A Six-Year Investigation of the Dynamics of Avirulence Allele Profiles, Blackleg Incidence, and Mating Type Alleles of Leptosphaeria maculans Populations Associated with Canola Crops in Manitoba, Canada

Whole genome sequencing reveals the genetic diversity and structure of Leptosphaeria maculans populations from the Western Cape province of South Africa

BACKGROUND

Leptosphaeria maculans is the causal agent of blackleg, a globally important disease of canola. Investigating the genetic diversity and structure of L. maculans populations can provide insight into its evolutionary potential and genetic variability, which is important to develop effective blackleg management strategies. In this study, whole genome sequence data was generated for 230 L. maculans isolates collected between 2020 and 2022 across the canola production regions of the Western Cape of South Africa. A total of 27 419 informative single nucleotide polymorphisms was used to investigate the genetic diversity and structure of the pathogen population.

RESULTS

Mating type distribution did not deviate statistically from a 1:1 ratio at any location, indicating no restriction on sexual reproduction. Genetic statistics calculated showed high genotypic diversity and evenness (Lambda and E.5 ≥ 0.98) and low linkage disequilibrium ( ≤ 2.71E-04) which is also associated with sexual reproduction. Discriminative analysis of principal components and sparse nonnegative matrix factorisation revealed genetic differentiation between the Swartland and Southern Cape canola production regions in the Western Cape. Analysis of molecular variance also indicated regions as the most important factor for population differentiation but suggested shallow population structure with only 3,71% of the total variation occurring between regions. To assess the phylogenomic position of South African isolates in the global context, data for 171 international isolates was included, and the clustering analyses repeated. Results showed a high similarity between Australian and Swartland isolates, while isolates from the Southern Cape formed a unique genetic cluster.

CONCLUSION

The results from this study provide the basis for blackleg research in South Africa and enhances understanding of the pathogen, which will assist in developing improved blackleg management strategies.

Artificial Intelligence: A Promising Tool in Exploring the Phytomicrobiome in Managing Disease and Promoting Plant Health

There is increasing interest in harnessing the microbiome to improve cropping systems. With the availability of high-throughput and low-cost sequencing technologies, gathering microbiome data is becoming more routine. However, the analysis of microbiome data is challenged by the size and complexity of the data, and the incomplete nature of many microbiome databases. Further, to bring microbiome data value, it often needs to be analyzed in conjunction with other complex data that impact on crop health and disease management, such as plant genotype and environmental factors. Artificial intelligence (AI), boosted through deep learning (DL), has achieved significant breakthroughs and is a powerful tool for managing large complex datasets such as the interplay between the microbiome, crop plants, and their environment. In this review, we aim to provide readers with a brief introduction to AI techniques, and we introduce how AI has been applied to areas of microbiome sequencing taxonomy, the functional annotation for microbiome sequences, associating the microbiome community with host traits, designing synthetic communities, genomic selection, field phenotyping, and disease forecasting. At the end of this review, we proposed further efforts that are required to fully exploit the power of AI in studying phytomicrobiomes.

Independent breakdown events of the Brassica napus Rlm7 resistance gene including via the off-target impact of a dual-specificity avirulence interaction

Protection of many crops is achieved through the use of genetic resistance. Leptosphaeria maculans, the causal agent of blackleg disease of Brassica napus, has emerged as a model for understanding gene-for-gene interactions that occur between plants and pathogens. Whilst many of the characterized avirulence effector genes interact with a single resistance gene in the host, the AvrLm4-7 avirulence gene is recognized by two resistance genes, Rlm4 and Rlm7. Here, we report the "breakdown" of the Rlm7 resistance gene in Australia, under two different field conditions. The first, and more typical, breakdown probably resulted from widescale use of Rlm7-containing cultivars whereby selection has led to an increase of individuals in the L. maculans population that have undergone repeat-induced point (RIP) mutations at the AvrLm4-7 locus. This has rendered the AvrLm4-7 gene ineffective and therefore these isolates have become virulent towards both Rlm4 and Rlm7. The second, more atypical, situation was the widescale use of Rlm4 cultivars. Whilst a single-nucleotide polymorphism is the more common mechanism of virulence towards Rlm4, in this field situation, RIP mutations have been selected leading to the breakdown of resistance for both Rlm4 and Rlm7. This is an example of a resistance gene being rendered ineffective without having grown cultivars with the corresponding resistance gene due to the dual specificity of the avirulence gene. These findings highlight the value of pathogen surveillance in the context of expanded knowledge about potential complexities for Avr-R interactions for the deployment of appropriate resistance gene strategies.

The Pid Family Has Been Diverged into Xian and Geng Type Resistance Genes against Rice Blast Disease

Rice blast (the causative agent the fungus Magnaporthe oryzae) represents a major constraint on the productivity of one of the world’s most important staple food crops. Genes encoding resistance have been identified in both the Xian and Geng subspecies genepools, and combining these within new cultivars represents a rational means of combating the pathogen. In this research, deeper allele mining was carried out on Pid2, Pid3, and Pid4 via each comprehensive FNP marker set in three panels consisting of 70 Xian and 58 Geng cultivars. Within Pid2, three functional and one non-functional alleles were identified; the former were only identified in Xian type entries. At Pid3, four functional and one non-functional alleles were identified; once again, all of the former were present in Xian type entries. However, the pattern of variation at Pid4 was rather different: here, the five functional alleles uncovered were dispersed across the Geng type germplasm. Among all the twelve candidate functional alleles, both Pid2-ZS and Pid3-ZS were predominant. Furthermore, the resistance functions of both Pid2-ZS and Pid3-ZS were assured by transformation test. Profiting from the merits of three comprehensive FNP marker sets, the study has validated all three members of the Pid family as having been strictly diverged into Xian and Geng subspecies: Pid2 and Pid3 were defined as Xian type resistance genes, and Pid4 as Geng type. Rather limited genotypes of the Pid family have been effective in both Xian and Geng rice groups, of which Pid2-ZS_Pid3-ZS has been central to the Chinese rice population.

Efficacy of Blackleg Major Resistance Genes in B. napus in Germany

Leptosphaeria maculans is one of the major pathogens of oilseed rape (B. napus). It causes blackleg disease, which accounts for significant yield losses worldwide. Using cultivars that harbor major resistance (R) genes is one of the most effective control methods. However, the efficacy of major R genes is related to the frequency of the corresponding avirulence (Avr) genes in a L. maculans population. In this paper, we report the Avr profiles of L. maculans populations and the ratio of its mating types in Northern and Central regions of Germany. Eleven Avr genes in five-hundred and seventy-four isolates were characterized either by applying cotyledon tests on a B. napus differential set or by amplifying avirulence gene-specific PCR markers. Fifty-two races were determined, among which the most dominant race was Avrlm6, -7, -11, AvrlepR1, -R2. Results showed that the resistance gene Rlm2 is 100% ineffective, some other major R genes such as Rlm1, Rlm3, Rlm4 and LepR3 are partially effective (with corresponding Avr frequencies ≤ 42%), while LepR1, LepR2, Rlm6, Rlm11 and Rlm7 can still provide relatively effective resistance in the German fields investigated (with corresponding Avr frequencies of 63-100%). Sexual reproduction is a factor that enhances the potential of L. maculans to evolve under selection pressure. Mating types of the L. maculans populations did not deviate from the ratio of 1:1 in the examined regions, indicating that sexual reproduction and ascospores play central roles in the L. maculans lifecycle. Overall, this study provides an important dataset for the establishment of a strategic plan to preserve the efficacies of major R genes in Germany by applying cultivar rotations of oilseed rape.

Leptosphaeria maculans-Brassica napus Battle: A Comparison of Incompatible vs. Compatible Interactions Using Dual RNASeq

Leptosphaeria maculans causes blackleg disease, which is one of the most destructive diseases of canola (Brassica napus L.). Due to the erosion of the current resistance in B. napus, it is pivotal to introduce new resistant genotypes to the growers. This study evaluated the potential of Rlm7 gene as resistance to its corresponding avirulence AvrLm7 gene is abundant. The Rlm7 line was inoculated with L. maculans isolate with AvrLm7; UMAvr7; and the CRISPR/Cas9 knockout AvrLm7 mutant, umavr7, of the same isolate to cause incompatible and compatible interactions, respectively. Dual RNA-seq showed differential gene expressions in both interactions. High expressions of virulence-related pathogen genes-CAZymes, merops, and effector proteins after 7-dpi in compatible interactions but not in incompatible interaction—confirmed that the pathogen was actively virulent only in compatible interactions. Salicyclic and jasmonic acid biosynthesis and signaling-related genes, defense-related PR1 gene (GSBRNA2T00150001001), and GSBRNA2T00068522001 in the NLR gene family were upregulated starting as early as 1- and 3-dpi in the incompatible interaction and the high upregulation of those genes after 7-dpi in compatible interactions confirmed the early recognition of the pathogen by the host and control it by early activation of host defense mechanisms in the incompatible interaction.

Remarkable recent changes in the genetic diversity of the avirulence gene AvrStb6 in global populations of the wheat pathogen Zymoseptoria tritici

Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is one of the most economically important diseases of wheat. Recently, both factors of a gene-for-gene interaction between Z. tritici and wheat, the wheat receptor-like kinase Stb6 and the Z. tritici secreted effector protein AvrStb6, have been identified. Previous analyses revealed a high diversity of AvrStb6 haplotypes present in earlier Z. tritici isolate collections, with up to c.18% of analysed isolates possessing the avirulence isoform of AvrStb6 identical to that originally identified in the reference isolate IPO323. With Stb6 present in many commercial wheat cultivars globally, we aimed to assess potential changes in AvrStb6 genetic diversity and the incidence of haplotypes allowing evasion of Stb6-mediated resistance in more recent Z. tritici populations. Here we show, using targeted resequencing of AvrStb6, that this gene is universally present in field isolates sampled from major wheat-growing regions of the world in 2013-2017. However, in contrast to the data from previous AvrStb6 population studies, we report a complete absence of the originally described avirulence isoform of AvrStb6 amongst modern Z. tritici isolates. Moreover, a remarkably small number of haplotypes, each encoding AvrStb6 protein isoforms conditioning virulence on Stb6-containing wheat, were found to predominate among modern Z. tritici isolates. A single virulence isoform of AvrStb6 was found to be particularly abundant throughout the global population. These findings indicate that, despite the ability of Z. tritici to sexually reproduce on resistant hosts, AvrStb6 avirulence haplotypes tend to be eliminated in subsequent populations.

Validating the Strategic Deployment of Blackleg Resistance Gene Groups in Commercial Canola Fields on the Canadian Prairies

Blackleg, caused by the fungal pathogen Leptosphaeria maculans, is a serious threat to canola (Brassica napus L.) production in western Canada. Crop scouting and extended crop rotation, along with the use of effective genetic resistance, have been key management practices available to mitigate the impact of the disease. In recent years, new pathogen races have reduced the effectiveness of some of the resistant cultivars deployed. Strategic deployment and rotation of major resistance (R) genes in cultivars have been used in France and Australia to help increase the longevity of blackleg resistance. Canada also introduced a grouping system in 2017 to identify blackleg R genes in canola cultivars. The main objective of this study was to examine and validate the concept of R gene deployment through monitoring the avirulence (Avr) profile of L. maculans population and disease levels in commercial canola fields within the Canadian prairies. Blackleg disease incidence and severity was collected from 146 cultivars from 53 sites across Manitoba, Saskatchewan, and Alberta in 2018 and 2019, and the results varied significantly between gene groups, which is likely influenced by the pathogen population. Isolates collected from spring and fall stubble residues were examined for the presence of Avr alleles AvrLm1, AvrLm2, AvrLm3, AvrLm4, AvrLm5, AvrLm6, AvrLm7, AvrLm9, AvrLm10, AvrLm11, AvrLepR1, AvrLepR2, AvrLep3, and AvrLmS using a set of differential host genotypes carrying known resistance genes or PCR-based markers. The Simpson's evenness index was very low, due to two dominant L. maculans races (AvrLm2-4-5-6-7-10-11 and AvrLm2-5-6-7-10-11) representing 49% of the population, but diversity of the population was high from the 35 L. maculans races isolated in Manitoba. AvrLm6 and AvrLm11 were found in all 254 L. maculans isolates collected in Manitoba. Knowledge of the blackleg disease levels in relation to the R genes deployed, along with the L. maculans Avr profile, helps to measure the effectiveness of genetic resistance.

Leptosphaeria maculans Isolates Reveal Their Allele Frequency in Western Canada

Blackleg, caused by Leptosphaeria maculans, is a major disease of canola in Canada, Australia, and Europe. For effective deployment of resistant varieties and disease management, it is crucial to understand the population structure of L. maculans. In this study, we analyzed L. maculans isolates from commercial fields in western Canada from 2014 to 2016 for the presence and frequency of avirulence (Avr) genes. A total of 1,584 isolates were examined for the presence of Avr genes AvrLm1, AvrLm2, AvrLm3, AvrLm4, AvrLm6, AvrLm7, AvrLm9, AvrLepR1, AvrLepR2, and AvrLmS via a set of differential host genotypes carrying known resistance genes and a PCR assay. Several Avr genes showed a higher frequency in the pathogen population, such as AvrLm6 and AvrLm7, which were present in >90% of isolates, whereas AvrLm3, AvrLm9, and AvrLepR2 showed frequencies of <10%. A total of 189 races (different combinations of Avr genes) were detected, with Avr-2-4-6-7-S, Avr-1-4-6-7, and Avr-2-4-6-7 as the three predominant races. When the effect of crop rotation was assessed, only a 3-year rotation showed a significantly higher frequency of AvrLm2 relative to shorter rotations. This study provides the information for producers to select effective canola varieties for blackleg management and for breeders to deploy new R genes in disease resistance breeding in western Canada.

Dynamics of the Rice Blast Fungal Population in the Field After Deployment of an Improved Rice Variety Containing Known Resistance Genes

Rice blast, caused by the fungus Magnaporthe oryzae, is one of the most destructive diseases of rice worldwide. Management through the deployment of host resistance genes would be facilitated by understanding the dynamics of the pathogen's population in the field. Here, to investigate the mechanism underlying the breakdown of disease resistance, we conducted a six-year field experiment to monitor the evolution of M. oryzae populations in Qujiang from Guangdong. The new variety of Xin-Yin-Zhan (XYZ) carrying R genes Pi50 and Pib was developed using the susceptible elite variety, Ma-Ba-Yin-Zhan (MBYZ), as the recurrent line. Field trials of disease resistance assessment revealed that the disease indices of XYZ in 2012, 2013, 2016, and 2017 were 0.19, 0.39, 0.70, and 0.90, respectively, indicating that XYZ displayed a very rapid increase of disease severity in the field. To investigate the mechanism underlying the quick erosion of resistance of XYZ, we collected isolates from both XYZ and MBYZ for pathogenicity testing against six different isogenic lines. The isolates collected from XYZ showed a similar virulence spectrum across four different years whereas those from MBYZ showed increasing virulence to the Pi50 and Pib isogenic lines from 2012 to 2017. Molecular analysis of AvrPib in the isolates from MBYZ identified four different AvrPib haplotypes, i.e., AvrPib-AP1-1, AvrPib-AP1-2, avrPib-AP2, and avrPib-AP3, verified by sequencing. AvrPib-AP1-1 and AvrPib-AP1-2 are avirulent to Pib whereas avrPib-AP2 and avrPib-AP3 are virulent. Insertions of a Pot3 and an Mg-SINE were identified in avrPib-AP2 and avrPib-AP3, respectively. Two major lineages based on rep-PCR analysis were further deduced in the field population, implying that the field population is composed of genetically related isolates. Our data suggest that clonal propagation and quick dominance of virulent isolates against the previously resistant variety could be the major genetic events contributing to the loss of varietal resistance against rice blast in the field.

Dynamics of Race Structures of Pyricularia oryzae Populations Across 18 Seasons in Guangdong Province, China

Rice blast, caused by Pyricularia oryzae, is one of the most damaging fungal diseases affecting rice. Understanding how the pathogen's race structure varies over time supports the efforts of rice breeders to develop improved cultivars. Here, the race structure of P. oryzae in Guangdong province, China, where rice is cropped twice per year, was assessed over 18 seasons from 1999 through 2008. The analysis was based on the reactions of a panel of seven differential Chinese cultivars to inoculation with a set of 1,248 isolates of P. oryzae in the province. The "total race frequency" parameter ranged from 14.7 to 39.7%, and the "race diversity index" ranged from 0.63 to 0.93. Twelve (ZA63, ZA31, ZA29, ZA21, ZA13, ZA9, ZB30, ZB17, ZB8, ZB2, ZC14, and ZC8) and two (ZD8 and ZD3) races were recognized as specific to indica and japonica rice types, respectively. Of the 59 distinct races identified, only two indica type races (ZC13 and ZC15) were identified as population-common, and nine indica type races (ZB1, ZB5, ZB6, ZB7, ZB13, ZB15, ZC5, ZC13, and ZC15) and one japonica type race (ZG1) were deemed to be population-dominant; the "total top two race isolate frequency" parameter ranged from 29.8 to 74.5%. On the host side, dynamics of resistance structures of the differential set were divided into three patterns: Both Tetep and Kanto 51 expressed the highest and most stable resistance, both Sifeng 43 and Lijiangxintuanheigu conveyed much lower and unstable resistance, and Zhenlong 13, Dongnong 363, and Heijiang 18 performed intermediate and seasonally dynamic resistance. Three interesting points distinguishing race structures of P. oryzae populations in southern and northeastern China were also discussed.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Development of a specific marker for detection of a functional AvrLm9 allele and validating the interaction between AvrLm7 and AvrLm9 in Leptosphaeria maculans

Blackleg, which is caused by the fungus Leptosphaeria maculans (L. maculans), is a major disease of canola in western Canada and worldwide. Long-term use of one source of resistance could cause the breakdown of its effectiveness. Therefore, appropriate use of R genes is very important, and knowledge about the distribution of avirulence genes is a prerequisite for effectively deploying resistance. Of the 14 avirulence genes identified in L. maculans, AvrLm5 and AvrLm9 were recognized as the two alleles of the same gene based on two single nucleotide polymorphisms, C⁸⁵T and G¹⁶⁴A/C. In this study, a specific marker was developed to identify AvrLm5 and AvrLm9 based on two single nucleotide polymorphisms, C⁸⁵T and G¹⁶⁴A/C, which are responsible for the function of AvrLm9. The specific marker can be used to discriminate the AvrLm9 from avrLm9 accurately in L. maculans isolates, which is consistent with inoculation tests in isolates without AvrLm4-7. This specific marker was used to screen 1229 isolates collected from fields in the years 2014 through 2016 in Manitoba. From 68 to 84% of the isolates were found to contain the AvrLm9 allele; while 4-7% of them were avirulent on the variety Goéland with Rlm9 loci. Furthermore, no isolates having both AvrLm9 and AvrLm7 were detected using a cotyledon test, while 67% to 84% of isolates contained both avirulence genes via PCR detection, implying suppression of AvrLm9 by AvrLm7. In addition, avirulence gene profiles of the other 10 avirulence alleles were examined with the 1229 isolates using cotyledon tests or PCR amplifications. Taken together, this research enables the fast identification of AvrLm5/9, provides the Avr genes' landscape of western Canada and elaborates the relationship between AvrLm9 and AvrLm7 using isolates from grower fields.

Generation and Characterization of a Virulent Leptosphaeria maculans Isolate Carrying a Mutated AvrLm7 Gene Using the CRISPR/Cas9 System

Blackleg, caused by the fungal pathogen Leptosphaeria maculans, is the most important disease affecting canola (Brassica napus) crops worldwide. We employed the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system to generate the mutant isolate umavr7 from a point mutation of the AvrLm7 coding region in a L. maculans isolate (UMAvr7). Reverse transcription PCR and transcriptome data confirmed that the AvrLm7 gene was knocked out in the mutant isolate. Pathogenicity tests indicated that umavr7 can cause large lesions on a set of Brassica differential genotypes that express different resistance (R) genes. Comparative pathogenicity tests between UMAvr7 (wild type) and umavr7 on the corresponding B. napus genotype 01-23-2-1 (with Rlm7) showed that umavr7 is a mutant isolate, producing large gray/green lesions on cotyledons. The pathogenicity of the mutant isolate was shifted from avirulent to virulent on the B. napus Rlm7 genotype. Therefore, this mutant is virulence on the identified resistant genes to blackleg disease in B. napus genotypes. Superoxide accumulated differently in cotyledons in response to infection with UMAvr7 and umavr7, especially in resistant B. napus genotype 01-23-2-1. Resistance/susceptibility was further evaluated on 123 B. napus genotypes with the mutant isolate, umavr7. Only 6 of the 123 genotypes showed resistance to umavr7. The identification of these six resistant B. napus genotypes will lead to further studies on the development of blackleg disease resistance through breeding and the identification of novel R genes.

Effect of Elevated CO2 Concentration on the Disease Severity of Compatible and Incompatible Interactions of Brassica napus-Leptosphaeria maculans Pathosystem

Global warming by increased atmospheric CO2 concentration has been widely accepted. Yet, there has not been any consistent conclusion on the doubled CO2 concentration that in the future will affect plant disease incidence and severity. Blackleg disease, mainly caused by Leptosphaeria maculans, is a major disease on canola production globally. Brassica napus and L. maculans have a gene-for-gene interaction, which causes an incompatible reaction between canola plants carrying resistance genes and L. maculans isolates carrying corresponding avirulence genes. In this study, B. napus varieties and lines inoculated with different Leptosphaeria isolates were subjected to simulated growth conditions, namely, growth chambers with normal environments and with controlled CO2 concentrations of 400, 600, and 800 ppm. The results indicated that the elevated CO2 concentrations have no noticeable effect on the inferred phenotypes of the canola-blackleg interactions. However, the disease severity decreased in most of the B. napus-L. maculans interactions at extremely high CO2 concentration (800 ppm). The varied pathogenicity changes of the B. napus-L. maculans pathosystem under elevated CO2 concentrations at 400 or 600 ppm may be due to the genetic background or physiological differences in plants and pathogenicity differences in L. maculans isolates having different Avr gene profiles. The mechanisms by which elevated CO2 concentrations affect the B. napus-L. maculans pathosystem will help us understand how climate change will impact crops and diseases.

Characterization of the Race Structure of Leptosphaeria maculans Causing Blackleg of Winter Canola in Oklahoma and Kansas

Blackleg, caused by the fungus Leptosphaeria maculans, is a widespread disease of winter canola (Brassica napus) in Oklahoma and Kansas. Deployment of genetic resistance is the primary strategy for managing blackleg. Resistance genes (Rlm) in canola interact with avirulence genes in the fungus (AvrLm) in a gene-for-gene manner. Little is known about the diversity and frequency of avirulence genes and the race structure in the region. Isolates of Leptosphaeria spp. were collected from diseased leaves in nine counties in Oklahoma and one county in Kansas from 2009 to 2013. Based on pathogenicity and PCR amplification of mating type and species-specific internal transcribed spacer loci, most isolates (n = 90) were L. maculans. The presence of avirulence genes was evaluated using phenotypic interactions on cotyledons of differential cultivars with Rlm1, Rlm2, Rlm3, and Rlm4 and amplification of AvrLm1, AvrLm4-7, and AvrLm6 by PCR. The avirulence alleles AvrLm6 and AvrLm7 were present in the entire L. maculans population. AvrLm1 was found in 34% of the population, AvrLm2 in 4%, and AvrLm4 in only 1%. A total of five races, defined as combinations of avirulence alleles, were identified that included AvrLm1-2-6-7, AvrLm2-6-7, AvrLm4-6-7, AvrLm1-6-7, and AvrLm6-7. Races virulent on the most Rlm genes, AvrLm1-6-7 at 32% and AvrLm6-7 at 62%, were predominant. Defining the avirulence allele frequency and race structure of L. maculans should be useful for the identification and development of resistant cultivars and hybrids for blackleg management in the region. The results suggest that Rlm6 and Rlm7 would be effective, although their deployment should be integrated with quantitative resistance and cultural practices, such as crop rotation, that limit selection pressure on Rlm genes.