosum, C.rhynchophora on Vignaunguiculata, C.vignae-subterraneae on Vignasubterranea, C.tentaculifera on Vignaunguiculata, C.zorniicola on Zorniaglochidiata, Pseudocercosporasennicola on Sennaoccidentalis and Pseudocercosporatabei on Vignaunguiculata. Eight species of cercosporoid fungi are reported for Benin for the first time, three of them, namely C.cf.canscorina, C.cf.fagopyri and C.phaseoli-lunati are new for West Africa. The presence of two species of cercosporoid fungi on Fabaceae previously reported from Benin, namely Nothopassalorapersonata and Passaloraarachidicola, is confirmed.

Drivers of Foliar Fungal Endophytic Communities of Kudzu (Pueraria montana var. lobata) in the Southeast United States

Fungal endophytes play important roles in plant fitness and plant–microbe interactions. Kudzu (Pueraria montana var. lobata) is a dominant, abundant, and highly aggressive invasive plant in the Southeast United States. Kudzu serves as a pathogen reservoir that impacts economically important leguminous crops. We conducted the first investigations on kudzu fungal endophytes (Illumina MiSeq—ITS2) to elucidate drivers of endophytic communities across the heart of the invasive range in the Southeast United States (TN, MS, AL, GA). We tested the impacts of multiple environmental parameters (Chlorophyll, NO3−, K+, soil pH, leaf area, host genotype, traffic intensity, and geographic location) on foliar endophyte communities. Endophytic communities were diverse and structured by many factors in our PerMANOVA analyses, but location, genotype, and traffic (proxy for pollution) were the strongest drivers of community composition (R2 = 0.152, p < 0.001, R2 = 0.129, p < 0.001, and R2 = 0.126, p < 0.001, respectively). Further, we examined the putative ecological interactions between endophytic fungi and plant pathogens. We identify numerous OTUs that are positively and strongly associated with pathogen occurrence, largely within the families Montagnulaceae and Tremellales incertae sedis. Taken together, these data suggest location, host genetics and local pollution play instrumental roles in structuring communities, and integrative plant management must consider these factors when developing management strategies.

The AVR4 effector is involved in cercosporin biosynthesis and likely affects the virulence of Cercospora cf. flagellaris on soybean

One of the most devastating fungal diseases of soybean in the southern USA is Cercospora leaf blight (CLB), which is caused mainly by Cercospora cf. flagellaris. Recent studies found that the fungal effector AVR4, originally identified in Cladosporium fulvum as a chitin-binding protein, is highly conserved among other Cercospora species. We wanted to determine whether it is present in C. cf. flagellaris and, if so, whether it plays a role in the pathogen infection of soybean. We cloned the Avr4 gene and created C. cf. flagellaris ∆avr4 mutants, which produced little cercosporin and significantly reduced expression of cercosporin biosynthesis genes. The ∆avr4 mutants were also more sensitive to chitinase and showed reduced virulence on soybean compared to the wild-type. The observed reduced virulence of C. cf. flagellaris ∆avr4 mutants on detached soybean leaves is likely due to reduced cercosporin biosynthesis. The phenotypes of reduced cercosporin production and cercosporin pathway gene expression, similar to those of the ∆avr4 mutants, were reproduced when wild-type C. cf. flagellaris was treated with double-stranded RNA targeting Avr4 in vitro. These two independent approaches demonstrated for the first time the direct involvement of AVR4 in the biosynthesis of cercosporin.

Evaluation of soybean genotypes for reaction to natural field infection by Cercospora species causing purple seed stain

Purple seed stain (PSS) of soybean (Glycine max (L.) Merr.) is a prevalent seed disease. It results in poor seed quality and reduced seed lot market grade, and thus undermines value of soybean worldwide. The objectives of this research were to evaluate the reaction of selected soybean genotypes collected from 15 countries representing maturity groups (MGs) III, IV, and V to PSS, and to identify new sources of resistance to PSS based on three years of evaluation of natural field infection by Cercospora spp. in the Mississippi Delta of the U. S. In this study, 42 soybean genotypes were evaluated in 2010, 2011, and 2012. Seventeen lines including six MG III (PI 88490, PI 504488, PI 417361, PI 548298, PI 437482, and PI 578486), seven MG IV (PI 404173, PI 346308, PI 355070, PI 416779, PI 80479, PI 346307, and PI 264555), and four MG V (PI 417567, PI 417420, PI 381659, and PI 407749) genotypes had significantly lower percent seed infection by Cercospora spp. than the susceptible checks and other genotypes evaluated (P ≤ 0.05). These genotypes of soybean can be used in developing soybean cultivars or germplasm lines with resistance to PSS and for genetic mapping of PSS resistance genes. In addition, among these 17 lines with different levels of resistance to PSS, nine soybean genotypes (PI 417361, PI 504488, PI 88490, PI 346308, PI 416779, PI 417567, PI 381659, PI 417567, and PI 407749) were previously reported as resistant to Phomopsis seed decay. Therefore, they could be useful in breeding programs to develop soybean cultivars with improved resistance to both seed diseases.

Cercospora cf. flagellaris and Cercospora cf. sigesbeckiae Are Associated with Cercospora Leaf Blight and Purple Seed Stain on Soybean in North America

Cercospora kikuchii has long been considered the causal agent of Cercospora leaf blight (CLB) and purple seed stain (PSS) on soybean, but a recent study found C. cf. flagellaris associated with CLB and PSS in Arkansas (United States) and Argentina. Here, we provide a broader perspective on the distribution of C. cf. flagellaris on soybean and alternate hosts within the United States (Arkansas, Louisiana, Mississippi, Missouri, and Kansas). We used a multilocus phylogenetic approach with data from actin, calmodulin, translation elongation factor 1-α, histone 3, the internal transcribed spacer region of rDNA and the mating-type locus to determine that two species, C. cf. flagellaris (200 of 205 isolates) and C. cf. sigesbeckiae (five of 205 isolates), are associated with CLB and PSS in the United States. In our phylogenetic analyses, species-level lineages were generally well-supported, though deeper-level evolutionary relationships remained unresolved, indicating that these genes do not possess sufficient phylogenetic signal to resolve the evolutionary history of Cercospora. We also investigated the potential for sexual reproduction in C. cf. flagellaris in Louisiana by determining the frequency of MAT1-1/MAT1-2 mating-type idiomorphs within the Louisiana population of C. cf. flagellaris. Though the MAT 1-2 idiomorph was significantly more common in our collection, the presence of both mating types suggests the potential for sexual reproduction exists.

More Cercospora Species Infect Soybeans across the Americas than Meets the Eye

Diseases of soybean caused by Cercospora spp. are endemic throughout the world's soybean production regions. Species diversity in the genus Cercospora has been underestimated due to overdependence on morphological characteristics, symptoms, and host associations. Currently, only two species (Cercospora kikuchii and C. sojina) are recognized to infect soybean; C. kikuchii causes Cercospora leaf blight (CLB) and purple seed stain (PSS), whereas C. sojina causes frogeye leaf spot. To assess cryptic speciation among pathogens causing CLB and PSS, phylogenetic and phylogeographic analyses were performed with isolates from the top three soybean producing countries (USA, Brazil, and Argentina; collectively accounting for ~80% of global production). Eight nuclear genes and one mitochondrial gene were partially sequenced and analyzed. Additionally, amino acid substitutions conferring fungicide resistance were surveyed, and the production of cercosporin (a polyketide toxin produced by many Cercospora spp.) was assessed. From these analyses, the long-held assumption of C. kikuchii as the single causal agent of CLB and PSS was rejected experimentally. Four cercosporin-producing lineages were uncovered with origins (about 1 Mya) predicted to predate agriculture. Some of the Cercospora spp. newly associated with CLB and PSS appear to represent undescribed species; others were not previously reported to infect soybeans. Lineage 1, which contained the ex-type strain of C. kikuchii, was monophyletic and occurred in Argentina and Brazil. In contrast, lineages 2 and 3 were polyphyletic and contained wide-host range species complexes. Lineage 4 was monophyletic, thrived in Argentina and the USA, and included the generalist Cercospora cf. flagellaris. Interlineage recombination was detected, along with a high frequency of mutations linked to fungicide resistance in lineages 2 and 3. These findings point to cryptic Cercospora species as underappreciated global considerations for soybean production and phytosanitary vigilance, and urge a reassessment of host-specificity as a diagnostic tool for Cercospora.

Evidence for Genetic Similarity of Vegetative Compatibility Groupings in Sclerotinia homoeocarpa

Vegetative compatibility groups (VCGs) are determined for many fungi to test for the ability of fungal isolates to undergo heterokaryon formation. In several fungal plant pathogens, isolates belonging to a VCG have been shown to share significantly higher genetic similarity than those of different VCGs. In this study we sought to examine the relationship between VCG and genetic similarity of an important cool season turfgrass pathogen, Sclerotinia homoeocarpa. Twenty-two S. homoeocarpa isolates from the Midwest and Eastern US, which were previously characterized in several studies, were all evaluated for VCG using an improved nit mutant assay. These isolates were also genotyped using 19 microsatellites developed from partial genome sequence of S. homoeocarpa. Additionally, partial sequences of mitochondrial genes cytochrome oxidase II and mitochondrial small subunit (mtSSU) rRNA, and the atp6-rns intergenic spacer, were generated for isolates from each nit mutant VCG to determine if mitochondrial haplotypes differed among VCGs. Of the 22 isolates screened, 15 were amenable to the nit mutant VCG assay and were grouped into six VCGs. The 19 microsatellites gave 57 alleles for this set. Unweighted pair group methods with arithmetic mean (UPGMA) tree of binary microsatellite data were used to produce a dendrogram of the isolate genotypes based on microsatellite alleles, which showed high genetic similarity of nit mutant VCGs. Analysis of molecular variance of microsatellite data demonstrates that the current nit mutant VCGs explain the microsatellite genotypic variation among isolates better than the previous nit mutant VCGs or the conventionally determined VCGs. Mitochondrial sequences were identical among all isolates, suggesting that this marker type may not be informative for US populations of S. homoeocarpa.

Development of a Quantitative Polymerase Chain Reaction Detection Protocol for Cercospora kikuchii in Soybean Leaves and Its Use for Documenting Latent Infection as Affected by Fungicide Applications

Cercospora leaf blight (CLB) of soybean, caused by Cercospora kikuchii, is a serious disease in the southern United States. A sensitive TaqMan probe-based real-time quantitative polymerase chain reaction (qPCR) assay was developed to specifically detect and quantify C. kikuchii in naturally infected soybean plants. The sensitivity was 1 pg of genomic DNA, which was equivalent to about 34 copies of genome of C. kikuchii. Using this qPCR assay, we documented a very long latent infection period for C. kikuchii in soybean leaves beginning at the V3 growth stage (as early as 22 days after planting). The levels of biomass of C. kikuchii remained low until R1, and a rapid increase was detected from the R2/R3 to R4/R5 growth stages shortly before the appearance of symptoms at R6. The efficacy of various fungicide regimens under field conditions also was evaluated over a 3-year period using this qPCR method. Our results showed that multiple fungicide applications beginning at R1 until late reproductive stages suppressed the development of C. kikuchii in leaves and delayed symptom expression. Different fungicide chemistries also had differential effects on the amount of latent infection and symptom expression during late reproductive growth stages.

Mating-type distribution and genetic diversity of Cercospora sojina populations on soybean from Arkansas: evidence for potential sexual reproduction

Cercospora sojina causes frogeye leaf spot of soybean, which can cause serious economic losses in the United States. In this study, 132 C. sojina isolates were collected from six fields (from two counties, Cross and Crawford) in Arkansas. To determine mating type, a multiplex polymerase chain reaction assay was developed with primers specific for C. sojina. Of the 132 isolates, 68 isolates had the MAT1-1-1 idiomorph and 64 isolates had the MAT1-2 idiomorph; no isolates possessed both idiomorphs. Both mating types were present in a variety of spatial scales, including separate lesions on individual leaves. Clone-corrected data from eight microsatellites indicated that mating-type loci were present in approximately equal proportions in all populations analyzed, which suggests that Arkansas populations of C. sojina are undergoing cryptic sexual reproduction. All six populations evaluated had high genotypic diversity of 26 to 79%. In addition, among strains isolated from a single leaf, multiple and distinct haplotypes were associated with both mating types, supporting the hypothesis that sexual reproduction occurs within the populations. Most populations showed significant gametic disequilibrium but levels of disequilibrium were relatively low, particularly in populations from Crawford County. A low differentiation index (GST) was observed for all simple-sequence repeat markers across all populations. Furthermore, the value of G statistics between populations suggests that significant genetic exchange exists among the populations. Taken together, these results demonstrate that C. sojina populations from Arkansas are genetically diverse and most likely undergoing sexual reproduction.

Genetic isolation among sympatric vegetative compatibility groups of the aflatoxin-producing fungus Aspergillus flavus

Aspergillus flavus, a fungal pathogen of animals and both wild and economically important plants, is most recognized for producing aflatoxin, a cancer-causing secondary metabolite that contaminates food and animal feed globally. Aspergillus flavus has two self/nonself recognition systems, a sexual compatibility system and a vegetative incompatibility system, and both play a role in directing gene flow in populations. Aspergillus flavus reproduces clonally in wild and agricultural settings, but whether a cryptic sexual stage exists in nature is currently unknown. We investigated the distribution of genetic variation in 243 samples collected over 4 years from three common vegetative compatibility groups (VCGs) in Arizona and Texas from cotton using 24 microsatellite loci and the mating type locus (MAT) to assess population structure and potential gene flow among A. flavus VCGs in sympatric populations. All isolates within a VCG had the same mating type with OD02 having MAT1-2 and both CG136 and MR17 having MAT1-1. Our results support the hypothesis that these three A. flavus VCGs are genetically isolated. We found high levels of genetic differentiation and no evidence of gene flow between VCGs, including VCGs of opposite mating-type. Our results suggest that these VCGs diverged before domestication of agricultural hosts (>10,000 yr bp).

Assessment of Lineages of Cercospora kikuchii in Louisiana for Aggressiveness and Screening Soybean Cultivars for Resistance to Cercospora Leaf Blight

Cercospora leaf blight (CLB) became much more prevalent in Louisiana beginning in 1999. A previous study showed that the Louisiana population of Cercospora kikuchii, the causal agent, was dominated by a new lineage that differed from those collected in other locations at earlier times. In this study, we tested whether the dominance of the new lineage was caused by higher aggressiveness and screened soybean cultivars for resistance to CLB. Representative isolates from both lineages were used individually to inoculate six soybean cultivars in the greenhouse. Contrary to expectations, the new lineage was less aggressive. Three virulence groups were defined in this pathogen based on correlation of the aggressiveness of individual isolates on soybean cultivars. Other possible causes that led to the dominance of the new lineage in Louisiana are discussed. Eleven soybean cultivars were tested for disease reaction at two locations over 3 years in the field. Two cultivars, AG5701 (Asgrow) and TV59R85 (Terral), were among the more resistant cultivars to CLB both in the greenhouse and in the field.