Combining Selective Pressures to Enhance the Durability of Disease Resistance Genes

Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola

The downy mildew disease caused by the oomycete Plasmopara viticola is a serious threat for grapevine and can cause enormous yield losses in viticulture. The quantitative trait locus Rpv12, mediating resistance against P. viticola, was originally found in Asian Vitis amurensis. This locus and its genes were analyzed here in detail. A haplotype-separated genome sequence of the diploid Rpv12-carrier Gf.99-03 was created and annotated. The defense response against P. viticola was investigated in an infection time-course RNA-seq experiment, revealing approximately 600 upregulated Vitis genes during host-pathogen interaction. The Rpv12 regions of the resistance and the sensitivity encoding Gf.99-03 haplotype were structurally and functionally compared with each other. Two different clusters of resistance-related genes were identified within the Rpv12 locus. One cluster carries a set of four differentially expressed genes with three ACCELERATED CELL DEATH 6-like genes. The other cluster carries a set of six resistance gene analogs related to qualitative pathogen resistance. The Rpv12 locus and its candidate genes for P. viticola resistance provide a precious genetic resource for P. viticola resistance breeding. Newly developed co-segregating simple sequence repeat markers in close proximity to the R-genes enable its improved applicability in marker-assisted grapevine breeding.

Antifungal alternation can be beneficial for durability but at the cost of generalist resistance

The evolution of resistance to pesticides is a major burden in agriculture. Resistance management involves maximizing selection pressure heterogeneity, particularly by combining active ingredients with different modes of action. We tested the hypothesis that alternation may delay the build-up of resistance not only by spreading selection pressure over longer periods, but also by decreasing the rate of evolution of resistance to alternated fungicides, by applying an experimental evolution approach to the economically important crop pathogen Zymoseptoria tritici. Our results show that alternation is either neutral or slows the overall resistance evolution rate, relative to continuous fungicide use, but results in higher levels of generalism in evolved lines. We demonstrate that the nature of the fungicides, and therefore their relative intrinsic risk of resistance may underly this trade-off, more so than the number of fungicides and the rhythm of alternation. This trade-off is also dynamic over the course of resistance evolution. These findings open up new possibilities for tailoring resistance management effectively while optimizing interplay between alternation components.

Mining legume germplasm for genetic gains: An Indian perspective

Legumes play a significant role in food and nutritional security and contribute to environmental sustainability. Although legumes are highly beneficial crops, it has not yet been possible to enhance their yield and production to a satisfactory level. Amid a rising population and low yield levels, per capita average legume consumption in India has fallen by 71% over the last 50 years, and this has led to protein-related malnutrition in a large segment of the Indian population, especially women and children. Several factors have hindered attempts to achieve yield enhancement in grain legumes, including biotic and abiotic pressures, a lack of good ideotypes, less amenability to mechanization, poorer responsiveness to fertilizer input, and a poor genetic base. Therefore, there is a need to mine the approximately 0.4 million ex situ collections of legumes that are being conserved in gene banks globally for identification of ideal donors for various traits. The Indian National Gene Bank conserves over 63,000 accessions of legumes belonging to 61 species. Recent initiatives have been undertaken in consortia mode with the aim of unlocking the genetic potential of ex situ collections and conducting large-scale germplasm characterization and evaluation analyses. We assume that large-scale phenotyping integrated with omics-based science will aid the identification of target traits and their use to enhance genetic gains. Additionally, in cases where the genetic base of major legumes is narrow, wild relatives have been evaluated, and these are being exploited through pre-breeding. Thus far, >200 accessions of various legumes have been registered as unique donors for various traits of interest.

Strong Genetic Differentiation between Generalist Populations of Venturia inaequalis and Populations from Partially Resistant Apple Cultivars Carrying Rvi3 or Rvi5

The ascomycete fungus Venturia inaequalis causes scab disease, a major problem in apple production. The utilization of resistant cultivars is hindered by emerging new pathogen races, which erode their resistance. Increasing our knowledge on the population genetic processes of the fungus can contribute to the development of resistance gene deployment strategies and more durable resistance. We investigated the effect of four scab race indicator cultivars, ‘Gala’ (no R-gene), ‘Golden Delicious’ (Rvi1), ‘Geneva’ (Rvi3, complex), and OR45t132 (Rvi5), on the V. inaequalis population genetic structure and diversity. Sixty-six monosporic fungal isolates from the four cultivars were genotyped with seven simple sequence repeat primers. Furthermore, the partial resistance of the indicators and the pathogenicity profile of the conidia from each host were assessed. The genetic diversity and structure of the investigated V. inaequalis subpopulations correspond to the partial resistance of the original hosts as well as the subpopulations’ pathogenicity profiles. Indicators carrying Rvi3 and Rvi5 had strongly diverged and specialized V. inaequalis populations on them and fewer symptoms on the field. In line with the complete breakdown of the Rvi1 gene, the population from ‘Golden Delicious’ did not segregate from the susceptible ‘Gala’, and virulence towards Rvi1 was present in all subpopulations.

Ectopic Expression of HbRPW8-a from Hevea brasiliensis Improves Arabidopsis thaliana Resistance to Powdery Mildew Fungi (Erysiphe cichoracearum UCSC1)

The RPW8s (Resistance to Powdery Mildew 8) are atypical broad-spectrum resistance genes that provide resistance to the powdery mildew fungi. Powdery mildew of rubber tree is one of the serious fungal diseases that affect tree growth and latex production. However, the RPW8 homologs in rubber tree and their role of resistance to powdery mildew remain unclear. In this study, four RPW8 genes, HbRPW8-a, b, c, d, were identified in rubber tree, and phylogenetic analysis showed that HbRPW8-a was clustered with AtRPW8.1 and AtRPW8.2 of Arabidopsis. The HbRPW8-a protein was localized on the plasma membrane and its expression in rubber tree was significantly induced upon powdery mildew infection. Transient expression of HbRPW8-a in tobacco leaves induced plant immune responses, including the accumulation of reactive oxygen species and the deposition of callose in plant cells, which was similar to that induced by AtRPW8.2. Consistently, overexpression of HbRPW8-a in Arabidopsis thaliana enhanced plant resistance to Erysiphe cichoracearum UCSC1 and Pseudomonas syringae pv. tomato DC30000 (PstDC3000). Moreover, such HbRPW8-a mediated resistance to powdery mildew was in a salicylic acid (SA) dependent manner. Taken together, we demonstrated a new RPW8 member in rubber tree, HbRPW8-a, which could potentially contribute the resistance to powdery mildew.

Insights into the Genetic Architecture and Genomic Prediction of Powdery Mildew Resistance in Flax (Linum usitatissimum L.)

Powdery mildew (PM), caused by the fungus Oidium lini in flax, can cause defoliation and reduce seed yield and quality. To date, one major dominant gene (Pm1) and three quantitative trait loci (QTL) on chromosomes 1, 7 and 9 have been reported for PM resistance. To fully dissect the genetic architecture of PM resistance and identify QTL, a diverse flax core collection of 372 accessions augmented with an additional 75 breeding lines were sequenced, and PM resistance was evaluated in the field for eight years (2010–2017) in Morden, Manitoba, Canada. Genome-wide association studies (GWAS) were performed using two single-locus and seven multi-locus statistical models with 247,160 single nucleotide polymorphisms (SNPs) and the phenotypes of the 447 individuals for each year separately as well as the means over years. A total of 349 quantitative trait nucleotides (QTNs) were identified, of which 44 large-effect QTNs (R² = 10–30%) were highly stable over years. The total number of favourable alleles per accession was significantly correlated with PM resistance (r = 0.74), and genomic selection (GS) models using all identified QTNs generated significantly higher predictive ability (r = 0.93) than those constructed using the 247,160 genome-wide random SNP (r = 0.69), validating the overall reliability of the QTNs and showing the additivity of PM resistance in flax. The QTNs were clustered on the distal ends of all 15 chromosomes, especially on chromosome 5 (0.4–5.6 Mb and 9.4–16.9 Mb) and 13 (4.7–5.2 Mb). To identify candidate genes, a dataset of 3230 SNPs located in resistance gene analogues (RGAs) was used as input for GWAS, from which an additional 39 RGA-specific QTNs were identified. Overall, 269 QTN loci harboured 445 RGAs within the 200 Kb regions spanning the QTNs, including 45 QTNs located within the RGAs. These RGAs supported by significant QTN/SNP allele effects were mostly nucleotide binding site and leucine-rich repeat receptors (NLRs) belonging to either coiled-coil (CC) NLR (CNL) or toll interleukin-1 (TIR) NLR (TNL), receptor-like kinase (RLK), receptor-like protein kinase (RLP), transmembrane-coiled-coil (TM-CC), WRKY, and mildew locus O (MLO) genes. These results constitute an important genomic tool for resistance breeding and gene cloning for PM in flax.

High Genetic Diversity in Predominantly Clonal Populations of the Powdery Mildew Fungus Podosphaera leucotricha from U.S. Apple Orchards

Apple powdery mildew (APM), caused by Podosphaera leucotricha, is a constant threat to apple production worldwide. Very little is known about the biology and population structure of this pathogen in the United States and other growing regions, which affects APM management. A total of 253 P. leucotricha isolates, sampled from 10 apple orchards in Washington, New York, and Virginia, were genetically characterized with novel single sequence repeat and mating type markers. Eighty-three multilocus genotypes (MLGs) were identified, most of which were unique to a given orchard. Each isolate carried either a MAT1-1 or a MAT1-2 idiomorph at the mating type locus, indicating that P. leucotricha is heterothallic. Virulence tests on detached apple leaves showed that the 10 most frequent P. leucotricha MLGs were avirulent on a line containing a major resistance gene. Analysis of molecular variance showed significant differentiation (P < 0.001) among populations, a result supported by principal coordinate analysis revealing three genetic groups, each represented by nonoverlapping MLGs from Washington, New York, and Virginia. A Bayesian cluster analysis showed genetic heterogeneity between Washington populations, and a relative migration analysis indicated substantial gene flow among neighboring orchards. Random mating tests indicated that APM epidemics during the active cycle were dominated by clonal reproduction. However, the presence of sexual structures in orchards, the likelihood that five repeated MLGs resulted from sexual reproduction, and high genotypic diversity observed in some populations suggest that sexual spores play some role in APM epidemics. IMPORTANCE Understanding the population biology and epidemiology of plant pathogens is essential to develop effective strategies for controlling plant diseases. Herein, we gathered insights into the population biology of P. leucotricha populations from conventional and organic apple orchards in the United States. We showed genetic heterogeneity between P. leucotricha populations in Washington and structure between populations from different U.S. regions, suggesting that short-distance spore dispersal plays an important role in the disease's epidemiology. We presented evidence that P. leucotricha is heterothallic and that populations likely result from a mixed (i.e., sexual and asexual) reproductive system, revealing that the sexual stage contributes to apple powdery mildew epidemics. We showed that the major resistance gene Pl-1 is valuable for apple breeding because virulent isolates have most likely not emerged yet in U.S. commercial orchards. These results will be important to achieve sustainability of disease management strategies and maintenance of plant health in apple orchards.

Clubroot in Brassica: recent advances in genomics, breeding, and disease management

Clubroot disease, caused by Plasmodiophora brassicae, affects Brassica oilseed and vegetable production worldwide. This review is focused on various aspects of clubroot disease and its management, including understanding the pathogen and resistance in the host plants. Advances in genetics, molecular biology techniques, and omics research have helped to identify several major loci, QTL, and genes from the Brassica genomes involved in the control of clubroot resistance. Transcriptomic studies have helped to extend our understanding of the mechanism of infection by the pathogen and the molecular basis of resistance/susceptibility in the host plants. A comprehensive understanding of the clubroot disease and host resistance would allow developing a better strategy by integrating the genetic resistance with cultural practices to manage this disease from a long-term perspective.

Breeding Strategies and Challenges in the Improvement of Blast Disease Resistance in Finger Millet. A Current Review

Climate change has significantly altered the biodiversity of crop pests and pathogens, posing a major challenge to sustainable crop production. At the same time, with the increasing global population, there is growing pressure on plant breeders to secure the projected food demand by improving the prevailing yield of major food crops. Finger millet is an important cereal crop in southern Asia and eastern Africa, with excellent nutraceutical properties, long storage period, and a unique ability to grow under arid and semi-arid environmental conditions. Finger millet blast disease caused by the filamentous ascomycetous fungus Magnaporthe oryzae is the most devastating disease affecting the growth and yield of this crop in all its growing regions. The frequent breakdown of blast resistance because of the susceptibility to rapidly evolving virulent genes of the pathogen causes yield instability in all finger millet-growing areas. The deployment of novel and efficient strategies that provide dynamic and durable resistance against many biotypes of the pathogen and across a wide range of agro-ecological zones guarantees future sustainable production of finger millet. Here, we analyze the breeding strategies currently being used for improving resistance to disease and discuss potential future directions toward the development of new blast-resistant finger millet varieties, providing a comprehensive understanding of promising concepts for finger millet breeding. The review also includes empirical examples of how advanced molecular tools have been used in breeding durably blast-resistant cultivars. The techniques highlighted are cost-effective high-throughput methods that strongly reduce the generation cycle and accelerate both breeding and research programs, providing an alternative to conventional breeding methods for rapid introgression of disease resistance genes into favorable, susceptible cultivars. New information and knowledge gathered here will undoubtedly offer new insights into sustainable finger millet disease control and efficient optimization of the crop's productivity.

Genetic mapping of Fusarium wilt resistance in a wild banana Musa acuminata ssp. malaccensis accession

Banana is an important fruit and food crop, but is threatened by Fusarium wilt, one of the most devastating soil-borne fungal diseases. Only host resistance facilitates banana cultivation in infested soils around the world, but the genetic basis of Fusarium wilt of banana (FWB) is unknown. We selfed a heterozygous wild banana accession Musa acuminata ssp. malaccensis (Mam, AA, 2n = 22) to generate a mapping population and to investigate the inheritance of resistance to Race 1 and tropical race 4 (TR4) that cause FWB. Phenotyping (N = 217) revealed segregation for resistance, and genotyping by sequencing resulted in 2802 high-quality single-nucleotide polymorphic markers (SNPs) that were used for genetic mapping. Combined analyses of these data showed that a single dominant resistance locus controls resistance to Race 1 and maps near the distal part of chromosome 10. Recombinants, together with the position of the putative resistance gene, were further analysed using graphical genotyping, which retrieved markers flanking a 360 kb genetic region that associates with Race 1 resistance. The region contains 165 putative genes on the reference genome, including 19 leucine-rich repeat receptor-like kinase-like genes. At the same position and phase, we also identified a QTL for TR4 resistance, showing that the locus for resistance against Race 1 provided partial resistance to TR4. However, this effect was far less significant and hence not included in the mapping. These data support the breeding of new banana varieties with resistance to Fusarium wilt.

Novel Aspects on The Interaction Between Grapevine and Plasmopara viticola: Dual-RNA-Seq Analysis Highlights Gene Expression Dynamics in The Pathogen and The Plant During The Battle For Infection

Mgaloblishvili, a Vitis vinifera cultivar, exhibits unique resistance traits against Plasmopara viticola, the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pinot noir (a V. vinifera susceptible cultivar), and Bianca (a resistant hybrid) leaves, inoculated and non-inoculated with the pathogen, were used to identify P. viticola effector-encoding genes and plant susceptibility/resistance genes. Multiple effector-encoding genes were identified in P. viticola transcriptome, with remarkable expression differences in relation to the inoculated grapevine cultivar. Intriguingly, five apoplastic effectors specifically associated with resistance in V. vinifera. Gene coexpression network analysis identified specific modules and metabolic changes occurring during infection in the three grapevine cultivars. Analysis of these data allowed, for the first time, the detection in V. vinifera of a putative P. viticola susceptibility gene, encoding a LOB domain-containing protein. Finally, the de novo assembly of Mgaloblishvili, Pinot noir, and Bianca transcriptomes and their comparison highlighted novel candidate genes that might be at the basis of the resistant phenotype. These results open the way to functional analysis studies and to new perspectives in molecular breeding of grapevine for resistance to P. viticola.

Rpv29, Rpv30 and Rpv31: Three Novel Genomic Loci Associated With Resistance to Plasmopara viticola in Vitis vinifera

Plasmopara viticola (Berk. et Curt.) Berl. and de Toni, the agent of downy mildew, is one of the most important pathogens of European grapevine (Vitis vinifera L.). Extensive evaluation of cultivated grapevine germplasm has highlighted the existence of resistant phenotypes in the Georgian (Southern Caucasus) germplasm. Resistance is shown as a reduction in disease severity. Unraveling the genetic architecture of grapevine response to P. viticola infection is crucial to develop resistant varieties and reduce the impact of disease management. The aim of this work was to apply a genome-wide association (GWA) approach to a panel of Georgian-derived accessions phenotyped for P. viticola susceptibility and genotyped with Vitis18kSNP chip array. GWA identified three highly significant novel loci on chromosomes 14 (Rpv29), 3 (Rpv30) and 16 (Rpv31) associated with a low level of pathogen sporulation. Rpv29, Rpv30, and Rpv31 loci appeared to be associated with plant defense genes against biotic stresses, such as genes involved in pathogen recognition and signal transduction. This study provides the first evidence of resistant loci against P. viticola in V. vinifera germplasm, and identifies potential target genes for breeding P. viticola resistant grapevine cultivars.

R-Loci Arrangement Versus Downy and Powdery Mildew Resistance Level: A Vitis Hybrid Survey

For the viticulture of the future, it will be an essential prerequisite to manage grapevine diseases with fewer chemical inputs. The development and the deployment of novel mildew resistant varieties are considered one of the most promising strategies towards a sustainable viticulture. In this regard, a collection of 102 accessions derived from crossing Vitis hybrids with V. vinifera varieties was studied. In addition to the true-to-type analysis, an exhaustive genetic characterization was carried out at the 11 reliable mildew resistance (R) loci available in the literature to date. Our findings highlight the pyramiding of R-loci against downy mildew in 15.7% and against powdery mildew in 39.2% of the total accessions. The genetic analysis was coupled with a three-year evaluation of disease symptoms in an untreated field in order to assess the impact of the R-loci arrangement on the disease resistance degree at leaf and bunch level. Overall, our results strongly suggest that R-loci pyramiding does not necessarily mean to increase the overall disease resistance, but it guarantees the presence of further barriers in case of pathogens overcoming the first. Moreover, our survey allows the discovery of new mildew resistance sources useful for novel QTL identifications towards marker-assisted breeding.

Mosaics, mixtures, rotations or pyramiding: What is the optimal strategy to deploy major gene resistance?

Once deployed uniformly in the field, genetically controlled plant resistance is often quickly overcome by pathogens, resulting in dramatic losses. Several strategies have been proposed to constrain the evolutionary potential of pathogens and thus increase resistance durability. These strategies can be classified into four categories, depending on whether resistance sources are varied across time (rotations) or combined in space in the same cultivar (pyramiding), in different cultivars within a field (cultivar mixtures) or among fields (mosaics). Despite their potential to differentially affect both pathogen epidemiology and evolution, to date the four categories of deployment strategies have never been directly compared together within a single theoretical or experimental framework, with regard to efficiency (ability to reduce disease impact) and durability (ability to limit pathogen evolution and delay resistance breakdown). Here, we used a spatially explicit stochastic demogenetic model, implemented in the R package landsepi, to assess the epidemiological and evolutionary outcomes of these deployment strategies when two major resistance genes are present. We varied parameters related to pathogen evolutionary potential (mutation probability and associated fitness costs) and landscape organization (mostly the relative proportion of each cultivar in the landscape and levels of spatial or temporal aggregation). Our results, broadly focused on qualitative resistance to rust fungi of cereal crops, show that evolutionary and epidemiological control are not necessarily correlated and that no deployment strategy is universally optimal. Pyramiding two major genes offered the highest durability, but at high mutation probabilities, mosaics, mixtures and rotations can perform better in delaying the establishment of a universally infective superpathogen. All strategies offered the same short-term epidemiological control, whereas rotations provided the best long-term option, after all sources of resistance had broken down. This study also highlights the significant impact of landscape organization and pathogen evolutionary ability in considering the optimal design of a deployment strategy.

Evolutionary emergence of infectious diseases in heterogeneous host populations

The emergence and re-emergence of pathogens remains a major public health concern. Unfortunately, when and where pathogens will (re-)emerge is notoriously difficult to predict, as the erratic nature of those events is reinforced by the stochastic nature of pathogen evolution during the early phase of an epidemic. For instance, mutations allowing pathogens to escape host resistance may boost pathogen spread and promote emergence. Yet, the ecological factors that govern such evolutionary emergence remain elusive because of the lack of ecological realism of current theoretical frameworks and the difficulty of experimentally testing their predictions. Here, we develop a theoretical model to explore the effects of the heterogeneity of the host population on the probability of pathogen emergence, with or without pathogen evolution. We show that evolutionary emergence and the spread of escape mutations in the pathogen population is more likely to occur when the host population contains an intermediate proportion of resistant hosts. We also show that the probability of pathogen emergence rapidly declines with the diversity of resistance in the host population. Experimental tests using lytic bacteriophages infecting their bacterial hosts containing Clustered Regularly Interspaced Short Palindromic Repeat and CRISPR-associated (CRISPR-Cas) immune defenses confirm these theoretical predictions. These results suggest effective strategies for cross-species spillover and for the management of emerging infectious diseases.

The probability that an epidemic will break out is highly dependent on the ability of the pathogen to acquire new adaptive mutations and to induce evolutionary emergence. Forecasting pathogen emergence thus requires a good understanding of the interplay between the epidemiology and evolution taking place at the onset of an outbreak. Here, we provide a comprehensive theoretical framework to analyze the impact of host population heterogeneity on the probability of pathogen evolutionary emergence. We use this model to predict the impact of the fraction of susceptible hosts, the inoculum size of the pathogen, and the diversity of host resistance on pathogen emergence. Our experiments using lytic bacteriophages and CRISPR-resistant bacteria support our theoretical predictions and demonstrate that manipulating the diversity of resistance alleles in a host population may be an effective way to limit the emergence of new pathogens.

Spatio-temporal connectivity and host resistance influence evolutionary and epidemiological dynamics of the canola pathogen Leptosphaeria maculans

Genetic, physiological and physical homogenization of agricultural landscapes creates ideal environments for plant pathogens to proliferate and rapidly evolve. Thus, a critical challenge in plant pathology and epidemiology is to design durable and effective strategies to protect cropping systems from damage caused by pathogens. Theoretical studies suggest that spatio-temporal variation in the diversity and distribution of resistant hosts across agricultural landscapes may have strong effects on the epidemiology and evolutionary potential of crop pathogens. However, we lack empirical tests of spatio-temporal deployment of host resistance to pathogens can be best used to manage disease epidemics and disrupt pathogen evolutionary dynamics in real-world systems. In a field experiment, we simulated how differences in Brassica napus resistance deployment strategies and landscape connectivity influence epidemic severity and Leptosphaeria maculans pathogen population composition. Host plant resistance, spatio-temporal connectivity [stubble loads], and genetic connectivity of the inoculum source [composition of canola stubble mixtures] jointly impacted epidemiology (disease severity) and pathogen evolution (population composition). Changes in population composition were consistent with directional selection for the ability to infect the host (infectivity), leading to changes in pathotype (multilocus phenotypes) and infectivity frequencies. We repeatedly observed decreases in the frequency of unnecessary infectivity, suggesting that carrying multiple infectivity genes is costly for the pathogen. From an applied perspective, our results indicate that varying resistance genes in space and time can be used to help control disease, even when resistance has already been overcome. Furthermore, our approach extends our ability to test not only for the efficacy of host varieties in a given year, but also for durability over multiple cropping seasons, given variation in the combination of resistance genes deployed.

Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens

Genetically-controlled plant resistance can reduce the damage caused by pathogens. However, pathogens have the ability to evolve and overcome such resistance. This often occurs quickly after resistance is deployed, resulting in significant crop losses and a continuing need to develop new resistant cultivars. To tackle this issue, several strategies have been proposed to constrain the evolution of pathogen populations and thus increase genetic resistance durability. These strategies mainly rely on varying different combinations of resistance sources across time (crop rotations) and space. The spatial scale of deployment can vary from multiple resistance sources occurring in a single cultivar (pyramiding), in different cultivars within the same field (cultivar mixtures) or in different fields (mosaics). However, experimental comparison of the efficiency (i.e. ability to reduce disease impact) and durability (i.e. ability to limit pathogen evolution and delay resistance breakdown) of landscape-scale deployment strategies presents major logistical challenges. Therefore, we developed a spatially explicit stochastic model able to assess the epidemiological and evolutionary outcomes of the four major deployment options described above, including both qualitative resistance (i.e. major genes) and quantitative resistance traits against several components of pathogen aggressiveness: infection rate, latent period duration, propagule production rate, and infectious period duration. This model, implemented in the R package landsepi, provides a new and useful tool to assess the performance of a wide range of deployment options, and helps investigate the effect of landscape, epidemiological and evolutionary parameters. This article describes the model and its parameterisation for rust diseases of cereal crops, caused by fungi of the genus Puccinia. To illustrate the model, we use it to assess the epidemiological and evolutionary potential of the combination of a major gene and different traits of quantitative resistance. The comparison of the four major deployment strategies described above will be the objective of future studies.

There are many recent examples which demonstrate the evolutionary potential of plant pathogens to overcome the resistances deployed in agricultural landscapes to protect our crops. Increasingly, it is recognised that how resistance is deployed spatially and temporally can impact on rates of pathogen evolution and resistance breakdown. Such deployment strategies are mainly based on the combination of several sources of resistance at different spatiotemporal scales. However, comparison of these strategies in a predictive sense is not an easy task, owing to the logistical difficulties associated with experiments involving the spread of a pathogen at large spatio-temporal scales. Moreover, both the durability of a strategy and the epidemiological protection it provides to crops must be assessed since these evaluation criteria are not necessarily correlated. Surprisingly, no current simulation model allows a thorough comparison of the different options. Here we describe a spatio-temporal model able to simulate a wide range of deployment strategies and resistance sources. This model, implemented in the R package landsepi, facilitates assessment of both epidemiological and evolutionary outcomes across simulated scenarios. In this work, the model is used to investigate the combination of different sources of resistance against fungal diseases such as rusts of cereal crops.

Pyramiding of transgenic Pm3 alleles in wheat results in improved powdery mildew resistance in the field

The combined effects of enhanced total transgene expression level and allele-specificity combination in transgenic allele-pyramided Pm3 wheat lines result in improved powdery mildew field resistance without negative pleiotropic effects. Allelic Pm3 resistance genes of wheat confer race-specific resistance to powdery mildew (Blumeria graminis f. sp. tritici, Bgt) and encode nucleotide-binding domain, leucine-rich repeat (NLR) receptors. Transgenic wheat lines overexpressing alleles Pm3a, b, c, d, f, and g have previously been generated by transformation of cultivar Bobwhite and tested in field trials, revealing varying degrees of powdery mildew resistance conferred by the transgenes. Here, we tested four transgenic lines each carrying two pyramided Pm3 alleles, which were generated by crossbreeding of lines transformed with single Pm3 alleles. All four allele-pyramided lines showed strongly improved powdery mildew resistance in the field compared to their parental lines. The improved resistance results from the two effects of enhanced total transgene expression levels and allele-specificity combinations. In contrast to leaf segment tests on greenhouse-grown seedlings, no allelic suppression was observed in the field. Plant development and yield scores of the pyramided lines were similar to the mean scores of the corresponding parental lines, and thus, the allele pyramiding did not cause any negative effects. On the contrary, in pyramided line, Pm3b × Pm3f normal plant development was restored compared to the delayed development and reduced seed set of parental line Pm3f. Allele-specific RT qPCR revealed additive transgene expression levels of the two Pm3 alleles in the pyramided lines. A positive correlation between total transgene expression level and powdery mildew field resistance was observed. In summary, allele pyramiding of Pm3 transgenes proved to be successful in enhancing powdery mildew field resistance.

Unlocking new alleles for leaf rust resistance in the Vavilov wheat collection

Thirteen potentially new leaf rust resistance loci were identified in a Vavilov wheat diversity panel. We demonstrated the potential of allele stacking to strengthen resistance against this important pathogen. Leaf rust (LR) caused by Puccinia triticina is an important disease of wheat (Triticum aestivum L.), and the deployment of genetically resistant cultivars is the most viable strategy to minimise yield losses. In this study, we evaluated a diversity panel of 295 bread wheat accessions from the N. I. Vavilov Institute of Plant Genetic Resources (St Petersburg, Russia) for LR resistance and performed genome-wide association studies (GWAS) using 10,748 polymorphic DArT-seq markers. The diversity panel was evaluated at seedling and adult plant growth stages using three P. triticina pathotypes prevalent in Australia. GWAS was applied to 11 phenotypic data sets which identified a total of 52 significant marker-trait associations representing 31 quantitative trait loci (QTL). Among them, 29 QTL were associated with adult plant resistance (APR). Of the 31 QTL, 13 were considered potentially new loci, whereas 4 co-located with previously catalogued Lr genes and 14 aligned to regions reported in other GWAS and genomic prediction studies. One seedling LR resistance QTL located on chromosome 3A showed pronounced levels of linkage disequilibrium among markers (r ² = 0.7), suggested a high allelic fixation. Subsequent haplotype analysis for this region found seven haplotype variants, of which two were strongly associated with LR resistance at seedling stage. Similarly, analysis of an APR QTL on chromosome 7B revealed 22 variants, of which 4 were associated with resistance at the adult plant stage. Furthermore, most of the tested lines in the diversity panel carried 10 or more combined resistance-associated marker alleles, highlighting the potential of allele stacking for long-lasting resistance.

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.