Category Archives: ORIGINAL ARTICLE

No safe haven: Loss of avirulence in the plant pathogen Leptosphaeria maculans by DNA duplication and repeat‐induced point mutation

Posted on 16 March 2024 by nAlexander Idnurm, nAlec J. McCallum, nAngela P. Van de Wouwn

Unlike other avirulence genes in canola pathogen Leptosphaeria maculans, AvrLm2 is protected from repeat-induced point mutation (RIP): here fungal populations were identified with RIP in AvrLm2, due to a DNA duplication event.

Abstract

Microbes can overcome the ability of plant resistance genes to confer protection against disease by mutating their corresponding avirulence genes. The fungus Leptosphaeria maculans causes blackleg disease on canola crops and subverts Brassica napus resistance genes through several DNA mutation mechanisms. One of these is repeat-induced point (RIP) mutation, which can ‘leak’ into the avirulence genes from the adjacent repetitive sequences that the mutation process is targeting. Here, we identified populations of L. maculans in Australia that have extensive RIP mutations in the avirulence gene AvrLm2 and show that this has been triggered by a duplication of the gene and surrounding DNA that includes the distant (>55 kb in total) AvrLm6 gene. This finding provides another mechanism of mutation by which pathogens can overcome host resistance, and more broadly contributes to understanding the complex balance between gene duplication and genome defence.

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.

Landscape‐scale patterns and predictors of potato viruses in Scotland

Posted on 15 March 2024 by nPeter Skelseyn

ArcGIS and machine learning are used to provide a comprehensive overview of potato viruses in Scotland, a deeper understanding of landscape epidemiology, and a model that could serve as the basis of a decision support tool.

Abstract

Virus diseases represent important economic threats to seed potato production worldwide, yet relatively little is known of their epidemiology at the landscape-scale. In this study, data was compiled from the Scottish national seed potato classification scheme on the incidence of 10 different potato viruses for the years 2009–2022. A co-occurrence analysis identified that 12 virus species pairs occurred together more often than expected by chance, and potato blackleg was positively associated with eight potato viruses. ArcGIS was used to investigate spatial and spatiotemporal variation in incidence rates of the three most prevalent viruses (potato virus Y, potato leaf roll virus and potato virus A), and this revealed prominent geographic differences in long-term disease outcomes. Focusing on potato virus Y as the most commonly occurring single infection, interpretable machine-learning techniques were used to investigate the influence of key crop, management and environmental factors on patterns of incidence in space and time. The results showed that health characteristics of seed stocks were among the most important predictors of incidence, along with blackleg infection, several management features, cultivar resistance, distance to the nearest seed and ware crop, temperature variables and several soil features. This approach provides a comprehensive overview of potato viruses in Scotland, a deeper understanding of epidemiological risk factors at the landscape-scale and a forecast model that could serve as the basis of a decision support tool for improved management of potato virus Y.

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.

Exploring the genomics of abiotic stress tolerance and crop resilience to climate change

Posted on 13 March 2024 by nRajeev K. Varshney, nRutwik Barmukh, nAlison Bentley, nHenry T. Nguyenn

The Plant Genome, EarlyView.

Ceratocystis fimbriata alters root system architecture and causes symptom development only in detached storage roots in Bayou Belle and Beauregard sweet potato

Posted on 13 March 2024 by nArthur Q. Villordon, nCatherine D. DeRobertis, nChristopher A. Clarkn

Ceratocystis fimbriata affected root system architecture of sweet potato even though it did not cause symptoms and was not isolated from roots until swollen storage roots were detached from the plant.

Abstract

Little is known about how the sweet potato (Ipomoea batatas) root system responds to Ceratocystis fimbriata in the growth substrate. Understanding whether the fungus affects the root system before harvest of storage roots (SR) could guide timing of management efforts. Cuttings of cultivars Bayou Belle and Beauregard, both previously considered susceptible to black rot, were in unamended or infested sand. At the onset of SR formation, effects on first- and second-order lateral root (LR) length and number among and within treatments, cultivars and replicate experiments were recorded. First-order LR length in inoculated Bayou Belle plants was 31% greater than in inoculated plants of cultivar Beauregard in Expt 1, but there were no differences in Expt 2. Second-order LR length varied among, and within, cultivars, inoculum treatments and experiments in Expts 1 and 2. At 49 days after planting in Expt 1, only inoculated plants had necrotic lesions on stems in both cultivars, with more than twice as many recorded on Bayou Belle than Beauregard. SR had no lesions at harvest. Detached SR originating from inoculated treatments and stored in sampling bags for 25 days developed black rot lesions at either end of the SR (45% and 31% of total in Expt 1 and Expt 2, respectively) or elsewhere, including those centred on LR emergence sites or lenticels (55% and 69%, respectively). Exposing developing plants to inoculation may reveal differences in SR susceptibility not found when harvested SR are wounded and inoculated.

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.