Insights into the Diaporthe/Phomopsis complex infecting soybeans in the United States

Diaporthe/Phomopsis species are pathogens on a wide range of hosts including soybeans (Glycine max L.), and responsible for several diseases, some of which are of economic importance. Under favorable environmental conditions, these diseases can result in in significant yield losses (Backman et al. 1985). For example, yield losses from Stem canker in the Midwest have ranged from minor to in excess of 50% (Hartman et al. 1999). Four Diaporthe species have been reported pathogenic on soybean – Diaporthe sojae, the causal agent of pod and stem blight; Diaporthe caulivora and Diaporthe aspalathi, causal agents of Northern and Southern stem cankers, respectively; and Diaporthe longicolla, causing seed decay (Hartman et al. 1999)

Phomopsis Stem Canker of Sunflower in North America: Correlation with Climate and Solutions Through Breeding and Management

Climate change is occurring in the central US and is interacting with agroecological factors to increase biotic stress in sunflower. Certain species of Diaporthe cause Phomopsis stem canker in sunflower and other dicotyledonous weeds and crops. The increase in precipitation already observed in the states of North Dakota, South Dakota, and Minnesota have increased the chances of outbreaks of necrotrophic pathogens, like Diaporthe. We discuss how climate trends, combined with technological, management, and economic interactions, are correlated with increasing incidence of Phomopsis stem canker in these and adjacent areas in North America. Further, we discuss management options and the role of improved sunflower genetics in reducing Phomopsis stem canker outbreak risk

Transcriptome Profiling of Interaction Effects of Soybean Cyst Nematodes and Soybean Aphids on Soybean

Soybean aphid (Aphis glycines; SBA) and soybean cyst nematode (Heterodera glycines; SCN) are two major pests of soybean (Glycine max) in the United States of America. This study aims to characterize three-way interactions among soybean, SBA, and SCN using both demographic and genetic datasets. SCN-resistant and SCN-susceptible soybean cultivars with a combination of soybean aphids (biotype 1) and SCN (HG type 0) in a randomized complete block design (RCBD) with six blocks were used to evaluate the three-way interactions in a greenhouse setup. Treatments receiving SCN were infested at planting with 2000 nematode eggs, and the treatments with soybean aphids were infested at second trifoliate growth stage (V2) with 15 soybean aphids. The whole roots were sampled from plants at 5 and 30 days post SBA infestation for RNA sequencing using Illumina Hiseq. 3000. The data comprises of 47 libraries that are useful for further analyses of important genes, which are involved in interaction effects of SBA and SCN on soybean

Phomopsis stem canker of sunflower in North America: correlation with climate and solutions through breeding and management☆ ☆☆

Climate change is occurring in the central US and is interacting with agroecological factors to increase biotic stress in sunflower. Certain species of Diaporthe cause Phomopsis stem canker in sunflower and other dicotyledonous weeds and crops. The increase in precipitation already observed in the states of North Dakota, South Dakota, and Minnesota have increased the chances of outbreaks of necrotrophic pathogens, like Diaporthe. We discuss how climate trends, combined with technological, management, and economic interactions, are correlated with increasing incidence of Phomopsis stem canker in these and adjacent areas in North America. Further, we discuss management options and the role of improved sunflower genetics in reducing Phomopsis stem canker outbreak risk

Population genomic analysis reveals geographic structure and climatic diversification for Macrophomina phaseolina isolated from soybean and dry bean across the United States, Puerto Rico, and Colombia

Macrophomina phaseolina causes charcoal rot, which can significantly reduce yield and seed quality of soybean and dry bean resulting from primarily environmental stressors. Although charcoal rot has been recognized as a warm climate-driven disease of increasing concern under global climate change, knowledge regarding population genetics and climatic variables contributing to the genetic diversity of M. phaseolina is limited. This study conducted genome sequencing for 95 M. phaseolina isolates from soybean and dry bean across the continental United States, Puerto Rico, and Colombia. Inference on the population structure using 76,981 single nucleotide polymorphisms (SNPs) revealed that the isolates exhibited a discrete genetic clustering at the continental level and a continuous genetic differentiation regionally. A majority of isolates from the United States (96%) grouped in a clade with a predominantly clonal genetic structure, while 88% of Puerto Rican and Colombian isolates from dry bean were assigned to a separate clade with higher genetic diversity. A redundancy analysis (RDA) was used to estimate the contributions of climate and spatial structure to genomic variation (11,421 unlinked SNPs). Climate significantly contributed to genomic variation at a continental level with temperature seasonality explaining the most variation while precipitation of warmest quarter explaining the most when spatial structure was accounted for. The loci significantly associated with multivariate climate were found closely to the genes related to fungal stress responses, including transmembrane transport, glycoside hydrolase activity and a heat-shock protein, which may mediate climatic adaptation for M. phaseolina. On the contrary, limited genome-wide differentiation among populations by hosts was observed. These findings highlight the importance of population genetics and identify candidate genes of M. phaseolina that can be used to elucidate the molecular mechanisms that underly climatic adaptation to the changing climate

Optimization and Application of a Quantitative Polymerase Chain Reaction Assay to Detect Diaporthe Species in Soybean Plant Tissue

Diaporthe caulivora and D. longicolla are the causal agents of stem canker of soybean (Glycine max L.). Accurate identification of stem canker pathogens upon isolation from infected soybean plants is difficult and unreliable based on morphology. In this study, two TaqMan probe-based quantitative polymerase chain reaction (qPCR) assays were optimized for detection of D. caulivora and D. longicolla in soybean plants. The assays used previously reported D. caulivora-specific (DPC-3) and D. longicolla-specific (PL-3) probe/primer sets. The sensitivity limit of the two assays was determined to be over a range of 100 pg to 10 fg of pure D. caulivora and D. longicolla genomic DNA. The qPCR assays were validated with plant samples collected from commercial soybean fields. The PL-3 set detected D. longicolla in soybean plants collected from the fields (quantification cycle value \u3c35), which was confirmed by isolation on potato dextrose agar (PDA). D. caulivora was detected only in low levels (quantification cycle value \u3c40) by DPC-3 set in a few of the symptomatic field samples, although the pathogen was not isolated on PDA. The qPCR assays were also useful in quantitatively phenotyping soybean plants for resistance to D. caulivora and D. longicolla under greenhouse conditions

First report of an Orobanche ludoviciana Parasitizing Sunflowers

In September 2014, a commercial field in western Nebraska was found exhibiting sunflower plants being parasitized by another flowering plant. Its presence was detected in approximately 25% of the field. The parasite was identified as Orobanche ludoviciana, and represents the first known report of any species of Orobanche attacking sunflowers in the Western Hemisphere

Phomopsis stem canker of sunflower in North America: correlation with climate and solutions through breeding and management

Climate change is occurring in the central US and is interacting with agroecological factors to increase biotic stress in sunflower. Certain species of Diaporthe cause Phomopsis stem canker in sunflower and other dicotyledonous weeds and crops. The increase in precipitation already observed in the states of North Dakota, South Dakota, and Minnesota have increased the chances of outbreaks of necrotrophic pathogens, like Diaporthe. We discuss how climate trends, combined with technological, management, and economic interactions, are correlated with increasing incidence of Phomopsis stem canker in these and adjacent areas in North America. Further, we discuss management options and the role of improved sunflower genetics in reducing Phomopsis stem canker outbreak risk

First Report of Brown Stem Rot of Soybean (Glycine max) Caused by Phialophora gregata in South Dakota

During late September 2010, soybean (Glycine max L.) plants exhibiting interveinal leaf necrosis and internal stem browning were received from Brookings (44°17.915′ N, 096°55.393′ W), Aurora (43°41.540′ N, 098°34.195′ W), and Hand (44°29.407′ N, 099°00.464′ W) counties for diagnosis. Isolations were made from the margins of the stem lesions by plating small pieces (5 mm) on a semiselective medium (GBA, Mengistu et al. 1991) amended with 0.02% streptomycin sulfate, followed by single-spore culturing and incubation at 20°C in the dark for 7 days

Molecular Basis of Soybean Resistance to Soybean Aphids and Soybean Cyst Nematodes

Soybean aphid (SBA; Aphis glycines Matsumura) and soybean cyst nematode (SCN; Heterodera glycines Ichninohe) are major pests of the soybean (Glycine max [L.] Merr.). Substantial progress has been made in identifying the genetic basis of limiting these pests in both model and non-model plant systems. Classical linkage mapping and genome-wide association studies (GWAS) have identified major and minor quantitative trait loci (QTLs) in soybean. Studies on interactions of SBA and SCN effectors with host proteins have identified molecular cues in various signaling pathways, including those involved in plant disease resistance and phytohormone regulations. In this paper, we review the molecular basis of soybean resistance to SBA and SCN, and we provide a synthesis of recent studies of soybean QTLs/genes that could mitigate the effects of virulent SBA and SCN populations. We also review relevant studies of aphid–nematode interactions, particularly in the soybean–SBA–SCN system