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Charcoal rot of soybean [Glycine max (L.) Merr.], caused by the soilborne fungus Macrophomina phaseolina (Tassi) Goid., has ranked among the most important soybean diseases in the United States. Disease management is typically done in a multifaceted approach through crop rotation, tillage, irrigation, and seed treatments aimed at minimizing damage caused by the pathogen. Development of genetic resistance to charcoal rot appears to be the most efficient strategy to control the disease; however, there are no reports of genetic regions associated with resistance to the disease. The objective of this study was to identify quantitative trait loci (QTLs) governing resistance to charcoal rot in soybean using a biparental population of PI 567562A (resistant) × PI 567437 (susceptible). A total of 140 F2–derived lines were genotyped with 5403 single nucleotide polymorphism (SNP) markers covering 20 chromosomes, of which 2283 were polymorphic. Resistance to charcoal rot was evaluated in the F2:3 lines using the cut‐stem inoculation technique under greenhouse conditions. The QTL mapping analysis indicated one QTL on chromosome 15 explaining 29.4% of phenotypic variation, and two QTLs on chromosome 16 explaining 25.4 and 8.4% of phenotypic variation for resistance to M. phaseliona. To our knowledge, this is the first report of genomic regions harboring resistance to charcoal rot in soybean, and it may facilitate breeding and molecular engineering progress to combat charcoal rot disease in the future. [ABSTRACT FROM AUTHOR]

Blue light plays an important role in the growth and development of fungi. Environmental cues enable plant pathogenic fungi to synchronise essential metabolic pathways to that of their hosts to gain a competitive advantage. Phylogenetic analysis of the LOV domain present in blue light receptors across all three kingdoms suggests that these receptors in fungal lineages have undergone convergent evolution to use the same domain for control and regulation of similar cellular and metabolic processes. In this review, the genetic basis of blue light photoperception in fungi, and the functions it regulates, will be discussed. Furthermore, the evolution of the light sensing domain and its role in pathogenesis is hypothesised concluding with how knowledge of conserved LOV domains may be exploited for fungal disease control in crop plants. [ABSTRACT FROM AUTHOR]

Peronospora effusa is an obligate pathogen that causes downy mildew on spinach and is considered the most economically important disease of spinach. The objective of the current research was to assess genetic diversity of known historical races and isolates collected in 2014 from production fields in Yuma, Arizona and Salinas Valley, California. Candidate neutral single nucleotide polymorphisms (SNPs) were identified by comparing sequence data from reference isolates of known races of the pathogen collected in 2009 and 2010. Genotypes were assessed using targeted sequencing on genomic DNA extracted directly from infected plant tissue. Genotyping 26 historical and 167 contemporary samples at 46 SNP loci revealed 82 unique multi-locus genotypes. The unique genotypes clustered into five groups and the majority of isolates collected in 2014 were genetically closely related, regardless of source location. The historical samples, representing several races, showed greater genetic differentiation. Overall, the SNP data indicate much of the genotypic variation found within fields was produced during asexual development, whereas overall genetic diversity may be influenced by sexual recombination on broader geographical and temporal scales. [ABSTRACT FROM AUTHOR]

The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed "mesosynteny" is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors. [ABSTRACT FROM AUTHOR]

Charcoal rot, caused by Macrophomina phaseolina in soybean [ Glycine max (L).Merr.] is a disease of economic significance in the United States. Chemical and cultural control are not effective and host resistance could be a potential method to control the disease. In this study we report the use of bulked-segregant analysis (BSA) to map the genetic basis of resistance to charcoal rot in soybean PI 567562A, using a QTL-seq approach. Resistant and susceptible bulks from progenies of a biparental population (PI 567562A and PI 567437) were sequenced, and reads were aligned to the PI 567562A genome and used to calculate the SNP-index at each SNP position for the resistant and susceptible bulks. The average distributions of the SNP-index and Δ SNP-index across the genome were estimated for genomic intervals using a sliding window analysis with 2-Mb window size and a 10-kb step. Three genomic regions on chromosomes 5, 8 and 14 were identified with positive values in Δ SNP-index plots that potentially correspond to QTL governing the difference between the R-bulk and S-bulk sub-populations. The current study is the first attempt employing QTL-seq to identify genomic regions that may contain QTL controlling charcoal rot disease resistance in soybean. • Genetic basis of resistance to charcoal rot in soybean. • QTL-seq approach with next-generation sequencing (NGS). • Bulked-segregant analysis (BSA). [ABSTRACT FROM AUTHOR]