Predicting airborne ascospores of Sclerotinia sclerotiorum through machine learning and statistical methods

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Predicting airborne ascospores of Sclerotinia sclerotiorum through machine learning and statistical methods

Across all statistical and machine learning models, the greatest predictor of ascospores released on a given day was the number of ascospores released on the previous day.


Abstract

A main biological constraint of dry bean (Phaseolus vulgaris) production in Canada is white mould, caused by the fungal pathogen Sclerotinia sclerotiorum. The primary infectious propagules of S. sclerotiorum are airborne ascospores and monitoring the air for inoculum levels could help predict the severity of white mould in bean fields. Daily air samples were collected in commercial dry bean fields in Alberta, Manitoba and Ontario and ascospores were quantified using quantitative PCR. Daily weather data was obtained from in-field weather stations. The number of ascospores on a given day was modelled using 63 different environmental variables and several modelling methods, both regression and classification approaches, were implemented with machine learning (ML) (random forests, logistic regression and support vector machines) and statistical (generalized linear models) approaches. Across all years and provinces, ascospores were most highly correlated with ascospore release from the previous day (r ranged from 0.15 to 0.6). This variable was also the only variable included in all models and had the greatest weight in all models. Models without this variable had much poorer performance than those with it. Correlations of ascospores with other environmental variables varied by province and sometimes by year. A comparison of ML and statistical models revealed that they both performed similarly, but that the statistical models were easier to interpret. However, the precise relationship between airborne ascospore levels and in-field disease severity remains unclear, and spore sampling methods will require further development before they can be deployed as a disease management tool.

Experimental warming and nitrogen deposition in clear‐cuts and forest edges: Assessing impacts on plant communities and tree seedling performance

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Experimental warming and nitrogen deposition in clear-cuts and forest edges: Assessing impacts on plant communities and tree seedling performance

With a field experiment, we studied nitrogen deposition and climate warming impacts on planted tree seedlings and associated understory plants in clear-cuts and forest edges. Microenvironments were assessed, including soil properties and edge effects. Microenvironmental effects on plants were habitat dependent. Moderate climate warming may enhance tree seedling performance and plant cover in a clear-cuts of Pacific Northwest coastal ecosystems.


Abstract

Questions

Do nitrogen deposition and climate warming affect tree seedlings and plant communities in different habitats? In these habitats, how do microenvironments, including soil properties and, when applicable, edge effects relate to plant performance?

Location

The University of British Columbia Malcolm Knapp Research Forest, Maple Ridge, British Columbia, Canada.

Methods

We assessed performance of Pseudotsuga menziesii (Mirb.) Franco, Thuja plicata Donn ex D. Don and Tsuga heterophylla (Raf.) Sarg. planted tree seedlings and associated vascular plant communities. Performance of tree seedlings (height) and under vascular plant communities (percent cover) were examined in an experiment with warming (open-top chambers) and nitrogen deposition (ammonium nitrate applied at 10 kg N ha−1 year−1) treatments applied to subplots in six forest edges and six clear-cuts (N = 298 total subplots).

Results

In clear-cuts, tree seedling height increased with experimental warming and differed among species, and vascular plant cover increased with warming. In clear-cuts, species identity, not soil variables, was a strong predictor of height, and plant cover was negatively related to pH. In forest edges, edge position and some soil variables were related to height, but not plant cover. There were no interaction effects found between experimental nitrogen deposition and warming.

Conclusions

Our results suggest that moderate warming can enhance tree seedling height and understorey vascular plant cover in clear-cuts in Pacific Northwest coastal ecosystems, but low nitrogen deposition may not have an effect alone or synergistically with warming.

Clavibacter tessellarius causing bacterial mosaic of wheat establishes in the Old World

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Clavibacter tessellarius causing bacterial mosaic of wheat establishes in the Old World

Using field surveys and samplings we confirmed widespread occurrence of the wheat pathogen Clavibacter tessellarius in southern Iran and establishment of the bacterium in the Old World.


Abstract

The genus Clavibacter (family Microbacteriaceae) includes gram-positive actinobacterial species infecting diverse agricultural crops such as alfalfa, maize, pepper, potato, tomato and wheat. Clavibacter tessellarius, causing bacterial mosaic of wheat, was reported for the first time in 1976 in Nebraska (United States). Since then, the pathogen was thought to be restricted to North America (Canada and the United States). While bacterial strains suspected to be C. tessellarius have occasionally been isolated from wheat samples outside North America, occurrence of the pathogen in the Old World has not yet been confirmed by the plant protection authorities. In spring 2020 (January to May) dozens of wheat fields with young plants showing leaf chlorosis and mild mosaic symptoms were surveyed and sampled in southern Iran. Among 192 surveyed wheat fields, gram-positive, orange-pigmented actinobacterial strains were isolated from samples of 53 fields. Altogether, 61 bacterial strains were identified as C. tessellarius based on the phenotypic features, PCR-based molecular tests and pathogenicity assays. Multilocus sequence analysis of five housekeeping genes (atpD, dnaK, gyrB, ppk and rpoB) using 10 representative strains from diverse geographic areas in southern Iran confirmed the phylogenetic status of the strains within C. tessellarius. Our data indicate that the bacterial mosaic pathogen occurs in four southern Iranian provinces including Bushehr, Fars, Kerman and Khuzestan. Thus, occurrence of C. tessellarius outside North America is confirmed. Potential risks associated with the emergence of the pathogen in the Old World, and the need for strict quarantine measures in the area, is further discussed.

Survey of Phyllosticta citricarpa mating type in the São Paulo citrus belt and optimization of in vitro ascospore production

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Survey of Phyllosticta citricarpa mating type in the São Paulo citrus belt and optimization of in vitro ascospore production

The two mating types of Phyllosticta citricarpa occurred in similar ratio in the São Paulo citrus belt; ascospores were produced in potato dextrose agar (PDA), ½ PDA and malt extract agar (MEA) at 15, 20 and 25°C, especially in MEA at 25°C.


Abstract

Phyllosticta citricarpa, the citrus black spot causal agent, requires both mating types, designated as MAT1-1 and MAT1-2, to produce ascospores. Mating-type ratio in some citrus-growing areas has been characterized but remains little known in the São Paulo (SP) citrus belt, the largest sweet orange producer worldwide. A protocol for in vitro ascospore production was developed recently; however, there are few studies regarding the optimal conditions for their production. Thus, this study aimed to determine the mating-type ratio in SP and quantify ascospores produced under different conditions in vitro. The mating types were identified by duplex PCR, and ascospore production was assessed in five culture media: potato dextrose agar (PDA), ½ PDA, malt extract agar (MEA), oatmeal agar (OMA) and citrus agar (CA), and at temperatures from 10 to 30°C. The ratio of MAT1-1 and MAT1-2 was similar to 1:1. Ascospore production reached peaks of 8.0, 7.0 and 3.0 × 103 ascospores/mL in MEA, PDA and ½ PDA, respectively. There were no ascospores observed in OMA and CA. P. citricarpa ascospores were observed only at 15, 20 and 25°C in PDA, with peaks of up to 2.0 × 103 ascospores/mL at 42, 35 and 21 days, respectively. There were no ascospores observed at 10 and 30°C. Both mating types are similarly distributed in the SP citrus belt, and in vitro ascospore production may be optimized by using MEA at 25°C. These data provide a better understanding of P. citricarpa sexual reproduction and a background for further studies with ascospores.

Genome‐wide association study of adult plant resistance to spot blotch in an elite Canadian two‐row barley germplasm collection

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Genome-wide association study of adult plant resistance to spot blotch in an elite Canadian two-row barley germplasm collection

Using elite Canadian two-row barley germplasm, GWAS identified several single-nucleotide polymorphism (SNP) molecular markers of multiple chromosomes that were associated with adult-plant resistance to Bipolaris sorokiniana.


Abstract

Spot blotch, caused by Bipolaris sorokiniana, is a growing concern for barley (Hordeum vulgare) production in most humid, temperate growing regions of the world. Under epidemic conditions, this disease can reduce yields significantly. Reduction of kernel plumpness is associated with lower malt extract and consequently grain quality. Enhanced resistance to this disease is a major goal of western Canadian two-row barley breeding programmes; however, two-row barley is considered to be more susceptible than six-row barley. Plant–pathogen interactions observed for Canadian germplasm are polygenic, where quantitative breeding methods could be beneficial for the development of resistant germplasm. A germplasm panel consisting of 200 two-row, spring barley genotypes with differential reaction to spot blotch was evaluated at Brandon, Manitoba (MB), and Melfort, Saskatchewan (SK), over eight site years. Genome-wide association study was conducted using a 50k single-nucleotide polymorphism (SNP) Illumina iSelect genotyping array. The most-resistant germplasm was found to carry Midwest Six-rowed Durable Resistant Haplotype (MSDRH) alleles at the loci located on chromosomes 1H (Rcs-qtl-1H-11_10764), 3H (Rcs-qtl-3H-11_10565) and 7H (Rcs-qtl-7H-11_20162, Rcs5 locus), where the 3H locus was found to be the most under-represented in Canadian germplasm. Additional marker-trait associations within nurseries were identified on chromosomes 1H, 2H and 4H. Several of the SNP markers identified were found to be polymorphic within the Canadian two-row germplasm panel and thus could be useful for enhancing spot blotch resistance in two-row barley for development of resistant cultivars.

Flavour improvement in early generations of fresh market tomatoes (Solanum lycopersicum): I. Identification of QTL for sensory attributes, physicochemical measurements and volatile compounds

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Abstract

Human sensory analysis is the most appropriate method for assessing the flavour of fresh market tomatoes, but it is very labour and time consuming. Therefore, sensory attributes are often neglected in early generations of breeding programmes and genetic studies, although there is a demand for tomatoes with improved flavour. In this study, the recently developed Breeders' Sensory Test was applied to an F2 mapping population derived from two parents with superior flavour. Sensory attributes, physicochemical measurements, volatiles and fruit weight were assessed in organic low-input and hydroponic cultivation. A linkage map spanning 1070 cM was developed. In total, 71 quantitative trait loci (QTL) were detected for the means of both cultivation systems, 61 for organic and 46 for hydroponic cultivation. A proportion of 27% of the loci were co-localized between both cultivation systems. Nine distinct QTL clusters for flavour-related traits were identified, including a large cluster on chromosome 6 comprising five sensory and nine volatile QTL. The sensory QTL on chromosomes 2, 5, 6, 10 and 11, partly within clusters, are recommended for marker-assisted selection.