Draft Genome Sequences of 14 Fungal Species from Alternaria Section Infectoriae.

Isolates representing 14 Alternaria section Infectoriae species collected from diverse hosts and locations were shotgun sequenced. These genome assemblies and annotations will improve the study of taxonomy and biology in this group of ubiquitous fungi.

First Report of Downy Mildew caused by Pseudoperonospora cannabina on Cannabis sativa in New York.

Hemp (Cannabis sativa <0.3% tetrahydrocannabinol) is an emerging crop used for grain, fiber, and cannabinoid production (Fike et al. 2020). In New York, hemp is grown both in controlled environment facilities, including greenhouses, and as a field crop. In August 2020, downy mildew-like symptoms were observed on leaves and inflorescence of hemp plants in a field research trial in Ithaca, NY. Several cultivars, including 'Auto CBD', were affected. Disease was severe with some plants reaching 75% disease severity at the individual plant level. In the most severely affected plots, there was no marketable yield. The disease was characterized by chlorotic and necrotic lesions producing sporangiophores under high humidity. Pigmented sporangia were produced on branched sporangiophores. On artificially inoculated leaves incubated at 18°C, 80% humidity, 12h light for 5d, sporangiophores produced 8-19 pigmented, lemon-shaped sporangia with mean ± SD dimensions of 25.2 ± 3.0 (18.9 to 30.4) x 18.2 ± 2.1 (14.6 to 23.2) µm (n=50). Each sporangium produced 2-5 zoospores after less than 45 min in water at room temperature (22°C). Sporangia were collected from sporulating lesions and DNA was extracted as outlined in Crowell et al. (2020). Fragments of the ribosomal internal transcribed spacer (ITS) region (White et al. 1990), the beta-tubulin ras-associated ypt1 gene (Moorman et al. 2002), and the mitochondrial cytochrome B oxidase subunit 2 (cox2) gene (Hudspeth et al. 2000) were amplified by PCR and sequenced bidirectionally. Sequences were deposited in GenBank under accession numbers OK086084, OM867581, and OM867580, respectively. BLAST searches using the amplified ITS and cox2 sequences resulted in 100% identity to Pseudoperonospora cannabina (HM636051.1, HM636003.1) with ypt1 aligning at 97.95% identity (382/390 bp) with P. cannabina (KJ651402.1). The molecular characterization identified the causal agent as P. cannabina. A representative isolate was deposited in the Cornell Plant Pathology Herbarium as CUP-070922. Sporangia were rinsed from detached leaves and used to confirm pathogenicity on whole plants. Ten 4-week-old 'Anka' plants were spray-inoculated until run off with a suspension of 1x104 sporangia mL-1. Ten control plants were sprayed with water. After inoculation, plants were placed in a 19˚C growth chamber with a 12-h photoperiod and misted for 30 min twice daily to maintain humidity above 80%. Sporangia and previously described symptoms were observed 7 days post-inoculation, while control plants were asymptomatic. The pathogen was reisolated onto detached leaves of 'Anka' from inoculated leaves where both sporangia and oospores were observed. The reisolated pathogen was confirmed morphologically and molecularly, through PCR amplification and bidirectional sequencing of the ITS, cox2, and ypt1 genes, as P. cannabina. To our knowledge, this is the first report of P. cannabina causing hemp downy mildew in New York. Depending on the severity and timing of infections, this disease could pose a significant threat to hemp production in the state. Other members of the genus, P. cubensis and P. humuli cause downy mildew on cucurbits and hops, respectively. As these can cause devastating diseases on their hosts, P. cannabina must be monitored with vigilance as an emerging pathogen (Purayannur et al. 2021; Savory et al. 2011). Literature Cited: Crowell, C. R., et al.2020. Plant Dis. 104:2949. DOI 10.1094/PDIS-04-20-0718-RE Fike, J. H., et al. 2020. Page 89 In: Sustainable Agriculture Reviews, vol 42. Springer, Cham, Switzerland. DOI 10.1007/978-3-030-41384-2_3 Hudspeth, D. S. S., et al. 2000. Mycologia 92:674. DOI 10.2307/3761425 Moorman, G. W., et al. 2002. Plant Dis. 86:1227. DOI 10.1094/PDIS.2002.86.11.1227 Purayannur, S., et al. 2021. Mol. Plant Pathol. 22:755. DOI 10.1111/mpp.13063 Savory, E. A., et al. 2011. Mol. Plant Pathol. 12:217. DOI 10.1111/j.1364-3703.2010.00670.x White, T. J., et al. 1990. Page 315 In: PCR Protocols. A Guide to Methods and Applications. Academic Press, San Diego, CA. DOI 10.1016/B978-0-12-372180-8.50042-1.

Genome-Wide Associations with Resistance to Bipolaris Leaf Spot (Bipolaris oryzae (Breda de Haan) Shoemaker) in a Northern Switchgrass Population (Panicum virgatum L.).

Switchgrass (Panicum virgatum L.), a northern native perennial grass, suffers from yield reduction from Bipolaris leaf spot caused by Bipolaris oryzae (Breda de Haan) Shoemaker. This study aimed to determine the resistant populations via multiple phenotyping approaches and identify potential resistance genes from genome-wide association studies (GWAS) in the switchgrass northern association panel. The disease resistance was evaluated from both natural (field evaluations in Ithaca, New York and Phillipsburg, Philadelphia) and artificial inoculations (detached leaf and leaf disk assays). The most resistant populations based on a combination of three phenotyping approaches-detached leaf, leaf disk, and mean from two locations-were 'SW788', 'SW806', 'SW802', 'SW793', 'SW781', 'SW797', 'SW798', 'SW803', 'SW795', 'SW805'. The GWAS from the association panel showed 27 significant SNPs on 12 chromosomes: 1K, 2K, 2N, 3K, 3N, 4N, 5K, 5N, 6N, 7K, 7N, and 9N. These markers accumulatively explained the phenotypic variance of the resistance ranging from 3.28 to 26.52%. Within linkage disequilibrium of 20 kb, these SNP markers linked with the potential resistance genes included the genes encoding for NBS-LRR, PPR, cell-wall related proteins, homeostatic proteins, anti-apoptotic proteins, and ABC transporter.

Phyllachora species infecting maize and other grass species in the Americas represents a complex of closely related species.

The genus Phyllachora contains numerous obligate fungal parasites that produce raised, melanized structures called stromata on their plant hosts referred to as tar spot. Members of this genus are known to infect many grass species but generally do not cause significant damage or defoliation, with the exception of P. maydis which has emerged as an important pathogen of maize throughout the Americas, but the origin of this pathogen remains unknown. To date, species designations for Phyllachora have been based on host associations and morphology, and most species are assumed to be host specific. We assessed the sequence diversity of 186 single stroma isolates collected from 16 hosts representing 15 countries. Samples included both herbarium and contemporary strains that covered a temporal range from 1905 to 2019. These 186 isolates were grouped into five distinct species with strong bootstrap support. We found three closely related, but genetically distinct groups of Phyllachora are capable of infecting maize in the United States, we refer to these as the P. maydis species complex. Based on herbarium specimens, we hypothesize that these three groups in the P. maydis species complex originated from Central America, Mexico, and the Caribbean. Although two of these groups were only found on maize, the third and largest group contained contemporary strains found on maize and other grass hosts, as well as herbarium specimens from maize and other grasses that include 10 species of Phyllachora. The herbarium specimens were previously identified based on morphology and host association. This work represents the first attempt at molecular characterization of Phyllachora species infecting grass hosts and indicates some Phyllachora species can infect a broad range of host species and there may be significant synonymy in the Phyllachora genus.

Fusarium graminearum Species Complex: A Bibliographic Analysis and Web-Accessible Database for Global Mapping of Species and Trichothecene Toxin Chemotypes.

Fusarium graminearum is ranked among the five most destructive fungal pathogens that affect agroecosystems. It causes floral diseases in small grain cereals including wheat, barley, and oats, as well as maize and rice. We conducted a systematic review of peer-reviewed studies reporting species within the F. graminearum species complex (FGSC) and created two main data tables. The first contained summarized data from the articles including bibliographic, geographic, methodological (ID methods), host of origin and species, while the second data table contains information about the described strains such as publication, isolate code(s), host/substrate, year of isolation, geographical coordinates, species and trichothecene genotype. Analyses of the bibliographic data obtained from 123 publications from 2000 to 2021 by 498 unique authors and published in 40 journals are summarized. We describe the frequency of species and chemotypes for 16,274 strains for which geographical information was available, either provided as raw data or extracted from the publications, and sampled across six continents and 32 countries. The database and interactive interface are publicly available, allowing for searches, summarization, and mapping of strains according to several criteria including article, country, host, species and trichothecene genotype. The database will be updated as new articles are published and should be useful for guiding future surveys and exploring factors associated with species distribution such as climate and land use. Authors are encouraged to submit data at the strain level to the database, which is accessible at https://fgsc.netlify.app.

Genome-wide association mapping of seedling and adult plant response to stem rust in a durum wheat panel.

Many of the major stem rust resistance genes deployed in commercial wheat (Triticum spp.) cultivars and breeding lines become ineffective over time because of the continuous emergence of virulent races. A genome-wide association study (GWAS) was conducted using 26,439 single nucleotide polymorphism (SNP) markers and 280 durum wheat [Triticum turgidum L. subsp. Durum (Desf.) Husnot] lines from CIMMYT to identify genomic regions associated with seedling resistance to races TTKSK, TKTTF, JRCQC, and TTRTF and field resistance to TKTTF and JRCQC. The phenotypic data analysis across environments revealed 61-91 and 59-77% of phenotypic variation was explained by the genotypic component for seedling and adult plant response of lines, respectively. For seedling resistance, mixed linear model (MLM) identified eight novel and nine previously reported quantitative trait loci (QTL) while a fixed and random model circulating probability unification (FarmCPU) detected 12 novel and eight previously reported QTL. For field resistance, MLM identified 12 novel and seven previously reported loci while FarmCPU identified seven novel and nine previously reported loci. The regions of Sr7a, Sr8155B1, Sr11, alleles of Sr13, Sr17, Sr22/Sr25, and Sr49 were identified. Novel loci on chromosomes 3B, 4A, 6A, 6B, 7A, and 7B could be used as sources of resistance to the races virulent on durum wheat. Two large-effect markers on chromosome 6A could potentially be used to differentiate resistant haplotypes of Sr13 (R1 and R3). Allelism tests for Sr13, breaking the deleterious effect associated with Sr22/Sr25 and retaining the resistance allele at the Sr49 locus, are needed to protect future varieties from emerging races.

Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex.

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.

The Incidence of Fusarium graminearum in Wild Grasses is Associated With Rainfall and Cumulative Host Density in New York.

The movement of plant pathogens between cultivated and natural host communities can result in lost agricultural production and altered microbial or plant biodiversity. Fusarium graminearum incidence was studied in wild grass hosts for 3 years to better understand the ecology of this plant pathogen at the interface of crop fields and nonagricultural environments. Research sites (n = 23) were spread between regions of high and low agricultural production and included both agricultural and nonagricultural fields. Pathogen incidence in living grass spikes and senesced, overwintered stems varied between regions of New York and was lowest in a region with sparser agricultural production (P = 0.001). However, pathogen incidence within regions was similar at both agricultural and nonagricultural sites. The groundcover of crop and wild hosts within 1 km of sample sites were equally effective predictors of pathogen incidence, indicating either host group may drive pathogen spread. Rainfall in the 8 weeks preceding sample collection was strongly correlated with F. graminearum incidence in grasses, as well as an increased prevalence of F. graminearum in Fusarium spp. communities (P = 0.001). Grass species diversity was not associated with a reduction in pathogen incidence, and F. graminearum incidence did not vary among the most well-sampled grasses. These results indicate the pathogen colonizes and spreads in noncultivated grasses in a manner consistent with existing concepts of pathogen epidemiology in cereal crops. Increasing host acreage, whether cultivated or not, could drive the colonization of grasses in remote or protected environments, potentially altering their microbial communities.

Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum).

Local adaptation is an important process in plant evolution, which can be impacted by differential pathogen pressures along environmental gradients. However, the degree to which pathogen resistance loci vary in effect across space and time is incompletely described. To understand how the genetic architecture of resistance varies across time and geographic space, we quantified rust (Puccinia spp.) severity in switchgrass (Panicum virgatum) plantings at eight locations across the central USA for 3 yr and conducted quantitative trait locus (QTL) mapping for rust progression. We mapped several variable QTLs, but two large-effect QTLs which we have named Prr1 and Prr2 were consistently associated with rust severity in multiple sites and years, particularly in northern sites. By contrast, there were numerous small-effect QTLs at southern sites, indicating a genotype-by-environment interaction in rust resistance loci. Interestingly, Prr1 and Prr2 had a strong epistatic interaction, which also varied in the strength and direction of effect across space. Our results suggest that abiotic factors covarying with latitude interact with the genetic loci underlying plant resistance to control rust infection severity. Furthermore, our results indicate that segregating genetic variation in epistatically interacting loci may play a key role in determining response to infection across geographic space.

Managing a Destructive, Episodic Crop Disease: A National Survey of Wheat and Barley Growers' Experience With Fusarium Head Blight.

The main techniques for minimizing Fusarium head blight (FHB, or scab) and deoxynivalenol in wheat and barley are well established and generally available: planting of moderately FHB-resistant cultivars, risk monitoring, and timely use of the most effective fungicides. Yet the adoption of these techniques remains uneven across the FHB-prone portions of the U.S. cereal production area. A national survey was undertaken by the U.S. Wheat and Barley Scab Initiative in 17 states where six market classes of wheat and barley are grown. In 2014, 5,107 usable responses were obtained. The highest percentages reporting losses attributable to FHB in the previous 5 years were in North Dakota, Maryland, Kentucky, and states bordering the Great Lakes but across all states, ≥75% of respondents reported no FHB-related losses in the previous 5 years. Adoption of cultivar resistance was uneven by state and market class and was low except among hard red spring wheat growers. In 13 states, a majority of respondents had not applied an FHB-targeted fungicide in the previous 5 years. Although the primary FHB information source varied by state, crop consultants were considered to be an important source or their primary source of information on risk or management of FHB by the largest percentage of respondents. Use of an FHB risk forecasting website was about twice as high in North Dakota as the 17-state average of 6%. The most frequently cited barriers to adopting FHB management practices were weather or logistics preventing timely fungicide application, difficulty in determining flowering timing for fungicide applications, and the impracticality of FHB-reducing rotations. The results highlight the challenges of managing an episodically damaging crop disease and point to specific areas for improvement.

Population Genetics of Fusarium graminearum at the Interface of Wheat and Wild Grass Communities in New York.

Fusarium graminearum is primarily understood as an agricultural pathogen affecting cereal crops, but its host range also includes diverse, noncultivated grasses ubiquitous across agricultural and natural environments. Wild grasses may select for the production of diverse toxin variants (chemotypes) and serve as reservoirs of genetic diversity or sources of disease-inciting inoculum. Populations at the intersection of wheat and wild grass communities were described using 909 isolates collected from wheat spikes, wild grass spikes, and overwintered wild grass stems found at natural and agricultural sites in regions of high and low crop production. Trichothecene (TRI) genotypes correlated to pathogen chemotype were predicted from two loci, and multilocus genotypes (MLGs) were determined using eight microsatellite loci. The genetic diversity of wild grass and wheat-derived populations was comparable, and their differentiation was low. Duplicate MLGs were rare even in samples collected from a single square meter, although they could be found in multiple hosts, environments, regions, and years. TRI genotype frequencies differed between region and land use. Admixture between TRI genotype-defined populations, which correspond to three previously described sympatric North American populations, was detected and was highest in a region with remote host communities and little agricultural production. Nonagricultural environments may maintain different pathogen TRI genotypes than wheat fields and provide an opportunity for recombination between isolates from different F. graminearum populations. A lack of structural barriers suggests that pathogen gene flow is uninhibited between wheat and wild grass communities, and the recovery of putative clones from multiple hosts and environments provides initial evidence that noncultivated grasses are a source of local and regional inoculum.

Effects of Pre- and Postanthesis Applications of Demethylation Inhibitor Fungicides on Fusarium Head Blight and Deoxynivalenol in Spring and Winter Wheat.

Anthesis is generally recommended as the optimum growth stage for applying a foliar fungicide to manage Fusarium head blight (FHB) and the Fusarium-associated toxin deoxynivalenol (DON) in wheat. However, because it is not always possible to treat fields at anthesis, studies were conducted to evaluate pre- and postanthesis treatment options for managing FHB and DON in spring and winter wheat. Network meta-analytical models were fitted to data from 19 years of fungicide trials, and log response ratio ([Formula: see text]) and approximate percent control ([Formula: see text]) relative to a nontreated check were estimated as measures of the effects of six treatments on FHB index (IND: mean percentage of diseased spikelets per spike) and DON. The evaluated treatments consisted of either Caramba (metconazole) applied early (at heading [CE]), at anthesis (CA), or late (5 to 7 days after anthesis; CL), or Prosaro (prothioconazole + tebuconazole) applied at the same three times and referred to as PE, PA, and PL, respectively. All treatments reduced mean IND and DON relative to the nontreated check, but the magnitude of the effect varied with timing and wheat type. CA and PA resulted in the highest [Formula: see text] values for IND, 52.2 and 51.5%, respectively, compared with 45.9% for CL, 41.3% for PL, and less than 33% for CE and PE. Anthesis and postanthesis treatments reduced mean IND by 14.9 to 29.7% relative to preanthesis treatments. The estimated effect size was also statistically significant for comparisons between CA and CL and PA and PL; CA reduced IND by 11.7% relative to CL, whereas PA reduced the disease by 17.4% relative to PL. Differences in efficacy against IND between pairs of prothioconazole + tebuconazole and metconazole treatments applied at the same timing (CE versus PE, CA versus PA, and CL versus PL) were not statistically significant. However, CA and CL outperformed PA and PL by 7 and 12.8%, respectively, in terms of efficacy against DON. All application programs had comparable efficacy against IND between spring and winter wheat types, but efficacy against DON was 10 to 16% greater for spring than winter wheat for applications made at or after anthesis. All programs led to an increase in mean grain yield and test weight relative to the nontreated check.

Malting of Fusarium Head Blight-Infected Rye (Secale cereale): Growth of Fusarium graminearum, Trichothecene Production, and the Impact on Malt Quality.

This project was initiated with the goal of investigating the malt quality of winter rye cultivars and hybrids grown in the United States in 2014 and 2015, but high levels of deoxynivalenol (DON) were subsequently found in many of the malt samples. DON levels in 75% of the investigated rye samples (n = 117) were actually below 1.0 mg/kg, as quantified by a gas chromatography combined with electron capture detector (GC-ECD). However, 83% of the samples had DON in excess of 1.0 mg/kg following malting, and the average DON level in malted rye was 10.6 mg/kg. In addition, relatively high levels of 3-acetate DON (3-ADON), 15-acetate DON (15-ADON), nivalenol (NIV), and DON-3-glucoside (D3G) were observed in some rye malts. Our results show that rye grain DON is likely a poor predicator of type B trichothecenes in malt in practice, because high levels of malt DON, 15-ADONm and D3G were produced, even when the rye samples with DON levels below 0.50 mg/kg were processed. Fusarium Tri5 DNA content in rye was highly associated with malt DON levels (r = 0.83) in a small subset of samples (n = 55). The impact of Fusarium infection on malt quality was demonstrated by the significant correlations between malt DON levels and wort viscosity, ß-glucan content, wort color, wort p-coumaric acid content, and total phenolic content. Additional correlations of rye Fusarium Tri5 DNA contents with malt diastatic power (DP), wort free amino nitrogen (FAN) content, and arabinoxylan content were observed.

Genome-wide association mapping for resistance to leaf rust, stripe rust and tan spot in wheat reveals potential candidate genes.

KEY MESSAGE: Genome-wide association mapping in conjunction with population sequencing map and Ensembl plants was used to identify markers/candidate genes linked to leaf rust, stripe rust and tan spot resistance in wheat. Leaf rust (LR), stripe rust (YR) and tan spot (TS) are some of the important foliar diseases in wheat (Triticum aestivum L.). To identify candidate resistance genes for these diseases in CIMMYT's (International Maize and Wheat Improvement Center) International bread wheat screening nurseries, we used genome-wide association studies (GWAS) in conjunction with information from the population sequencing map and Ensembl plants. Wheat entries were genotyped using genotyping-by-sequencing and phenotyped in replicated trials. Using a mixed linear model, we observed that seedling resistance to LR was associated with 12 markers on chromosomes 1DS, 2AS, 2BL, 3B, 4AL, 6AS and 6AL, and seedling resistance to TS was associated with 14 markers on chromosomes 1AS, 2AL, 2BL, 3AS, 3AL, 3B, 6AS and 6AL. Seedling and adult plant resistance (APR) to YR were associated with several markers at the distal end of chromosome 2AS. In addition, YR APR was also associated with markers on chromosomes 2DL, 3B and 7DS. The potential candidate genes for these diseases included several resistance genes, receptor-like serine/threonine-protein kinases and defense-related enzymes. However, extensive LD in wheat that decays at about 5 × 107 bps, poses a huge challenge for delineating candidate gene intervals and candidates should be further mapped, functionally characterized and validated. We also explored a segment on chromosome 2AS associated with multiple disease resistance and identified seventeen disease resistance linked genes. We conclude that identifying candidate genes linked to significant markers in GWAS is feasible in wheat, thus creating opportunities for accelerating molecular breeding.

Fusarium graminearum-induced shoot elongation and root reduction in maize seedlings correlate with later seedling blight severity.

Fusarium graminearum seedling blight is a common disease of maize (Zea mays). Development of genetic resistance to seedling blight in maize germplasm requires efficient and accurate quantitative assessment of disease severity. Through artificial inoculation experiments under controlled growth conditions, we determined that host genotype, pathogen genotype, and infection dose influence the extent to which F. graminearum induces shoot elongation and inhibits root growth in maize seedlings. A comparison of 15 maize inbred lines showed independent variation of these two fungus-induced effects on seedling growth. In a broader survey with nine commercial maize hybrids and three field-collected fungal isolates, there was significant correlation between these seedling growth responses, as well as with later seedling blight severity. Analysis of variance suggested that this variation and the observed correlative relationships were primarily driven by differing pathogenicity of the three fungal isolates. Together, our results indicate that F. graminearum-induced shoot elongation and root reduction in maize seedlings have distinct underlying physiological mechanisms, and that early observations of seedling growth responses can serve as a proxy for investigating natural variation in host resistance and pathogen aggressiveness at later growth stages.

Comparison of Models and Whole-Genome Profiling Approaches for Genomic-Enabled Prediction of Septoria Tritici Blotch, Stagonospora Nodorum Blotch, and Tan Spot Resistance in Wheat.

The leaf spotting diseases in wheat that include Septoria tritici blotch (STB) caused by , Stagonospora nodorum blotch (SNB) caused by , and tan spot (TS) caused by pose challenges to breeding programs in selecting for resistance. A promising approach that could enable selection prior to phenotyping is genomic selection that uses genome-wide markers to estimate breeding values (BVs) for quantitative traits. To evaluate this approach for seedling and/or adult plant resistance (APR) to STB, SNB, and TS, we compared the predictive ability of least-squares (LS) approach with genomic-enabled prediction models including genomic best linear unbiased predictor (GBLUP), Bayesian ridge regression (BRR), Bayes A (BA), Bayes B (BB), Bayes Cπ (BC), Bayesian least absolute shrinkage and selection operator (BL), and reproducing kernel Hilbert spaces markers (RKHS-M), a pedigree-based model (RKHS-P) and RKHS markers and pedigree (RKHS-MP). We observed that LS gave the lowest prediction accuracies and RKHS-MP, the highest. The genomic-enabled prediction models and RKHS-P gave similar accuracies. The increase in accuracy using genomic prediction models over LS was 48%. The mean genomic prediction accuracies were 0.45 for STB (APR), 0.55 for SNB (seedling), 0.66 for TS (seedling) and 0.48 for TS (APR). We also compared markers from two whole-genome profiling approaches: genotyping by sequencing (GBS) and diversity arrays technology sequencing (DArTseq) for prediction. While, GBS markers performed slightly better than DArTseq, combining markers from the two approaches did not improve accuracies. We conclude that implementing GS in breeding for these diseases would help to achieve higher accuracies and rapid gains from selection.

Genomic and pedigree-based prediction for leaf, stem, and stripe rust resistance in wheat.

KEY MESSAGE: Genomic prediction for seedling and adult plant resistance to wheat rusts was compared to prediction using few markers as fixed effects in a least-squares approach and pedigree-based prediction. The unceasing plant-pathogen arms race and ephemeral nature of some rust resistance genes have been challenging for wheat (Triticum aestivum L.) breeding programs and farmers. Hence, it is important to devise strategies for effective evaluation and exploitation of quantitative rust resistance. One promising approach that could accelerate gain from selection for rust resistance is 'genomic selection' which utilizes dense genome-wide markers to estimate the breeding values (BVs) for quantitative traits. Our objective was to compare three genomic prediction models including genomic best linear unbiased prediction (GBLUP), GBLUP A that was GBLUP with selected loci as fixed effects and reproducing kernel Hilbert spaces-markers (RKHS-M) with least-squares (LS) approach, RKHS-pedigree (RKHS-P), and RKHS markers and pedigree (RKHS-MP) to determine the BVs for seedling and/or adult plant resistance (APR) to leaf rust (LR), stem rust (SR), and stripe rust (YR). The 333 lines in the 45th IBWSN and the 313 lines in the 46th IBWSN were genotyped using genotyping-by-sequencing and phenotyped in replicated trials. The mean prediction accuracies ranged from 0.31-0.74 for LR seedling, 0.12-0.56 for LR APR, 0.31-0.65 for SR APR, 0.70-0.78 for YR seedling, and 0.34-0.71 for YR APR. For most datasets, the RKHS-MP model gave the highest accuracies, while LS gave the lowest. GBLUP, GBLUP A, RKHS-M, and RKHS-P models gave similar accuracies. Using genome-wide marker-based models resulted in an average of 42% increase in accuracy over LS. We conclude that GS is a promising approach for improvement of quantitative rust resistance and can be implemented in the breeding pipeline.

Detection and phylogenetic relationships of Puccinia emaculata and Uromyces graminicola (Pucciniales) on switchgrass in New York State using rDNA sequence information.

The species of rust fungi (Pucciniales) inciting disease on switchgrass (Panicum virgatum) grown in bioenergy feedstock systems across the north-central and eastern United States remain unclear. In the present study, the species number and phylogenetic relationships of rust species affecting switchgrass were examined in 2011-2013 at two sites in New York State as well as selected sites in Alabama, Iowa, Nebraska, Pennsylvania, South Dakota, and West Virginia using ribosomal RNA gene data (partial internal transcribed spacer [ITS] 1, complete 5.8 subunit [S] and ITS2, and partial 28S). Uredinial group and teliospore morphology were also utilized to delimit taxa in collection years 2012 and 2013. Maximum likelihood, maximum parsimony, and Bayesian analyses demonstrated two monophyletic clades. Clade I consisted of Puccinia emaculata and included the majority of single-sorus samples across sites, whereas, Clade II included multiple samples from Iowa, Nebraska, and South Dakota. Single-telial samples for Clade I possessed only two-celled teliospores while Clade II samples possessed only one-celled teliospores, and hence, were readily diagnosed morphologically to P. emaculata and Uromyces graminicola, respectively. No U. graminicola sequences exist in GenBank to compare with our Clade II samples; however, based on teliospore morphology, the identity of Clade II taxa is U. graminicola.

Trichothecene Genotype Composition of Fusarium graminearum Not Differentiated Among Isolates from Maize Stubble, Maize Ears, Wheat Spikes, and the Atmosphere in New York.

In order to test the hypothesis that the trichothecene genotype composition of local populations of Fusarium graminearum is structured by specific habitats, a collection of 1,407 isolates was obtained from overwintered maize stubble, mature maize ears and wheat spikes, and the atmosphere 1.5 m aboveground during the flowering stage of these crops. These isolates were sampled at three diverse agricultural locations in New York State: namely, Aurora (sampled in 2012 and 2013) in central New York, Belmont (sampled in 2013) in southwestern New York, and Willsboro (sampled in 2013) in northeastern New York. Approximately 100 isolates of F. graminearum from each habitat were collected within a 10-mile2 area in each location. Polymerase chain reaction assays were used to identify three main B-trichothecene genotypes--3-acetyldeoxynivalenol (3-ADON), 15-ADON, or nivalenol (NIV)--based on amplification of portions of Tri3 and Tri12 genes. All but the NIV genotype were detected. The 15-ADON genotype predominated in most locations; frequencies were 92% (652/709) at Aurora, 78% (332/379) at Belmont, and 53% (167/319) at Willsboro. Frequencies of any genotype did not differ in general among the four habits in each location. An exception was in Aurora 2012, where only 5 in 24 3-ADON isolates were found in samplings from the air and grains of both crops. As viewed by the composition of trichothecene genotypes, local populations of F. graminearum appear not to be structured by these four habitats inclusive of pathogenic and saprophytic phases of the fungus life cycle. The similar frequency of 3-ADON and 15-ADON in eastern New York (Willsboro), which is less than 400 km away from the Aurora sampling location in the central area of the state, suggests that regional populations may be differentiated based on selection associated with climatic or landscape features not currently identified.

Disease Risk, Spatial Patterns, and Incidence-Severity Relationships of Fusarium Head Blight in No-till Spring Wheat Following Maize or Soybean.

The first large-scale survey of Fusarium head blight (FHB) in commercial wheat fields in southern Brazil was conducted over three years (2009 to 2011). The objectives were to: (i) evaluate whether increased FHB risk is associated with within-field maize residue; (ii) determine the spatial pattern of FHB incidence; and (iii) quantify the relationship between FHB incidence and severity. FHB was assessed in a total of 160 fields between early milk and dough. Incidence ranged from 1.0 to 89.9% (median = 25%) and severity from 0.02 to 18.6% (median = 1.3%). FHB risk was neither lower nor higher in wheat following maize than in wheat following soybean. Only 18% of fields were classified as having aggregated patterns of FHB-symptomatic spikes. A binary power law description of the variances was consistent with an overall random pattern of the disease. These results conform with the hypothesis that FHB epidemics in southern Brazil are driven by sufficient atmospherically-transported inoculum from regional sources. The incidence-severity relationship was coherent across growing season, growth stage, and previous crop; one common fitted curve described the relationship across all observations. Estimating severity from incidence may be useful in reducing the workload in epidemiological surveys.