High Genetic Diversity in Predominantly Clonal Populations of the Powdery Mildew Fungus Podosphaera leucotricha from U.S. Apple Orchards

Population Genetic Structure of the Rubber Tree Powdery Mildew Pathogen (Erysiphe quercicola) from China

In order to manage agricultural pathogens, it is crucial to understand the population structure underlying epidemics. Rubber tree powdery mildew, caused by Erysiphe quercicola, is a serious threat to rubber plantations worldwide, especially in subtropical environments including all rubber tree-growing regions in China. However, the population structure of the pathogen is uncertain. In this study, 16 polymorphic microsatellite markers were used to genotype powdery mildew samples from the main rubber tree-growing regions including Yunnan (YN), Hainan (HN), western Guangdong (WG), and eastern Guangdong (EG). YN had higher genotypic diversity (Simpson's indices), genotypic evenness, Nei's gene diversity, allelic richness, and private allelic richness than the other regions. Cluster analysis, discriminant analysis of principal components, pairwise divergence, and shared multilocus genotype analyses all showed that YN differed significantly from the other regions. The genetic differentiation was small among the other three regions (HN, WG, and EG). Analysis of molecular variance indicated that the variability among regions accounted for 22.37% of the total variability. Genetic differentiation was significantly positively correlated (Rxy = 0.772, P = 0.001) with geographic distance. Linkage equilibrium analysis suggested possible occurrence of sexual recombination although asexual reproduction predominates in E. quercicola. The results suggested that although significant genetic differentiation of E. quercicola occurred between YN and the other regions, pathogen populations from the other three regions lacked genetic differentiation.

Assessment of Fungicide Resistance via Molecular Assay in Populations of Podosphaera leucotricha, Causal Agent of Apple Powdery Mildew, in New York

Podosphaera leucotricha, causal agent of apple powdery mildew, is a pathogen endemic worldwide where apples are produced. In the absence of durable host resistance, the disease is most effectively managed in conventional orchards with single-site fungicides. In New York State, increasingly erratic precipitation patterns and warmer temperatures due to climate change may create a regional environment more conducive to apple powdery mildew development and spread. In this scenario, outbreaks of apple powdery mildew may supplant the apple diseases of current management concern: apple scab and fire blight. Presently, there have been no reports from producers of fungicide control failures for apple powdery mildew, though increased disease incidence has been reported to and observed by the authors. As such, action was needed to assess the fungicide resistance status of populations of P. leucotricha to ensure key classes of single-site fungicides (FRAC 3, demethylation inhibitors, DMI; FRAC 11, quinone outside inhibitors, QoI; and FRAC 7, succinate dehydrogenase inhibitors, SDHI) remain effective. In a 2-year survey (2021 to 2022), we collected 160 samples of P. leucotricha from 43 orchards, representing conventional, organic, low-input, and unmanaged orchards from New York's primary production regions. Samples were screened for mutations in the target genes (CYP51, cytb, and sdhB) historically known to confer fungicide resistance in other fungal pathogens to the DMI, QoI, and SDHI fungicide classes, respectively. Across all samples, no nucleotide sequence mutations that translated into problematic amino acid substitutions were found in the target genes, suggesting that New York populations of P. leucotricha remain sensitive to the DMI, QoI, and SDHI fungicide classes, provided no other fungicide resistance mechanism is at play in the population.

Evaluation of Malus Germplasm Identifies Genetic Sources of Powdery Mildew and Frogeye Leaf Spot Resistance for Apple Breeding

Apple is an important fruit crop of temperate regions. The narrow genetic base of commercially cultivated apples has resulted in its vulnerability to a large number of fungal, bacterial, and viral pathogens. Apple breeders are always seeking new sources of resistance within the cross-compatible Malus species that can be deployed into elite genetic backgrounds. We have evaluated resistance to two major fungal diseases of apples: powdery mildew and frogeye leaf spot, using a germplasm collection of 174 Malus accessions to identify novel sources of genetic resistance. In 2020 and 2021, we evaluated these accessions for the incidence and severity of powdery mildew and frogeye leaf spot diseases at Cornell AgriTech, Geneva, New York, in a partially managed orchard. The severity and incidence of powdery mildew and frogeye leaf spot, as well as weather parameters were recorded in June, July, and August. Total incidence of powdery mildew and frogeye leaf spot infections increased from 33 to 38%, and 56 to 97% in 2020 and 2021, respectively. Our analysis showed that relative humidity and precipitation correlate with powdery mildew and frogeye leaf spot susceptibility. The predictor variables with highest impact to the variability of powdery mildew were accessions and relative humidity in May. A total of 65 Malus accessions were found to be resistant to powdery mildew, and only one accession showed moderate resistance to frogeye leaf spot. Several of these accessions belong to Malus hybrid species and domesticated apples and can therefore be potential sources of novel resistance alleles for apple breeding.

Genetic Relationships of Puccinia striiformis f. sp. tritici in Southwestern and Northwestern China

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a crucial disease for wheat worldwide and constantly threatens wheat production in southwestern and northwestern China, where the environment is a good fit for Pst oversummering and overwintering. However, the underlying genetic dynamics of spring epidemic Pst populations across large areas of continuous planting in the southwestern and northwestern regions are poorly understood. A total of 2,103 Pst isolates were sampled in the spring of 2019 from the two agroecosystems and grouped into three horizontal spatial scales (countywide, provincial, and regional subpopulations) and two vertical spatial scales that consisted of elevational and geomorphic subpopulations. A total of 776 multilocus genotypes were identified, with the highest genetic diversity found in the northern and Sichuan populations, particularly in the Ningxia and Sichuan Basins, while the lowest genetic diversity was found in the Yunnan and Guizhou populations. Multivariate discriminant analysis of principal components (DAPC) and STRUCTURE (STRUCTURE 2.3.4) analyses revealed variation in the genotypic compositions of the molecular groups on horizontal and vertical dimensions from north to south or vice versa and from low to high or vice versa, respectively. The regional neighbor-joining tree revealed three large spatial structures consisting of the southwestern, the northwestern, and the Xinjiang regions, while the Tibetan population connected the southwestern and northwestern regions. The isolates of the Sichuan Basin were scattered over the four quartiles by principal coordinate analysis, which indicated frequent genotype interchange with others. Greater genetic differentiation was observed between the southwestern and northwestern regions. Linkage equilibrium (P ≥ 0.05) was detected on different spatial scales, suggesting that Pst populations are using sexual reproduction or mixed reproduction (sexual and clonal reproduction) in southwestern and northwestern China. IMPORTANCE Understanding the epidemiology and population genetics of plant pathogens is crucial to formulate efficient predictions of disease outbreaks and achieve sustainable integrated disease management, especially for pathogens with migratory capability. Here, this study covers the genetic homogeneity and heterogeneity of different geographical Pst populations on broad to fine spatial scales from the key epidemic regions of the two agroecosystems in China, where wheat stripe rust occurs annually. We provide knowledge of the population genetics of Pst and reveal that, for instance, there is greater genetic diversity in northwestern China, there are close genetic relationships between Yunnan and Guizhou and between Gansu-Ningxia and Qinghai, and there are effects of altitude on genetic compositions, etc. All of these findings clarify the genetic relationships and expand the insights into the population dynamics and evolutionary mechanisms of Pst in southwestern and northwestern China, providing a theoretical basis for achieving sustainable control of wheat stripe rust in key epidemic regions.