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Estimating the frequency of virulence against an Stb gene in Zymoseptoria tritici populations by bulk phenotyping on checkerboard microcanopies of wheat near‐isogenic lines

Posted on 16 March 2024 by

The BCP method leverages the relationship between the ratio of Zymoseptoria tritici lesions on wheat near-isogenic lines differing by one resistance gene (Stb16q) and the frequency of virulent strains in the inoculated population.

Abstract

Monitoring virulent strains within pathogen populations is crucial to improve host resistance deployment strategies. Such monitoring increasingly involves field pathogenomics studies of molecular polymorphisms in pathogen genomes based on high-throughput screening technologies. However, it is not always straightforward to predict virulence phenotypes from these polymorphisms, and in planta phenotyping remains necessary. We developed a method for ‘bulk phenotyping on checkerboard microcanopies of wheat near-isogenic lines’ (BPC) for estimating the frequency of virulence against a resistance gene in mixed populations of the fungal pathogen Zymoseptoria tritici, the causal agent of Septoria tritici blotch (STB) in wheat, without the need for strain-by-strain pathogen phenotyping. Our method involves the uniform inoculation of a microcanopy of two wheat lines—one with the target resistance gene and the other without it—with a multistrain mixture of isolates representative of the population to be characterized, followed by the differential quantification of infection points (lesions). Using Stb16q, a wheat resistance gene that has recently broken down in Europe, we found a robust correlation between the ratio of the mean number of lesions on each wheat line and the frequency of virulent strains in the inoculum. Using pairs of virulent and avirulent strains, as well as synthetic populations consisting of 10 virulent strains and 10 avirulent strains mixed in different proportions, we validated the principle of the method and established standard curves at virulence frequencies close to those observed in natural conditions. We discuss the potential of this method for virulence monitoring in combination with molecular methods.

All‐in‐one Xylella detection and identification: A nanopore sequencing‐compatible conventional PCR

Posted on 15 March 2024 by

A new diagnostic PCR assay assesed with an Interlaboratory Test Performance Study (TPS) by five plant pathology laboratories that can accurately detect and differentiate all species and subspecies in Xylella genus.

Abstract

Xylella fastidiosa is a plant-pathogenic bacterium that poses a serious threat to the production of economically important plant species including grapes, almonds, olives and a broad range of amenity plants, causing significant economic losses worldwide. While multiple molecular detection assays have been developed for X. fastidiosa, there is a lack of molecular tools available for detection and differentiation of the closely related pear pathogen, Xylella taiwanensis. In this study, we present a novel conventional PCR assay with primers that can amplify both Xylella species. The amplified product could be sequenced and used for discrimination between the two species and the subspecies within the fastidiosa species. This PCR assay was designed using a genome-informed approach to target the ComEC/Rec2 gene of both Xylella species, ensuring a higher specificity than other previously developed PCR assays. A test performance study across five national plant diagnostic laboratories in Australia and New Zealand demonstrated this assay's high sensitivity and specificity to all known species and subspecies within the Xylella genus. This PCR assay can be used for Xylella identification at the species and subspecies level and is compatible with Sanger sequencing and nanopore sequencing for rapid turnaround time. The newly developed conventional PCR assay presented here offers rapid detection and accurate identification of both Xylella species from plant, insect vector or bacterial samples, enabling timely implementation of biosecurity measures or disease management responses.

Inheritance and genetic mapping of the first CPMMV tolerance locus in common bean

Posted on 15 March 2024 by

A QTL locus for CPMMV tolerance in common bean cv. BRS Sublime was mapped to the terminal region on chromosome Pv08, linked to the SNP_Ch_8_62396711 marker. Two LRR genes and one protein kinase were located within the confidence interval.

Abstract

Although cowpea mild mottle virus (CPMMV) has been reported in Brazil since 1983, it has only become a significant concern for researchers and farmers in recent years. The objective of this work was to investigate the genetic basis of CPMMV tolerance, mapping and reporting the first loci associated with this trait in common bean (cv. BRS Sublime). Phenotypic assays were carried out on 180 individual plants (F₂ generation) and 180 F_2:3 progenies comprising 12 plants per family and their parents (BRS Sublime, tolerant parent × CNFCT 16207, susceptible parent). CPMMV was mechanically inoculated and symptoms were evaluated at 35 days after inoculation, using a 1–5 scoring scale. A linkage map was constructed using 1695 single-nucleotide polymorphism (SNP) and SilicoDArT markers that segregated in the F₂ and F_2:3 generations as expected. Markers were distributed across 11 common bean chromosomes, resulting in a total length of 2864 cM, with an average distance between markers of 1.8 cM. Phenotypic observations revealed that tolerance in cv. BRS Sublime is controlled by a single dominant gene. The main effect quantitative trait locus (QTL; CPMMV.Pv08) associated with CPMMV tolerance was identified in the terminal region on chromosome 8 (Pv08). This QTL explained approximately 77% of phenotypic variation, indicating that the inheritance of tolerance to CPMMV is monogenic, controlled by a major locus. As far as we know, this study represents the first investigation into the inheritance and genetic mapping of CPMMV tolerance in common bean, with potential for the development of elite lines with multiple virus resistance/tolerance.

Effect of water movement in frozen soil on long-term hydrological simulation of Soil and Water Assessment Tool in cold climate watershed in Hokkaido, Japan

Posted on 15 March 2024 by

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Genome assembly and multi‐omic analyses reveal the mechanisms underlying flower color formation in Torenia fournieri

Posted on 14 March 2024 by

Abstract

Torenia fournieri Lind. is an ornamental plant that is popular for its numerous flowers and variety of colors. However, its genomic evolutionary history and the genetic and metabolic bases of flower color formation remain poorly understood. Here, we report the first T. fournieri reference genome, which was resolved to the chromosome scale and was 164.4 Mb in size. Phylogenetic analyses clarified relationships with other plant species, and a comparative genomic analysis indicated that the shared ancestor of T. fournieri and Antirrhinum majus underwent a whole genome duplication event. Joint transcriptomic and metabolomic analyses identified many metabolites related to pelargonidin, peonidin, and naringenin production in rose (TfR)-colored flowers. Samples with blue (TfB) and deep blue (TfD) colors contained numerous derivatives of petunidin, cyanidin, quercetin, and malvidin; differences in the abundances of these metabolites and expression levels of the associated genes were hypothesized to be responsible for variety-specific differences in flower color. Furthermore, the genes encoding flavonoid 3-hydroxylase, anthocyanin synthase, and anthocyanin reductase were differentially expressed between flowers of different colors. Overall, we successfully identified key genes and metabolites involved in T. fournieri flower color formation. The data provided by the chromosome-scale genome assembly establish a basis for understanding the differentiation of this species and will facilitate future genetic studies and genomic-assisted breeding.

Genome‐wide scanning to identify and validate single nucleotide polymorphism markers associated with drought tolerance in spring wheat seedlings

Posted on 13 March 2024 by

Abstract

Unlike other growth stages of wheat, very few studies on drought tolerance have been done at the seedling stage, and this is due to the complexity and sensitivity of this stage to drought stress resulting from climate change. As a result, the drought tolerance of wheat seedlings is poorly understood and very few genes associated with drought tolerance at this stage were identified. To address this challenge, a set of 172 spring wheat genotypes representing 20 different countries was evaluated under drought stress at the seedling stage. Drought stress was applied on all tested genotypes by water withholding for 13 days. Two types of traits, namely morphological and physiological traits were scored on the leaves of all tested genotypes. Genome-wide association study (GWAS) is one of the effective genetic analysis methods that was used to identify target single nucleotide polymorphism (SNP) markers and candidate genes for later use in marker-assisted selection. The tested plant materials were genotyped using 25k Infinium iSelect array (25K) (herein after it will be identified as 25K) (for 172 genotypes) and genotyping-by-sequencing (GBS) (for 103 genotypes), respectively. The results of genotyping revealed 21,093 25K and 11,362 GBS-SNPs, which were used to perform GWAS analysis for all scored traits. The results of GWAS revealed that 131 and 55 significant SNPs were controlling morphological and physiological traits, respectively. Moreover, a total of eight and seven SNP markers were found to be associated with more than one morphological and physiological trait under drought stress, respectively. Remarkably, 10 significant SNPs found in this study were previously reported for their association with drought tolerance in wheat. Out of the 10 validated SNP markers, four SNPs were associated with drought at the seedling stage, while the remaining six SNPs were associated with drought stress at the reproductive stage. Moreover, the results of gene enrichment revealed 18 and six pathways as highly significant biological and molecular pathways, respectively. The selection based on drought-tolerant alleles revealed 15 genotypes with the highest number of different drought-tolerant alleles. These genotypes can be used as candidate parents in future breeding programs to produce highly drought-tolerant genotypes with high genetic diversity. Our findings in this study provide novel markers and useful information on the genetic basis of drought tolerance at early growth stages.

The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed

Posted on 13 March 2024 by

Abstract

Ambrosia artemisiifolia and Ambrosia trifida (Asteraceae) are important pest species and the two greatest sources of aeroallergens globally. Here, we took advantage of a hybrid to simplify genome assembly and present chromosome-level assemblies for both species. These assemblies show high levels of completeness with Benchmarking Universal Single-Copy Ortholog (BUSCO) scores of 94.5% for A. artemisiifolia and 96.1% for A. trifida and long terminal repeat (LTR) Assembly Index values of 26.6 and 23.6, respectively. The genomes were annotated using RNA data identifying 41,642 genes in A. artemisiifolia and 50,203 in A. trifida. More than half of the genome is composed of repetitive elements, with 62% in A. artemisiifolia and 69% in A. trifida. Single copies of herbicide resistance-associated genes PPX2L, HPPD, and ALS were found, while two copies of the EPSPS gene were identified; this latter observation may reveal a possible mechanism of resistance to the herbicide glyphosate. Ten of the 12 main allergenicity genes were also localized, some forming clusters with several copies, especially in A. artemisiifolia. The evolution of genome structure has differed among these two species. The genome of A. trifida has undergone greater rearrangement, possibly the result of chromoplexy. In contrast, the genome of A. artemisiifolia retains a structure that makes the allotetraploidization of the most recent common ancestor of the Heliantheae Alliance the clearest feature of its genome. When compared to other Heliantheae Alliance species, this allowed us to reconstruct the common ancestor's karyotype—a key step for furthering of our understanding of the evolution and diversification of this economically and allergenically important group.

Rice resistance against Bipolaris oryzae infection is mediated by lower foliar potassium concentration

Posted on 13 March 2024 by

Lower foliar potassium concentration reduced brown spot symptoms and was linked to stronger biochemical defence reactions, a robust antioxidative system and less damage to photosynthesis.

Abstract

Brown spot, caused by Bipolaris oryzae, is a very important disease of rice. This study investigated the effect of potassium (K) on rice resistance to brown spot. The working hypothesis tested was that higher foliar K concentration could allow plants to respond more efficiently against fungal infection. Plants were grown in nutrient solution amended with three K rates (0.5, 1.0 and 2.5 mM) and noninoculated or inoculated with B. oryzae. The photosynthetic performance of plants, activities of defence and antioxidant enzymes and the concentrations of reactive oxygen species, phenolics and lignin were determined. Foliar K concentration was significantly higher by 38% and 91% for plants supplied with 1.0 and 2.5 mM K, respectively, compared to plants supplied with 0.5 mM K. Brown spot severity was significantly higher (≥20%) for plants supplied with 1.0 and 2.5 mM K than those supplied with 0.5 mM K (≤15%). Higher brown spot severity for plants supplied with 2.5 mM K resulted in changes in the photosynthetic apparatus, reduced chlorophyll a + b and carotenoids concentrations, and higher production of hydrogen peroxide and superoxide anion radical. In contrast, higher activities of defence and antioxidant enzymes and more production of phenolics for plants supplied with 0.5 mM K helped them to cope with B. oryzae infection more efficiently. In conclusion, rice resistance against brown spot was achieved by keeping a lower foliar K concentration linked to more active defence reactions, a robust antioxidative system and less damage to the photosynthetic apparatus.

Phenotype and genotype characterization of Botrytis cinerea isolates from cut roses in Yunnan, China

Posted on 13 March 2024 by

One hundred Botrytis cinerea strains from cut roses were classified into phylogenetic Group II based on polymorphisms in Bc-hch; four subpopulations showed significant variation in morphology, pathogenicity and fungicide resistance.

Abstract

Botrytis cinerea is considered to be the second most destructive fungal pathogen worldwide, causing severe pre- and postharvest losses in cut roses. However, to date, no systematic research on its characteristics in cut roses has been reported. In our study, a total of 100 isolates from cut roses from Yunnan, China, were analysed. A combination of morphological characteristics and phylogenetic analysis of RPB2 revealed that 100 isolates were of the species B. cinerea. These isolates were pathogenic on unwounded detached rose petals. Pathogenicity was evaluated according to the size of petal spots and categorized into grades 0–5, from weak to strong. The inhibition rate varied greatly following the addition of procymidone (21.9%–100%) and cyprodinil (25.0%–92.3%). Analysis of Bc-hch sequences revealed all isolates belong to phylogenetic Group II. According to the presence or absence of transposable elements, 87, 5, 4 and 4 isolates were identified as transposa, vacuma, Boty-only and Flipper-only types, respectively. Detection of mating type indicated that all isolates were heterothallic with 45% belonging to MAT1-1 and 55% to MAT1-2. Isolates were divided into four subpopulations when analysing single-nucleotide polymorphisms at the genomic level, with a significant difference in pathogenicity between subpopulations 1 and 4. The evolutionary tree indicated that isolates AN-02, AN-22 and SM-C18 were clustered in the root, suggesting an earlier evolutionary time than other isolates; moreover, they all exhibited low pathogenicity (grade 1). This systematic study of the characteristics of B. cinerea will provide significant support for grey mould control and further research.

A high‐throughput analysis of high‐resolution X‐ray CT images of stems of olive and citrus plants resistant and susceptible to Xylella fastidiosa

Posted on 13 March 2024 by

Though morphological traits of resistant olives (narrow vessels) and citrus' (connected vessels) are distinct, across both taxa, susceptible cultivars have many more vessels; representing a potentially broader-reaching trend.

Abstract

The bacterial plant pathogen Xylella fastidiosa causes disease in several globally important crops. However, some cultivars harbour reduced bacterial loads and express few symptoms. Evidence considering plant species in isolation suggests xylem structure influences cultivar susceptibility to X. fastidiosa. We test this theory more broadly by analysing high-resolution synchrotron X-ray computed tomography of healthy and infected plant vasculature from two taxonomic groups containing susceptible and resistant varieties: two citrus cultivars (sweet orange cv. Pera, tangor cv. Murcott) and two olive cultivars (Koroneiki, Leccino). Results found the susceptible plants had more vessels than resistant ones, which could promote within-host pathogen spread. However, features associated with resistance were not shared by citrus and olive. While xylem vessels in resistant citrus stems had comparable diameters to those in susceptible plants, resistant olives had narrower vessels that could limit biofilm spread. And while differences among olive cultivars were not detected, results suggest greater vascular connectivity in resistant compared to susceptible citrus plants. We hypothesize that this provides alternate flow paths for sustaining hydraulic functionality under infection. In summary, this work elucidates different physiological resistance mechanisms between two taxonomic groups, while supporting the existence of an intertaxonomical metric that could speed up the identification of candidate-resistant plants.