Downy mildew, caused by the obligate pathogen Peronospora effusa, can have a devastating economic impact on spinach production. Growing resistant cultivars is the most economical way to manage this disease and the only viable management practice for organic spinach production. However, rapidly emerging races or novel strains may result in a breakdown of the resistance deployed. It is therefore critical to monitor the population dynamics of P. effusa and to determine the disease reactions of newly released cultivars to the new races and novel strains. In this study, 74 isolates of P. effusa were examined for their pathogenicity on differential host cultivars, resulting in the identification of three new races and 18 novel strains with unique virulence pathotypes. Of those identified, race 19 of P. effusa could infect many widely grown cultivars with resistance to P. effusa races 1 to 17. Targeted sequencing of DNA isolated from lesions of P. effusa race 19 isolates revealed genetic variations among isolates and within isolates of P. effusa race 19. The isolates showed either no genetic variation (only one genotype was found from multiple lesions of an isolate tested), limited, or abundant genetic variation (multiple genotypes were found within an isolate tested). Additionally, 70 commercial spinach cultivars were tested with two P. effusa races, 18 and 19, and four novel strains. The results of this study are helpful for growers in selecting suitable cultivars for production and for breeders in developing downy mildew-resistant cultivars.

California is the leading producer of lettuce and spinach in the United States. Production of these crops is beset by a continual challenge from downy mildews caused by the obligate oomycete pathogens Bremia lactucae and Peronospora effusa, respectively. Managing these diseases requires repeated fungicide applications that are costly and increase the risk of fungicide resistance developing in the pathogen populations. Increased understanding of the dispersal patterns of sporangia in California is necessary to support more judicious application of fungicides. In this study, qPCR was used to estimate the numbers of airborne sporangia of P. effusa and B. lactucae from three valleys in California, one on the central coast and two in the southern desert, from September through March of 2021/2022 and 2022/2023. The analyses of these data uncovered a relationship between estimated airborne sporangia concentration and maximum and minimum temperatures. In consecutive seasons, airborne sporangia of both pathogens were not detected during 3- to 4-week periods of high temperatures in the Imperial Valley early in the growing season, suggesting that the primary inoculum was not from distant airborne sporangia that were introduced into the system. This work provides insight on lettuce and spinach downy mildew sporangia numbers in different California agricultural production valleys that may be useful to improve downy mildew management and the strategic timing of fungicide applications.The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2026.

Fusarium wilt of spinach, caused by Fusarium oxysporum f. sp. spinaciae (Fos), leads to substantial losses in spinach (Spinacia oleracea) seed production in the only region of the USA suitable for growing spinach seed crops, the maritime Pacific Northwest. Accessions of wild spinach, S. turkestanica, serve as a major source of resistance to multiple spinach diseases. In this study, 84 Spinacia genotypes (all 68 S. turkestanica accessions available publicly and 16 S. oleracea) were evaluated for reactions to Fos at medium and high densities of inoculum comprising a mix of isolates of races 1 and 2, using a factorial experimental design of genotypes (n = 84) and Fos inoculum density (0, 12,500, and 37,500 CFU/ml potting medium) with two replicates. The area under the disease progress curve (AUDPC) calculated for wilt severity 28, 35, and 42 days after planting (DAP) ranged from 0.0 to 11.0 and 1.5 to 13.3 at medium and high inoculum densities, respectively. Of the 68 S. turkestanica accessions, 17 and 8 showed high levels of resistance at medium and high inoculum densities, respectively. Single nucleotide polymorphism (SNP) markers (n = 7,065) identified with genotyping-by-sequencing (GBS) were used for genome wide association studies (GWAS) using multiple models tested with GAPIT and TASSEL software. Twelve SNPs were associated significantly with Fusarium wilt resistance in 10 QTL regions located on chromosomes 1, 3, 4, and 6. SNP S6_38110665 on chromosome 6 was validated across multiple GWAS models and demonstrated a major effect (-2.48 to -2.79) at reducing Fusarium wilt severity. SNP S6_38110665 can be used to introduce Fusarium wilt resistance QTL into cultivated spinach (S. oleracea) using marker-assisted selection, thereby enhancing breeding programs for improved disease resistance.

Numerous hybrid spinach cultivars are released annually by commercial seed companies. These novel cultivars typically include a combination of known or new resistance genes to the pathogen of downy mildew disease, Peronospora effusa. Annual sentinel plots provide an insight into how the cultivars perform under field conditions with naturally occurring endemic inoculum of P. effusa. A field evaluation of resistance to the downy mildew pathogen of spinach was conducted in Yuma, AZ, in 2023. Disease development was due to naturally occurring inoculum. The disease incidence (DI) was recorded 57 days after the wet date for 70 cultivars. The DI varied considerably among the cultivars tested, and the range was 0.0 to 98.3% infected leaves.

A field evaluation of resistance to the downy mildew pathogen of spinach ( Peronospora effusa) was conducted in San Juan Bautista, CA, in 2023. Disease development was due to naturally occurring inoculum. The disease incidence was recorded 46 days after the wet-date for 70 cultivars. The disease incidence varied considerably among the cultivars tested, and the range was 0.0 to 100.0% infected leaves.

Annual sentinel field trials expose spinach cultivars to naturally occurring endemic inoculum, providing insight into the performance of new and existing commercial varieties under field conditions. The evaluated hybrid cultivars incorporate a broad combination of resistance genes from both the male and female parent. A field evaluation for resistance to the downy mildew pathogen of spinach (Peronospora effusa) was conducted in Yuma, AZ, in 2024. Disease development was due to naturally occurring inoculum. The disease incidence was recorded 41 days after the wet date for 70 cultivars. The disease incidence varied considerably among the cultivars tested, and the range was 0.0 to 96.7% infected leaves.

Downy mildews are major constraints on spinach and lettuce production globally. Disease management can be achieved with fungicides, but routine applications are costly and can lead to pathogen resistance. Detection of airborne spores could guide sustainable fungicide application, and, considering that spinach and lettuce are often grown in the same cycles, simultaneous detection of both pathogens is practical. Here, a multiplex hydrolysis probe quantitative PCR assay was designed using single copy mitochondrial DNA targets for spinach downy mildew ( Peronospora effusa) and lettuce downy mildew ( Bremia lactucae). To quantify P. effusa and B. lactucae sporangia, a standard curve was developed for each pathogen using the multiplex qPCR to amplify DNA obtained from known dilutions of sporangia. Analysis of these curves revealed a greater sensitivity for B. lactucae, indicating that the sporangia of B. lactucae may harbor more mitochondria than those of P. effusa, providing insight into the biology of these pathogens. The multiplex qPCR assay was partnered with two different spore trap types: a cyclone spore trap and an impaction spore trap. Results from air sampling revealed that the cyclone spore traps collect significantly more sporangia compared with impaction traps. Exposure of P. effusa sporangia to desiccation was performed to assess the environmental impact on the assay, and although detection levels were reduced, they were still apparent. This detection and quantification tool will be useful in efforts to improve the accuracy of downy mildew forecasting, which in return may reduce fungicide usage or improve its efficiency. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.

Abstract Background Spinach downy mildew, caused by the obligate oomycete pathogen, Peronospora effusa remains a major concern for spinach production. Disease control is predominantly based on development of resistant spinach cultivars. However, new races and novel isolates of the pathogen continue to emerge and overcome cultivar resistance. Currently there are 20 known races of P. effusa. Here we characterized the transcriptomes of spinach, Spinacia oleracea, and P. effusa during disease progression using the spinach cultivar Viroflay, the near isogenic lines NIL1 and NIL3, and P. effusa races, R13 and R19, at 24 h post inoculation and 6 days post inoculation. A total of 54 samples were collected and subjected to sequencing and transcriptomic analysis. Results Differentially expressed gene (DEG) analysis in resistant spinach interactions of R13-NIL1 and R19-NIL3 revealed spinach DEGs from protein kinase-like and P-loop containing families, which have roles in plant defense. The homologous plant defense genes included but were not limited to, receptor-like protein kinases (Spiol0281C06495, Spiol06Chr21559 and Spiol06Chr24027), a BAK1 homolog (Spiol0223C05961), genes with leucine rich repeat motifs (Spiol04Chr08771, Spiol04Chr01972, Spiol05Chr26812, Spiol04Chr11049, Spiol0084S08137, Spiol03Chr20299) and ABC-transporters (Spiol02Chr28975, Spiol06Chr22112, Spiol06Chr03998 and Spiol04Chr09723). Additionally, analysis of the expression of eight homologous to previously reported downy mildew resistance genes revealed that some are differentially expressed during resistant reactions but not during susceptible reactions. Examination of P. effusa gene expression during infection of susceptible cultivars identified expressed genes present in R19 or R13 including predicted RxLR and Crinkler effector genes that may be responsible for race-specific virulence on NIL1 or NIL3 spinach hosts, respectively. Conclusions These findings deliver foundational insight to gene expression in both spinach and P. effusa during susceptible and resistant interactions and provide a library of candidate genes for further exploration and functional analysis. Such resources will be beneficial to spinach breeding efforts for disease resistance in addition to better understanding the virulence mechanisms of this obligate pathogen.

Spinach downy mildew, caused by the obligate oomycete pathogen Peronospora effusa, is a worldwide constraint on spinach production. The role of airborne sporangia in the disease cycle of P. effusa is well established, but the role of the sexual oospores in the epidemiology of P. effusa is less clear and has been a major challenge to examine experimentally. To evaluate seed transmission of spinach downy mildew via oospores in this study, isolated glass chambers were employed in two independent experiments to grow out oospore-infested spinach seed and noninfested seeds mixed with oospore-infested crop debris. Downy mildew diseased spinach plants were observed 37 and 34 days after planting in the two isolator experiments, respectively, in the chambers that contained one of two oospore-infested seed lots or seeds coated with oospore-infested leaves. Spinach plants in isolated glass chambers initiated from seeds without oospores did not show downy mildew symptoms. Similar findings were obtained using the same seed lot samples in a third experiment conducted in a growth chamber. In direct grow out tests to examine oospore infection on seedlings performed in a containment greenhouse with oospore-infested seed of two different cultivars, characteristic Peronospora sporangiophores were observed growing from a seedling of each cultivar. The frequency of seedlings developing symptoms from 82 of these oospore-infested seed indicated that approximately 2.4% of seedlings from infested seed developed symptoms, and 0.55% of seedlings from total seeds assayed developed symptoms. The results provide evidence that oospores can serve as a source of inoculum for downy mildew and provide further evidence of direct seed transmission of the downy mildew pathogen to seedlings in spinach via seedborne oospores.

Four isolates of Neofusicoccum parvum, collected from diseased hemp (Cannabis sativa) plants over a period of 2 years and shown to be pathogenic on C. sativa, were examined in this study. Their genome sizes ranged between 42.8 and 44.4 Mb, with 16,499 ± 72 predicted genes across the four isolates.

Commercial production of spinach (Spinacia oleracea L.) is centered in California and Arizona in the US, where downy mildew caused by Peronospora effusa is the most destructive disease. Nineteen typical races of P. effusa have been reported to infect spinach, with 16 identified after 1990. The regular appearance of new pathogen races breaks the resistance gene introgressed in spinach. We attempted to map and delineate the RPF2 locus at a finer resolution, identify linked single nucleotide polymorphism (SNP) markers, and report candidate downy mildew resistance (R) genes. Progeny populations segregating for RPF2 locus derived from resistant differential cultivar Lazio were infected using race 5 of P. effusa and were used to study for genetic transmission and mapping analysis in this study. Association analysis performed with low coverage whole genome resequencing-generated SNP markers mapped the RPF2 locus between 0.47 to 1.46 Mb of chromosome 3 with peak SNP (Chr3_1, 221, 009) showing a LOD value of 61.6 in the GLM model in TASSEL, which was within 1.08 Kb from Spo12821, a gene that encodes CC-NBS-LRR plant disease resistance protein. In addition, a combined analysis of progeny panels of Lazio and Whale segregating for RPF2 and RPF3 loci delineated the resistance section in chromosome 3 between 1.18-1.23 and 1.75-1.76 Mb. This study provides valuable information on the RPF2 resistance region in the spinach cultivar Lazio compared to RPF3 loci in the cultivar Whale. The RPF2 and RPF3 specific SNP markers, plus the resistant genes reported here, could add value to breeding efforts to develop downy mildew resistant cultivars in the future.

There is a recent unparalleled increase in demand for rice in sub-Saharan Africa, yet its production is affected by blast disease. Characterization of blast resistance in adapted African rice cultivars can provide important information to guide growers and rice breeders. We used molecular markers for known blast resistance genes (Pi genes; n = 21) to group African rice genotypes (n = 240) into similarity clusters. We then used greenhouse-based assays to challenge representative rice genotypes (n = 56) with African isolates (n = 8) of Magnaporthe oryzae which varied in virulence and genetic lineage. The markers grouped rice cultivars into five blast resistance clusters (BRC) which differed in foliar disease severity. Using stepwise regression, we found that the Pi genes associated with reduced blast severity were Pi50 and Pi65, whereas Pik-p, Piz-t, and Pik were associated with increased susceptibility. All rice genotypes in the most resistant cluster, BRC 4, possessed Pi50 and Pi65, the only genes that were significantly associated with reduced foliar blast severity. Cultivar IRAT109, which contains Piz-t, was resistant against seven African M. oryzae isolates, whereas ARICA 17 was susceptible to eight isolates. The popular Basmati 217 and Basmati 370 were among the most susceptible genotypes. These findings indicate that most tested genes were not effective against African blast pathogen collections. Pyramiding genes in the Pi2/9 multifamily blast resistance cluster on chromosome 6 and Pi65 on chromosome 11 could confer broad-spectrum resistance capabilities. To gain further insights into genomic regions associated with blast resistance, gene mapping could be conducted with resident blast pathogen collections. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

White rust, caused by Albugo occidentalis, is one of the major yield-limiting diseases of spinach (Spinacia oleracea) in some major commercial production areas, particularly in southern Texas in the United States. The use of host resistance is the most economical and environment-friendly approach to managing white rust in spinach production. The objectives of this study were to conduct a genome-wide associating study (GWAS), to identify single nucleotide polymorphism (SNP) markers associated with white rust resistance in spinach, and to perform genomic prediction (GP) to estimate the prediction accuracy (PA). A GWAS panel of 346 USDA (US Dept. of Agriculture) germplasm accessions was phenotyped for white rust resistance under field conditions and GWAS was performed using 13 235 whole-genome resequencing (WGR) generated SNPs. Nine SNPs, chr2_53 049 132, chr3_58 479 501, chr3_95 114 909, chr4_9 176 069, chr4_17 807 168, chr4_83 938 338, chr4_87 601 768, chr6_1 877 096, and chr6_31 287 118, located on chromosomes 2, 3, 4, and 6 were associated with white rust resistance in this GWAS panel. Four scenarios were tested for PA using Pearson's correlation coefficient (r) between the genomic estimation breeding value (GEBV) and the observed values: (1) different ratios between the training set and testing set (fold), (2) different GP models, (3) different SNP numbers in three different SNP sets, and (4) the use of GWAS-derived significant SNP markers. The results indicated that a 2- to 10-fold difference in the various GP models had similar, although not identical, averaged r values in each SNP set; using GWAS-derived significant SNP markers would increase PA with a high r-value up to 0.84. The SNP markers and the high PA can provide valuable information for breeders to improve spinach by marker-assisted selection (MAS) and genomic selection (GS).

Downy mildew, commercially the most important disease of spinach, is caused by the obligate oomycete Peronospora effusa. In the past two decades, new pathogen races have repeatedly overcome the resistance used in newly released cultivars, urging the need for more durable resistance. Commercial spinach cultivars are bred with major R genes to impart resistance to downy mildew pathogens and are effective against some pathogen races/isolates. This work aimed to evaluate the worldwide USDA spinach germplasm collections and commercial cultivars for resistance to downy mildew pathogen in the field condition under natural inoculum pressure and conduct genome wide association analysis (GWAS) to identify resistance-associated genomic regions (alleles). Another objective was to evaluate the prediction accuracy (PA) using several genomic prediction (GP) methods to assess the potential implementation of genomic selection (GS) to improve spinach breeding for resistance to downy mildew pathogen. More than four hundred diverse spinach genotypes comprising USDA germplasm accessions and commercial cultivars were evaluated for resistance to downy mildew pathogen between 2017-2019 in Salinas Valley, California and Yuma, Arizona. GWAS was performed using single nucleotide polymorphism (SNP) markers identified via whole genome resequencing (WGR) in GAPIT and TASSEL programs; detected 14, 12, 5, and 10 significantly associated SNP markers with the resistance from four tested environments, respectively; and the QTL alleles were detected at the previously reported region of chromosome 3 in three of the four experiments. In parallel, PA was assessed using six GP models and seven unique marker datasets for field resistance to downy mildew pathogen across four tested environments. The results suggest the suitability of GS to improve field resistance to downy mildew pathogen. The QTL, SNP markers, and PA estimates provide new information in spinach breeding to select resistant plants and breeding lines through marker-assisted selection (MAS) and GS, eventually helping to accumulate beneficial alleles for durable disease resistance.