Assessing quantitative resistance against Leptosphaeria maculans (phoma stem canker) in Brassica napus (oilseed rape) in young plants

Breeding and management of major resistance genes to stem canker/blackleg in Brassica crops

Blackleg (also known as Phoma or stem canker) is a major, worldwide disease of Brassica crop species, notably B. napus (rapeseed, canola), caused by the ascomycete fungus Leptosphaeria maculans. The outbreak and severity of this disease depend on environmental conditions and management practices, as well as a complex interaction between the pathogen and its hosts. Genetic resistance is a major method to control the disease (and the only control method in some parts of the world, such as continental Europe), but efficient use of genetic resistance is faced with many difficulties: (i) the scarcity of germplasm/genetic resources available, (ii) the different history of use of resistance genes in different parts of the world and the different populations of the fungus the resistance genes are exposed to, (iii) the complexity of the interactions between the plant and the pathogen that expand beyond typical gene-for-gene interactions, (iv) the incredible evolutionary potential of the pathogen and the importance of knowing the molecular processes set up by the fungus to "breakdown' resistances, so that we may design high-throughput diagnostic tools for population surveys, and (v) the different strategies and options to build up the best resistances and to manage them so that they are durable. In this paper, we aim to provide a comprehensive overview of these different points, stressing the differences between the different continents and the current prospects to generate new and durable resistances to blackleg disease.

Effective control of Leptosphaeria maculans increases importance of L. biglobosa as a cause of phoma stem canker epidemics on oilseed rape

BACKGROUND

Phoma stem canker is a damaging disease of oilseed rape caused by two related fungal species, Leptosphaeria maculans and L. biglobosa. However, previous work has mainly focused on L. maculans and there has been little work on L. biglobosa. This work provides evidence of the importance of L. biglobosa to stem canker epidemics in the UK.

RESULTS

Quantification of L. maculans and L. biglobosa DNA using species-specific quantitative PCR showed that L. biglobosa caused both upper stem lesions and stem base cankers on nine oilseed rape cultivars in the UK. Upper stem lesions were mainly caused by L. biglobosa. For stem base cankers, there was more L. maculans DNA than L. biglobosa DNA in the susceptible cultivar Drakkar, while there was more L. biglobosa DNA than L. maculans DNA in cultivars with the resistance gene Rlm7 against L. maculans. The frequency of L. biglobosa detected in stem base cankers increased from 14% in 2000 to 95% in 2013. Ascospores of L. biglobosa and L. maculans were mostly released on the same days and the number of L. biglobosa ascospores in air samples increased from the 2010/2011 to 2012/2013 growing seasons.

CONCLUSION

Effective control of L. maculans increased infection by L. biglobosa, causing severe upper stem lesions and stem base cankers, leading to yield losses. The importance of L. biglobosa to phoma stem canker epidemics can no longer be ignored. Effective control of phoma stem canker epidemics needs to target both L. maculans and L. biglobosa. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Efficient qPCR estimation and discrimination of airborne inoculum of Leptosphaeria maculans and L. biglobosa, the causal organisms of phoma leaf spotting and stem canker of oilseed rape

BACKGROUND

Detection of the inoculum of phytopathogens greatly assists in the management of diseases, but is difficult for pathogens with airborne fungal propagules. Here, we present experiments to determine the abundance and distribution frequencies of the ascospores of Leptosphaeria (Plenodomus) species that were collected on the tapes of volumetric Hirst-type traps near oilseed rape fields in Poznan, Poland and Harpenden, UK. Fungal detection and species discrimination were achieved using a SYBR-Green quantitative polymerase chain reaction (qPCR) with two different pairs of primers previously reported to differentiate Leptosphaeria maculans (Plenodomus lingam) or L. biglobosa (P. biglobosus).

RESULTS

Detection was successful even at fewer than five spores per m3 of air. The primer pairs differed in the correlation coefficients obtained between DNA yields and the daily abundance of ascospores that were quantified by microscopy on duplicate halves of the spore trap tapes. Important differences in the specificity and sensitivity of the published SYBR-Green assays were also found, indicating that the Liu primers did not detect L. biglobosa subclade 'canadensis', whereas the Mahuku primers detected L. biglobosa subclade 'canadensis' and also the closely related Plenodomus dezfulensis.

CONCLUSIONS

Comparisons confirmed that application of qPCR assays to spore trap samples can be used for the early detection, discrimination and quantification of aerially dispersed L. maculans and L. biglobosa propagules before leaf spot symptoms are visible in winter oilseed rape fields. The specificity of the primers must be taken into consideration because the final result will greatly depend on the local population of the pathogen. © 2023 Society of Chemical Industry.

Co-inoculation timing affects the interspecific interactions between phoma stem canker pathogens Leptosphaeria maculans and Leptosphaeria biglobosa

BACKGROUND

Phoma stem canker is an economically important disease of oilseed rape, caused by two co-existing fungal pathogen species, Leptosphaeria maculans (Plenodomus lingam) and Leptosphaeria biglobosa (Plenodomus biglobosus). Leptosphaeria maculans produces a phytotoxin called sirodesmin PL. Our previous work showed that L. biglobosa has an antagonistic effect on the production of sirodesmin PL if it is simultaneously co-inoculated with L. maculans. However, the effects of sequential co-inoculation on interspecific interactions between the two pathogens are not understood.

RESULTS

The interactions between L. maculans and L. biglobosa were investigated in liquid culture by inoculation with L. maculans first, followed by L. biglobosa sequentially at 1, 3, 5 or 7 days later and vice versa; the controls were inoculated with L. maculans only, L. biglobosa only, or L. maculans and L. biglobosa simultaneously. The results showed that L. biglobosa inhibited the growth of L. maculans, the production of both sirodesmin PL and its precursors if L. biglobosa was inoculated before, or simultaneously with, L. maculans. However, the antagonistic effects of L. biglobosa were lost if it was co-inoculated 5 or 7 days after L. maculans.

CONCLUSION

For the first time, the results of this study provided evidence that the timing when L. maculans and L. biglobosa meet significantly influences the outcome of the interspecific competition between them. Leptosphaeria biglobosa can inhibit the production of sirodesmin PL and the growth of L. maculans if it is inoculated before L. maculans or less than 3 days after L. maculans in liquid culture. There is a need to further investigate the timing of co-inoculation on interactions between L. maculans and L. biglobosa in their host plants for improving the control of phoma stem canker. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Identification of candidate genes for LepR1 resistance against Leptosphaeria maculans in Brassica napus

Utilising resistance (R) genes, such as LepR1, against Leptosphaeria maculans, the causal agent of blackleg in canola (Brassica napus), could help manage the disease in the field and increase crop yield. Here we present a genome wide association study (GWAS) in B. napus to identify LepR1 candidate genes. Disease phenotyping of 104 B. napus genotypes revealed 30 resistant and 74 susceptible lines. Whole genome re-sequencing of these cultivars yielded over 3 million high quality single nucleotide polymorphisms (SNPs). GWAS in mixed linear model (MLM) revealed a total of 2,166 significant SNPs associated with LepR1 resistance. Of these SNPs, 2108 (97%) were found on chromosome A02 of B. napus cv. Darmor bzh v9 with a delineated LepR1_mlm1 QTL at 15.11-26.08 Mb. In LepR1_mlm1, there are 30 resistance gene analogs (RGAs) (13 nucleotide-binding site-leucine rich repeats (NLRs), 12 receptor-like kinases (RLKs), and 5 transmembrane-coiled-coil (TM-CCs)). Sequence analysis of alleles in resistant and susceptible lines was undertaken to identify candidate genes. This research provides insights into blackleg resistance in B. napus and assists identification of the functional LepR1 blackleg resistance gene.

Molecular Interactions Between Leptosphaeria maculans and Brassica Species

Canola is an important oilseed crop, providing food, feed, and fuel around the world. However, blackleg disease, caused by the ascomycete Leptosphaeria maculans, causes significant yield losses annually. With the recent advances in genomic technologies, the understanding of the Brassica napus-L. maculans interaction has rapidly increased, with numerous Avr and R genes cloned, setting this system up as a model organism for studying plant-pathogen associations. Although the B. napus-L. maculans interaction follows Flor's gene-for-gene hypothesis for qualitative resistance, it also puts some unique spins on the interaction. This review discusses the current status of the host-pathogen interaction and highlights some of the future gaps that need addressing moving forward.

Orphan legumes: harnessing their potential for food, nutritional and health security through genetic approaches

Legumes, being angiosperm's third-largest family as well as the second major crop family, contributes beyond 33% of human dietary proteins. The advent of the global food crisis owing to major climatic concerns leads to nutritional deprivation, hunger and hidden hunger especially in developing and underdeveloped nations. Hence, in the wake of promoting sustainable agriculture and nutritional security, apart from the popular legumes, the inclusion of lesser-known and understudied local crop legumes called orphan legumes in the farming systems of various tropical and sub-tropical parts of the world is indeed a need of the hour. Despite possessing tremendous potentialities, wide adaptability under diverse environmental conditions, and rich in nutritional and nutraceutical values, these species are still in a neglected and devalued state. Therefore, a major re-focusing of legume genetics, genomics, and biology is much crucial in pursuance of understanding the yield constraints, and endorsing underutilized legume breeding programs. Varying degrees of importance to these crops do exist among researchers of developing countries in establishing the role of orphan legumes as future crops. Under such circumstances, this article assembles a comprehensive note on the necessity of promoting these crops for further investigations and sustainable legume production, the exploitation of various orphan legume species and their potencies. In addition, an attempt has been made to highlight various novel genetic, molecular, and omics approaches for the improvement of such legumes for enhancing yield, minimizing the level of several anti-nutritional factors, and imparting biotic and abiotic stress tolerance. A significant genetic enhancement through extensive research in 'omics' areas is the absolute necessity to transform them into befitting candidates for large-scale popularization around the globe.

Influence of Elevated Temperatures on Resistance Against Phoma Stem Canker in Oilseed Rape

Cultivar resistance is an important tool in controlling pathogen-related diseases in agricultural crops. As temperatures increase due to global warming, temperature-resilient disease resistance will play an important role in crop protection. However, the mechanisms behind the temperature-sensitivity of the disease resistance response are poorly understood in crop species and little is known about the effect of elevated temperatures on quantitative disease resistance. Here, we investigated the effect of temperature increase on the quantitative resistance of Brassica napus against Leptosphaeria maculans. Field experiments and controlled environment inoculation assays were done to determine the influence of temperature on R gene-mediated and quantitative resistance against L. maculans; of specific interest was the impact of high summer temperatures on the severity of phoma stem canker. Field experiments were run for three consecutive growing seasons at various sites in England and France using twelve winter oilseed rape breeding lines or cultivars with or without R genes and/or quantitative resistance. Stem inoculation assays were done under controlled environment conditions with four cultivars/breeding lines, using avirulent and virulent L. maculans isolates, to determine if an increase in ambient temperature reduces the efficacy of the resistance. High maximum June temperature was found to be related to phoma stem canker severity. No temperature effect on stem canker severity was found for the cultivar ES Astrid (with only quantitative resistance with no known R genes). However, in the controlled environmental conditions, the cultivar ES Astrid had significantly smaller amounts of necrotic tissue at 20°C than at 25°C. This suggests that, under a sustained temperature of 25°C, the efficacy of quantitative resistance is reduced. Findings from this study show that temperature-resilient quantitative resistance is currently available in some oilseed cultivars and that efficacy of quantitative resistance is maintained at increased temperature but not when these elevated temperatures are sustained for a long period.

Comparison of non-subjective relative fungal biomass measurements to quantify the Leptosphaeria maculans-Brassica napus interaction

BACKGROUND

Blackleg disease, caused by the fungal pathogen Leptosphaeria maculans, is a serious threat to canola (Brassica napus) production worldwide. Quantitative resistance to this disease is a highly desirable trait but is difficult to precisely phenotype. Visual scores can be subjective and are prone to assessor bias. Methods to assess variation in quantitative resistance more accurately were developed based on quantifying in planta fungal biomass, including the Wheat Germ Agglutinin Chitin Assay (WAC), qPCR and ddPCR assays.

RESULTS

Disease assays were conducted by inoculating a range of canola cultivars with L. maculans isolates in glasshouse experiments and assessing fungal biomass in cotyledons, petioles and stem tissue harvested at different timepoints post-inoculation. PCR and WAC assay results were well correlated, repeatable across experiments and host tissues, and able to differentiate fungal biomass in different host-isolate treatments. In addition, the ddPCR assay was shown to differentiate between L. maculans isolates.

CONCLUSIONS

The ddPCR assay is more sensitive in detecting pathogens and more adaptable to high-throughput methods by using robotic systems than the WAC assay. Overall, these methods proved accurate and non-subjective, providing alternatives to visual assessments to quantify the L. maculans-B. napus interaction in all plant tissues throughout the progression of the disease in seedlings and mature plants and have potential for fine-scale blackleg resistance phenotyping in canola.

Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene Rlm9 in Elite Brassica napus

Blackleg is one of the major fungal diseases in oilseed rape/canola worldwide. Most commercial cultivars carry R gene-mediated qualitative resistances that confer a high level of race-specific protection against Leptosphaeria maculans, the causal fungus of blackleg disease. However, monogenic resistances of this kind can potentially be rapidly overcome by mutations in the pathogen's avirulence genes. To counteract pathogen adaptation in this evolutionary arms race, there is a tremendous demand for quantitative background resistance to enhance durability and efficacy of blackleg resistance in oilseed rape. In this study, we characterized genomic regions contributing to quantitative L. maculans resistance by genome-wide association studies in a multiparental mapping population derived from six parental elite varieties exhibiting quantitative resistance, which were all crossed to one common susceptible parental elite variety. Resistance was screened using a fungal isolate with no corresponding avirulence (AvrLm) to major R genes present in the parents of the mapping population. Genome-wide association studies revealed eight significantly associated quantitative trait loci (QTL) on chromosomes A07 and A09, with small effects explaining 3-6% of the phenotypic variance. Unexpectedly, the qualitative blackleg resistance gene Rlm9 was found to be located within a resistance-associated haploblock on chromosome A07. Furthermore, long-range sequence data spanning this haploblock revealed high levels of single-nucleotide and structural variants within the Rlm9 coding sequence among the parents of the mapping population. The results suggest that novel variants of Rlm9 could play a previously unknown role in expression of quantitative disease resistance in oilseed rape.

Engineering Multigenerational Host-Modulated Microbiota against Soilborne Pathogens in Response to Global Climate Change

Crop migration caused by climatic events has favored the emergence of new soilborne diseases, resulting in the colonization of new niches (emerging infectious diseases, EIDs). Soilborne pathogens are extremely persistent in the environment. This is in large part due to their ability to reside in the soil for a long time, even without a host plant, using survival several strategies. In this regard, disease-suppressive soils, characterized by a low disease incidence due to the presence of antagonist microorganisms, can be an excellent opportunity for the study mechanisms of soil-induced immunity, which can be applied in the development of a new generation of bioinoculants. Therefore, here we review the main effects of climate change on crops and pathogens, as well as the potential use of soil-suppressive microbiota as a natural source of biocontrol agents. Based on results of previous studies, we also propose a strategy for the optimization of microbiota assemblages, selected using a host-mediated approach. This process involves an increase in and prevalence of specific taxa during the transition from a conducive to a suppressive soil. This strategy could be used as a model to engineer microbiota assemblages for pathogen suppression, as well as for the reduction of abiotic stresses created due to global climate change.

A gene-for-gene interaction involving a 'late' effector contributes to quantitative resistance to the stem canker disease in Brassica napus

The control of stem canker disease of Brassica napus (rapeseed), caused by the fungus Leptosphaeria maculans is based largely on plant genetic resistance: single-gene specific resistance (Rlm genes) or quantitative, polygenic, adult-stage resistance. Our working hypothesis was that quantitative resistance partly obeys the gene-for-gene model, with resistance genes 'recognizing' fungal effectors expressed during late systemic colonization. Five LmSTEE (stem-expressed effector) genes were selected and placed under the control of the AvrLm4-7 promoter, an effector gene highly expressed at the cotyledon stage of infection, for miniaturized cotyledon inoculation test screening of a gene pool of 204 rapeseed genotypes. We identified a rapeseed genotype, 'Yudal', expressing hypersensitive response to LmSTEE98. The LmSTEE98-RlmSTEE98 interaction was further validated by inactivation of the LmSTEE98 gene with a CRISPR-Cas9 approach. Isolates with mutated versions of LmSTEE98 induced more severe stem symptoms than the wild-type isolate in 'Yudal'. This single-gene resistance was mapped in a 0.6 cM interval of the 'Darmor_bzh' × 'Yudal' genetic map. One typical gene-for-gene interaction contributes partly to quantitative resistance when L. maculans colonizes the stems of rapeseed. With numerous other effectors specific to stem colonization, our study provides a new route for resistance gene discovery, elucidation of quantitative resistance mechanisms and selection for durable resistance.

Genome-wide transcriptome reveals mechanisms underlying Rlm1-mediated blackleg resistance on canola

Genetic resistance to blackleg (Leptosphaeria maculans, Lm) of canola (Brassica napus, Bn) has been extensively studied, but the mechanisms underlying the host-pathogen interaction are still not well understood. Here, a comparative transcriptome analysis was performed on a resistant doubled haploid Bn line carrying the resistance gene Rlm1 following inoculation with a virulent (avrLm1) or avirulent (AvrLm1) Lm isolate on cotyledons. A total of 6999 and 3015 differentially expressed genes (DEGs) were identified, respectively, in inoculated local tissues with compatible (susceptible) and incompatible (resistant) interactions. Functional enrichment analysis found several biological processes, including protein targeting to membrane, ribosome and negative regulation of programmed cell death, were over-represented exclusively among up-regulated DEGs in the resistant reaction, whereas significant enrichment of salicylic acid (SA) and jasmonic acid (JA) pathways observed for down-regulated DEGs occurred only in the susceptible reaction. A heat-map analysis showed that both biosynthesis and signaling of SA and JA were induced more significantly in the resistant reaction, implying that a threshold level of SA and JA signaling is required for the activation of Rlm1-mediated resistance. Co-expression network analysis revealed close correlation of a gene module with the resistance, involving DEGs regulating pathogen-associated molecular pattern recognition, JA signaling and transcriptional reprogramming. Substantially fewer DEGs were identified in mock-inoculated (control) cotyledons, relative to those in inoculated local tissues, including those involved in SA pathways potentially contributing to systemic acquired resistance (SAR). Pre-inoculation of cotyledon with either an avirulent or virulent Lm isolate, however, failed to induce SAR on remote tissues of same plant despite elevated SA and PR1 protein. This study provides insights into the molecular mechanism of Rlm1-mediated resistance to blackleg.

Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives

Among the Brassica oilseeds, canola (Brassica napus) is the most economically significant globally. However, its production can be limited by blackleg disease, caused by the fungal pathogen Lepstosphaeria maculans. The deployment of resistance genes has been implemented as one of the key strategies to manage the disease. Genetic resistance against blackleg comes in two forms: qualitative resistance, controlled by a single, major resistance gene (R gene), and quantitative resistance (QR), controlled by numerous, small effect loci. R-gene-mediated blackleg resistance has been extensively studied, wherein several genomic regions harbouring R genes against L. maculans have been identified and three of these genes were cloned. These studies advance our understanding of the mechanism of R gene and pathogen avirulence (Avr) gene interaction. Notably, these studies revealed a more complex interaction than originally thought. Advances in genomics help unravel these complexities, providing insights into the genes and genetic factors towards improving blackleg resistance. Here, we aim to discuss the existing R-gene-mediated resistance, make a summary of candidate R genes against the disease, and emphasise the role of players involved in the pathogenicity and resistance. The comprehensive result will allow breeders to improve resistance to L. maculans, thereby increasing yield.

Inheritance Pattern and Molecular Markers for Resistance to Blackleg Disease in Cabbage

The inheritance and causal loci for resistance to blackleg, a devastating disease of Brassicaceous crops, are yet to be known in cabbage (Brassica oleracea L.). Here, we report the pattern of inheritance and linked molecular marker for this trait. A segregating BC₁ population consisting of 253 plants was raised from resistant and susceptible parents, L29 (♀) and L16 (♂), respectively. Cotyledon resistance bioassay of BC₁ population, measured based on a scale of 0-9 at 12 days after inoculation with Leptosphaeria maculans isolate 03-02 s, revealed the segregation of resistance and ratio, indicative of dominant monogenic control of the trait. Investigation of potential polymorphism in the previously identified differentially expressed genes within the collinear region of 'B. napus blackleg resistant loci Rlm1' in B. oleracea identified two insertion/deletion (InDel) mutations in the intron and numerous single nucleotide polymorphisms (SNPs) throughout the LRR-RLK gene Bol040029, of which six SNPs in the first exon caused the loss of two LRR domains in the susceptible line. An InDel marker, BLR-C-InDel based on the InDel mutations, and a high resolution melting (HRM) marker, BLR-C-2808 based on the SNP C²⁸⁰⁸T in the second exon were developed, which predicated the resistance status of the BC₁ population with 80.24%, and of 24 commercial inbred lines with 100% detection accuracy. This is the first report of inheritance and molecular markers linked with blackleg resistance in cabbage. This study will enhance our understanding of the trait, and will be helpful in marker assisted breeding aiming at developing resistant cabbage varieties.

Oilseed rape (Brassica napus) resistance to growth of Leptosphaeria maculans in leaves of young plants contributes to quantitative resistance in stems of adult plants

Key message: One QTL for resistance against Leptosphaeria maculans growth in leaves of young plants in controlled environments overlapped with one QTL detected in adult plants in field experiments. The fungal pathogen Leptosphaeria maculans initially infects leaves of oilseed rape (Brassica napus) in autumn in Europe and then grows systemically from leaf lesions along the leaf petiole to the stem, where it causes damaging phoma stem canker (blackleg) in summer before harvest. Due to the difficulties of investigating resistance to L. maculans growth in leaves and petioles under field conditions, identification of quantitative resistance typically relies on end of season stem canker assessment on adult plants. To investigate whether quantitative resistance can be detected in young plants, we first selected nine representative DH (doubled haploid) lines from an oilseed rape DY ('Darmor-bzh' × 'Yudal') mapping population segregating for quantitative resistance against L. maculans for controlled environment experiment (CE). We observed a significant correlation between distance grown by L. maculans along the leaf petiole towards the stem (r = 0.91) in CE experiments and the severity of phoma stem canker in field experiments. To further investigate quantitative trait loci (QTL) related to resistance against growth of L. maculans in leaves of young plants in CE experiments, we selected 190 DH lines and compared the QTL detected in CE experiments with QTL related to stem canker severity in stems of adult plants in field experiments. Five QTL for resistance to L. maculans growth along the leaf petiole were detected; collectively they explained 35% of the variance. Two of these were also detected in leaf lesion area assessments and each explained 10-12% of the variance. One QTL on A02 co-localized with a QTL detected in stems of adult plants in field experiments. This suggests that resistance to the growth of L. maculans from leaves along the petioles towards the stems contributes to the quantitative resistance assessed in stems of adult plants in field experiments at the end of the growing season.

Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses

Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.

Stable Quantitative Resistance Loci to Blackleg Disease in Canola (Brassica napus L.) Over Continents

The hemibiotrophic fungus, Leptosphaeria maculans is the most devastating pathogen, causing blackleg disease in canola (Brassica napus L). To study the genomic regions involved in quantitative resistance (QR), 259-276 DH lines from Darmor-bzh/Yudal (DYDH) population were assessed for resistance to blackleg under shade house and field conditions across 3 years. In different experiments, the broad sense heritability varied from 43 to 95%. A total of 27 significant quantitative trait loci (QTL) for QR were detected on 12 chromosomes and explained between 2.14 and 10.13% of the genotypic variance. Of the significant QTL, at least seven were repeatedly detected across different experiments on chromosomes A02, A07, A09, A10, C01, and C09. Resistance alleles were mainly contributed by 'Darmor-bzh' but 'Yudal' also contributed few of them. Our results suggest that plant maturity and plant height may have a pleiotropic effect on QR in our conditions. We confirmed that Rlm9 which is present in 'Darmor-bzh' is not effective to confer resistance in our Australian field conditions. Comparative mapping showed that several R genes coding for nucleotide-binding leucine-rich repeat (LRR) receptors map in close proximity (within 200 Kb) of the significant trait-marker associations on the reference 'Darmor-bzh' genome assembly. More importantly, eight significant QTL regions were detected across diverse growing environments: Australia, France, and United Kingdom. These stable QTL identified herein can be utilized for enhancing QR in elite canola germplasm via marker- assisted or genomic selection strategies.

Effectiveness of Rlm7 resistance against Leptosphaeria maculans (phoma stem canker) in UK winter oilseed rape cultivars

The Rlm7 gene in Brassica napus is an important source of resistance for control of phoma stem canker on oilseed rape caused by the fungus Leptosphaeria maculans. This study shows the first report of L. maculans isolates virulent against Rlm7 in the UK. Leptosphaeria maculans isolates virulent against Rlm7 represented 3% of the pathogen population when cultivars with the Rlm7 gene represented 5% of the UK oilseed rape area in 2012/13. However, the Rlm7 gene has been widely used since then, representing >15% of the UK oilseed rape area in 2015/16. Winter oilseed rape field experiments included cultivars with the Rlm7 gene, with the Rlm4 gene or without Rlm genes and took place at five sites in the UK over four cropping seasons. An increase in phoma leaf spotting severity on Rlm7 cultivars in successive seasons was observed. Major resistance genes played a role in preventing severe phoma leaf spotting at the beginning of the cropping season and, in addition, quantitative resistance (QR) in the cultivars examined made an important contribution to control of phoma stem canker development at the end of the cropping season. Deployment of the Rlm7 resistance gene against L. maculans in cultivars with QR in combination with sustainable disease management practices will prolong the use of this gene for effective control of phoma stem canker epidemics.

Multi-year linkage and association mapping confirm the high number of genomic regions involved in oilseed rape quantitative resistance to blackleg

A repertoire of the genomic regions involved in quantitative resistance to Leptosphaeria maculans in winter oilseed rape was established from combined linkage-based QTL and genome-wide association (GWA) mapping. Linkage-based mapping of quantitative trait loci (QTL) and genome-wide association studies are complementary approaches for deciphering the genomic architecture of complex agronomical traits. In oilseed rape, quantitative resistance to blackleg disease, caused by L. maculans, is highly polygenic and is greatly influenced by the environment. In this study, we took advantage of multi-year data available on three segregating populations derived from the resistant cv Darmor and multi-year data available on oilseed rape panels to obtain a wide overview of the genomic regions involved in quantitative resistance to this pathogen in oilseed rape. Sixteen QTL regions were common to at least two biparental populations, of which nine were the same as previously detected regions in a multi-parental design derived from different resistant parents. Eight regions were significantly associated with quantitative resistance, of which five on A06, A08, A09, C01 and C04 were located within QTL support intervals. Homoeologous Brassica napus genes were found in eight homoeologous QTL regions, which corresponded to 657 pairs of homoeologous genes. Potential candidate genes underlying this quantitative resistance were identified. Genomic predictions and breeding are also discussed, taking into account the highly polygenic nature of this resistance.

Combining R gene and quantitative resistance increases effectiveness of cultivar resistance against Leptosphaeria maculans in Brassica napus in different environments

Using cultivar resistance against pathogens is one of the most economical and environmentally friendly methods for control of crop diseases. However, cultivar resistance can be easily rendered ineffective due to changes in pathogen populations or environments. To test the hypothesis that combining R gene-mediated resistance and quantitative resistance (QR) in one cultivar can provide more effective resistance than use of either type of resistance on its own, effectiveness of resistance in eight oilseed rape (Brassica napus) cultivars with different R genes and/or QR against Leptosphaeria maculans (phoma stem canker) was investigated in 13 different environments/sites over three growing seasons (2010/2011, 2011/2012 and 2012/2013). Cultivar Drakkar with no R genes and no QR was used as susceptible control and for sampling L. maculans populations. Isolates of L. maculans were obtained from the 13 sites in 2010/2011 to assess frequencies of avirulent alleles of different effector genes (AvrLm1, AvrLm4 or AvrLm7) corresponding to the resistance genes (Rlm1, Rlm4 or Rlm7) used in the field experiments. Results of field experiments showed that cultivars DK Cabernet (Rlm1 + QR) and Adriana (Rlm4 + QR) had significantly less severe phoma stem canker than cultivars Capitol (Rlm1) and Bilbao (Rlm4), respectively. Results of controlled environment experiments confirmed the presence of Rlm genes and/or QR in these four cultivars. Analysis of L. maculans populations from different sites showed that the mean frequencies of AvrLm1 (10%) and AvrLm4 (41%) were less than that of AvrLm7 (100%), suggesting that Rlm1 and Rlm4 gene-mediated resistances were partially rendered ineffective while Rlm7 resistance was still effective. Cultivar Excel (Rlm7 + QR) had less severe canker than cultivar Roxet (Rlm7), but the difference between them was not significant due to influence of the effective resistance gene Rlm7. For the two cultivars with only QR, Es-Astrid (QR) had less severe stem canker than NK Grandia (QR). Analysis of the relationship between severity of stem canker and weather data among the 13 sites in the three growing seasons showed that increased severity of stem canker was associated with increased rainfall during the phoma leaf spot development stage and increased temperature during the stem canker development stage. Further analysis of cultivar response to environmental factors showed that cultivars with both an Rlm gene and QR (e.g. DK Cabernet, Adriana and Excel) were less sensitive to a change in environment than cultivars with only Rlm genes (e.g. Capitol, Bilbao) or only QR (e.g. DK Grandia). These results suggest that combining R gene and QR can provide effective, stable control of phoma stem canker in different environments.

Azole sensitivity in Leptosphaeria pathogens of oilseed rape: the role of lanosterol 14α-demethylase

Lanosterol 14-α demethylase is a key enzyme intermediating the biosynthesis of ergosterol in fungi, and the target of azole fungicides. Studies have suggested that Leptosphaeria maculans and L. biglobosa, the causal agents of phoma stem canker on oilseed rape, differ in their sensitivity to some azoles, which could be driving pathogen frequency change in crops. Here we used CYP51 protein modelling and heterologous expression to determine whether there are interspecific differences at the target-site level. Moreover, we provide an example of intrinsic sensitivity differences exhibited by both Leptosphaeria spp. in vitro and in planta. Comparison of homologous protein models identified highly conserved residues, particularly at the azole binding site, and heterologous expression of LmCYP51B and LbCYP51B, with fungicide sensitivity testing of the transformants, suggests that both proteins are similarly sensitive to azole fungicides flusilazole, prothioconazole-desthio and tebuconazole. Fungicide sensitivity testing on isolates shows that they sometimes have a minor difference in sensitivity in vitro and in planta. These results suggest that azole fungicides remain a useful component of integrated phoma stem canker control in the UK due to their effectiveness on both Leptosphaeria spp. Other factors, such as varietal resistance or climate, may be driving observed frequency changes between species.

Current Status and Challenges in Identifying Disease Resistance Genes in Brassica napus

Brassica napus is an economically important crop across different continents including temperate and subtropical regions in Europe, Canada, South Asia, China and Australia. Its widespread cultivation also brings setbacks as it plays host to fungal, oomycete and chytrid pathogens that can lead to serious yield loss. For sustainable crop production, identification of resistance (R) genes in B. napus has become of critical importance. In this review, we discuss four key pathogens affecting Brassica crops: Clubroot (Plasmodiophora brassicae), Blackleg (Leptosphaeria maculans and L. biglobosa), Sclerotinia Stem Rot (Sclerotinia sclerotiorum), and Downy Mildew (Hyaloperonospora parasitica). We first review current studies covering prevalence of these pathogens on Brassica crops and highlight the R genes and QTL that have been identified from Brassica species against these pathogens. Insights into the relationships between the pathogen and its Brassica host, the unique host resistance mechanisms and how these affect resistance outcomes is also presented. We discuss challenges in identification and deployment of R genes in B. napus in relation to highly specific genetic interactions between host subpopulations and pathogen pathotypes and emphasize the need for common or shared techniques and research materials or tighter collaboration between researchers to reconcile the inconsistencies in the research outcomes. Using current genomics tools, we provide examples of how characterization and cloning of R genes in B. napus can be carried out more effectively. Lastly, we put forward strategies to breed resistant cultivars through introgressions supported by genomic approaches and suggest prospects that can be implemented in the future for a better, pathogen-resistant B. napus.

Quantitative Resistance to Plant Pathogens in Pyramiding Strategies for Durable Crop Protection

Quantitative resistance has gained interest in plant breeding for pathogen control in low-input cropping systems. Although quantitative resistance frequently has only a partial effect and is difficult to select, it is considered more durable than major resistance (R) genes. With the exponential development of molecular markers over the past 20 years, resistance QTL have been more accurately detected and better integrated into breeding strategies for resistant varieties with increased potential for durability. This review summarizes current knowledge on the genetic inheritance, molecular basis, and durability of quantitative resistance. Based on this knowledge, we discuss how strategies that combine major R genes and QTL in crops can maintain the effectiveness of plant resistance to pathogens. Combining resistance QTL with complementary modes of action appears to be an interesting strategy for breeding effective and potentially durable resistance. Combining quantitative resistance with major R genes has proven to be a valuable approach for extending the effectiveness of major genes. In the plant genomics era, improved tools and methods are becoming available to better integrate quantitative resistance into breeding strategies. Nevertheless, optimal combinations of resistance loci will still have to be identified to preserve resistance effectiveness over time for durable crop protection.

A Major Locus for Manganese Tolerance Maps on Chromosome A09 in a Doubled Haploid Population of Brassica napus L

Soil acidity poses a major threat to productivity of several crops; mainly due to the prevalence of toxic levels of Al³⁺ and Mn²⁺. Crop productivity could be harnessed on acid soils via the development of plant varieties tolerant to phytotoxic levels of these cations. In this study, we investigated the extent of natural variation for Mn²⁺ tolerance among ten parental lines of the Australian and International canola mapping populations. Response to Mn²⁺ toxicity was measured on the bases of cotyledon chlorosis, shoot biomass, and leaf area in nutrient solution under control (9 μM of MnCl₂⋅4H₂O) and Mn treatment (125 μM of MnCl₂⋅4H₂O). Among parental lines, we selected Darmor-bzh and Yudal that showed significant and contrasting variation in Mn²⁺ tolerance to understand genetic control and identify the quantitative trait loci (QTL) underlying Mn²⁺ tolerance. We evaluated parental lines and their doubled haploid (DH) progenies (196 lines) derived from an F₁ cross, Darmor-bzh/Yudal for Mn²⁺ tolerance. Mn²⁺-tolerant genotypes had significantly higher shoot biomass and leaf area compared to Mn²⁺-sensitive genotypes. A genetic linkage map based on 7,805 DArTseq markers corresponding to 2,094 unique loci was constructed and further utilized for QTL identification. A major locus, BnMn²⁺.A09 was further mapped with a SNP marker, Bn-A09-p29012402 (LOD score of 34.6) accounting for most of the variation in Mn²⁺ tolerance on chromosome A09. This is the first report on the genomic localization of a Mn²⁺ tolerance locus in B. napus. Additionally, an ortholog of A. thaliana encoding for cation efflux facilitator transporter was located within 3,991 bp from significant SNP marker associated with BnMn²⁺.A09. A suite of genome sequence based markers (DArTseq and Illumina Infinium SNPs) flanking the BnMn²⁺.A09 locus would provide an invaluable tool for various molecular breeding applications to improve canola production and profitability on Mn²⁺ toxic soils.

Multi-environment QTL studies suggest a role for cysteine-rich protein kinase genes in quantitative resistance to blackleg disease in Brassica napus

BACKGROUND

Resistance to the blackleg disease of Brassica napus (canola/oilseed rape), caused by the hemibiotrophic fungal pathogen Leptosphaeria maculans, is determined by both race-specific resistance (R) genes and quantitative resistance loci (QTL), or adult-plant resistance (APR). While the introgression of R genes into breeding material is relatively simple, QTL are often detected sporadically, making them harder to capture in breeding programs. For the effective deployment of APR in crop varieties, resistance QTL need to have a reliable influence on phenotype in multiple environments and be well defined genetically to enable marker-assisted selection (MAS).

RESULTS

Doubled-haploid populations produced from the susceptible B. napus variety Topas and APR varieties AG-Castle and AV-Sapphire were analysed for resistance to blackleg in two locations over 3 and 4 years, respectively. Three stable QTL were detected in each population, with two loci appearing to be common to both APR varieties. Physical delineation of three QTL regions was sufficient to identify candidate defense-related genes, including a cluster of cysteine-rich receptor-like kinases contained within a 49 gene QTL interval on chromosome A01. Individual L. maculans isolates were used to define the physical intervals for the race-specific R genes Rlm3 and Rlm4 and to identify QTL common to both field studies and the cotyledon resistance response.

CONCLUSION

Through multi-environment QTL analysis we have identified and delineated four significant and stable QTL suitable for MAS of quantitative blackleg resistance in B. napus, and identified candidate genes which potentially play a role in quantitative defense responses to L. maculans.

Identification of environmentally stable QTL for resistance against Leptosphaeria maculans in oilseed rape (Brassica napus)

Six stable QTL for resistance against L. maculans (phoma stem canker) have been identified by QTL × environment interaction analysis using data from five winter oilseed rape field experiments. Phoma stem canker, caused by Leptosphaeria maculans, is a disease of worldwide importance on oilseed rape (Brassica napus). Quantitative trait loci (QTL)-mediated resistance against L. maculans in B. napus is considered to be race non-specific and potentially durable. Identification and evaluation of QTL for resistance to L. maculans is important for breeding oilseed rape cultivars with durable resistance. An oilseed rape mapping population was used to detect QTL for resistance against L. maculans in five winter oilseed rape field experiments under different environments. A total of 17 QTL involved in 'field' quantitative resistance against L. maculans were detected and collectively explained 51% of the phenotypic variation. The number of QTL detected in each experiment ranged from two to nine and individual QTL explained 2-25% of the phenotypic variation. QTL × environment interaction analysis suggested that six of these QTL were less sensitive to environmental factors, so they were considered to be stable QTL. Markers linked to these stable QTL will be valuable for selection to breed for effective resistance against L. maculans in different environments, which will contribute to sustainable management of the disease.

Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects

Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.

Methods to study PAMP-triggered immunity in Brassica species

The first layer of active defense in plants is based on the perception of pathogen-associated molecular patterns (PAMPs) leading to PAMP-triggered immunity (PTI). PTI is increasingly being investigated in crop plants, where it may have potential to provide durable disease resistance in the field. Limiting this work, however, is an absence of reliable bioassays to investigate PAMP responses in some species. Here, we present a series of methods to investigate PTI in Brassica napus. The assays allow measuring early responses such as the oxidative burst, mitogen-activated protein kinase phosphorylation, and PAMP-induced marker gene expression. Illumina-based RNA sequencing analysis produced a genome-wide survey of transcriptional changes upon PAMP treatment seen in both the A and C genomes of the allotetraploid B. napus. Later responses characterized include callose deposition and lignification at the cell wall, seedling growth inhibition, and PAMP-induced resistance to Pseudomonas syringae and Botrytis cinerea. Furthermore, using these assays, we demonstrated substantial variation in PAMP responses within a collection of diverse B. napus cultivars. The assays reported here could have widespread application in B. napus breeding and mapping programs to improve selection for broad-spectrum disease resistance.

Assessing quantitative resistance against Leptosphaeria maculans (phoma stem canker) in Brassica napus (oilseed rape) in young plants

Quantitative resistance against Leptosphaeria maculans in Brassica napus is difficult to assess in young plants due to the long period of symptomless growth of the pathogen from the appearance of leaf lesions to the appearance of canker symptoms on the stem. By using doubled haploid (DH) lines A30 (susceptible) and C119 (with quantitative resistance), quantitative resistance against L. maculans was assessed in young plants in controlled environments at two stages: stage 1, growth of the pathogen along leaf veins/petioles towards the stem by leaf lamina inoculation; stage 2, growth in stem tissues to produce stem canker symptoms by leaf petiole inoculation. Two types of inoculum (ascospores; conidia) and three assessment methods (extent of visible necrosis; symptomless pathogen growth visualised using the GFP reporter gene; amount of pathogen DNA quantified by PCR) were used. In stage 1 assessments, significant differences were observed between lines A30 and C119 in area of leaf lesions, distance grown along veins/petioles assessed by visible necrosis or by viewing GFP and amount of L. maculans DNA in leaf petioles. In stage 2 assessments, significant differences were observed between lines A30 and C119 in severity of stem canker and amount of L. maculans DNA in stem tissues. GFP-labelled L. maculans spread more quickly from the stem cortex to the stem pith in A30 than in C119. Stem canker symptoms were produced more rapidly by using ascospore inoculum than by using conidial inoculum. These results suggest that quantitative resistance against L. maculans in B. napus can be assessed in young plants in controlled conditions. Development of methods to phenotype quantitative resistance against plant pathogens in young plants in controlled environments will help identification of stable quantitative resistance for control of crop diseases.

Quantitative resistance affects the speed of frequency increase but not the diversity of the virulence alleles overcoming a major resistance gene to Leptosphaeria maculans in oilseed rape

Quantitative resistance mediated by multiple genetic factors has been shown to increase the potential for durability of major resistance genes. This was demonstrated in the Leptosphaeria maculans/Brassica napus pathosystem in a 5year recurrent selection field experiment on lines harboring the qualitative resistance gene Rlm6 combined or not with quantitative resistance. The quantitative resistance limited the size of the virulent isolate population. In this study we continued this recurrent selection experiment in the same way to examine whether the pathogen population could adapt and render the major gene ineffective in the longer term. The cultivars Eurol, with a susceptible background, and Darmor, with quantitative resistance, were used. We confirmed that the combination of qualitative and quantitative resistance is an effective approach for controlling the pathogen epidemics over time. This combination did not prevent isolates virulent against the major gene from amplifying in the long term but the quantitative resistance significantly delayed for 5years the loss of effectiveness of the qualitative resistance and disease severity was maintained at a low level on the genotype with both types of resistance after the fungus population had adapted to the major gene. We also showed that diversity of AvrLm6 virulence alleles was comparable in isolates recovered after the recurrent selection on lines carrying either the major gene alone or in combination with quantitative resistance: a single repeat-induced point mutation and deletion events were observed in both situations. Breeding varieties which combine qualitative and quantitative resistance can effectively contribute to disease control by increasing the potential for durability of major resistance genes.

Pathogenesis, parasitism and mutualism in the trophic space of microbe-plant interactions

Microbe-host interactions can be categorised as pathogenic, parasitic or mutualistic, but in practice few examples exactly fit these descriptions. New molecular methods are providing insights into the dynamics of microbe-host interactions, with most microbes changing their relationship with their host at different life-cycle stages or in response to changing environmental conditions. Microbes can transition between the trophic states of pathogenesis and symbiosis and/or between mutualism and parasitism. In plant-based systems, an understanding of the true ecological niche of organisms and the dynamic state of their trophic interactions with their hosts has important implications for agriculture, including crop rotation, disease control and risk management.

Quantitative resistance increases the durability of qualitative resistance to Leptosphaeria maculans in Brassica napus

It has frequently been hypothesized that quantitative resistance increases the durability of qualitative (R-gene mediated) resistance but supporting experimental evidence is rare. To test this hypothesis, near-isogenic lines with/without the R-gene Rlm6 introduced into two Brassica napus cultivars differing in quantitative resistance to Leptosphaeria maculans were used in a 5-yr field experiment. Recurrent selection of natural fungal populations was done annually on each of the four plant genotypes, using crop residues from each genotype to inoculate separately the four series of field trials for five consecutive cropping seasons. Severity of phoma stem canker was measured on each genotype and frequencies of avirulence alleles in L. maculans populations were estimated. Recurrent selection of virulent isolates by Rlm6 in a susceptible background rendered the resistance ineffective by the third cropping season. By contrast, the resistance was still effective after 5 yr of selection by the genotype combining this gene with quantitative resistance. No significant variation in the performance of quantitative resistance alone was noted over the course of the experiment. We conclude that quantitative resistance can increase the durability of Rlm6. We recommend combining quantitative resistance with R-gene mediated resistance to enhance disease control and crop production.