Fungal plant pathogens cause major crop losses worldwide, with many featuring compartmentalised genomes that include both core and accessory regions, which are believed to drive adaptation. The highly host-specific fungus Colletotrichum lupini greatly impacts lupin (Lupinus spp.) cultivation. This pathogen is part of clade 1 of the C. acutatum species complex and comprises four genetically uniform, presumably clonal, lineages (I-IV). Despite this, variation in virulence and morphology has been observed within these lineages. To investigate the potential sources of genetic variability in this asexual fungus, we compared the genomes of 16 C. lupini strains and 17 related Colletotrichum species. Phylogenomics confirmed the presence of four distinct lineages, but further examination based on genome size, gene content, transposable elements (TEs), and deletions revealed that lineage II could be split into two groups, II-A and II-B. TE content varied between lineages and correlated strongly with genome size variation, supporting a role for TEs in genome expansion in this species. Pangenome analysis revealed a highly variable accessory genome, including a minichromosome present in lineages II, III, and IV, but absent in lineage I. Accessory genes and effectors appeared to cluster in proximity to TEs. Presence/absence variation of putative effectors was lineage-specific, suggesting that these genes play a crucial role in determining host range. Notably, no effectors were found on the TE-rich minichromosome. Our findings shed light on the potential mechanisms generating genetic diversity in this asexual fungal pathogen that could aid future disease management.

AbstractColletotrichum lupini, the causative agent of lupin anthracnose, affects lupin cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective of this study was to employ population genetics to investigate the diversity, evolutionary dynamics, and molecular basis of the interaction of this notorious lupin pathogen with its host. A collection of globally representative C. lupini isolates was genotyped through triple digest restriction site‐associated DNA sequencing, resulting in a data set of unparalleled resolution. Phylogenetic and structural analysis could distinguish four independent lineages (I–IV). The strong population structure and high overall standardized index of association (r̅d) indicates that C. lupini reproduces clonally. Different morphologies and virulence patterns on white lupin (Lupinus albus) and Andean lupin (Lupinus mutabilis) were observed between and within clonal lineages. Isolates belonging to lineage II were shown to have a minichromosome that was also partly present in lineage III and IV, but not in lineage I isolates. Variation in the presence of this minichromosome could imply a role in host–pathogen interaction. All four lineages were present in the South American Andes region, which is suggested to be the centre of origin of this species. Only members of lineage II have been found outside South America since the 1990s, indicating it as the current pandemic population. As a seedborne pathogen, C. lupini has mainly spread through infected but symptomless seeds, stressing the importance of phytosanitary measures to prevent future outbreaks of strains that are yet confined to South America.

White lupin (Lupinus albus L.) is a promising crop to meet the rising global demand for plant-based protein. The seed-borne pathogen Colletotrichum lupini, however, threatens lupin cultivation worldwide. Seed dressings using synthetic fungicides were shown effective to reduce infection levels, but their negative environmental impact and exclusion from organic production calls for more sustainable solutions. In this study, a total of eleven different alternative seed treatments were tested in field trials in Switzerland between 2018 and 2021. Treatment types consisted of: hot water, steam, electron, long-term storage, elevated partial pressure of oxygen (EPPO), vinegar, plant extracts and biological control agents (BCAs). The BCAs were tested for potential antagonistic activity against C. lupini during white lupin infection under controlled conditions prior to field trials. Long-term storage and vinegar treatments successfully reduced disease incidence and increased yield to levels similar to those observed for certified seeds, without significantly affecting germination rate. Although promising, effectiveness of these treatments needs further validation. Four BCAs showed significant disease reductions under controlled conditions. Besides lowering disease severity, two BCAs also reduced C. lupini DNA in stem tissue. These reductions, however, were not observed in the field, highlighting the importance of field validations. The treatments identified in this study provide a solid basis for the development of sustainable and effective seed protection strategies in white lupin to control C. lupini successfully.

GWAS identifies candidate gene controlling resistance to anthracnose disease in white lupin. White lupin (Lupinus albus L.) is a promising grain legume to meet the growing demand for plant-based protein. Its cultivation, however, is severely threatened by anthracnose disease caused by the fungal pathogen Colletotrichum lupini. To dissect the genetic architecture for anthracnose resistance, genotyping by sequencing was performed on white lupin accessions collected from the center of domestication and traditional cultivation regions. GBS resulted in 4611 high-quality single-nucleotide polymorphisms (SNPs) for 181 accessions, which were combined with resistance data observed under controlled conditions to perform a genome-wide association study (GWAS). Obtained disease phenotypes were shown to highly correlate with overall three-year disease assessments under Swiss field conditions (r > 0.8). GWAS results identified two significant SNPs associated with anthracnose resistance on gene Lalb_Chr05_g0216161 encoding a RING zinc-finger E3 ubiquitin ligase which is potentially involved in plant immunity. Population analysis showed a remarkably fast linkage disequilibrium decay, weak population structure and grouping of commercial varieties with landraces, corresponding to the slow domestication history and scarcity of modern breeding efforts in white lupin. Together with 15 highly resistant accessions identified in the resistance assay, our findings show promise for further crop improvement. This study provides the basis for marker-assisted selection, genomic prediction and studies aimed at understanding anthracnose resistance mechanisms in white lupin and contributes to improving breeding programs worldwide.

White lupin (Lupinus albus) could contribute to the recent increase of organic grain legume production in Switzerland. However, its production is impaired by anthracnose (Colletotrichum lupini), against which FiBL is running a resistance pre-breeding project. In 2019, 196 new genetic resources and 60 F4 breeding lines were compared on-farm to the progeny of 288 accessions selected from 2015 to 2018. Relative disease scores compared to reference cultivar Amiga (mean score 6.9 on a scale from 1 (no symptoms) to 9 (plants completely dead) were calculated and ranged from -2.25 to +2. Mean relative scores of selected genotypes and breeding lines were -0.7 and -0.5, respectively, compared to -0.33 in the new accessions. The frequency of more resistant genotypes was about twice as high in the selected accessions and breeding lines than in the new accessions. These are valuable data for breeding as well as for development and validation of genetic markers for resistance screening.

White lupin (Lupinus albus) represents an important legume crop in Europe and other parts of the world due to its high protein content and potential for low-input agriculture. However, most cultivars are susceptible to anthracnose caused by Colletotrichum lupini, a seed- and air-borne fungal pathogen that causes severe yield losses. The aim of this work was to develop a C. lupini-specific quantitative real-time TaqMan PCR assay that allows for quick and reliable detection and quantification of the pathogen in infected seed and plant material. Quantification of C. lupini DNA in dry seeds allowed us to distinguish infected and certified (non-infected) seed batches with DNA loads corresponding to the disease score index and yield of the mother plants. Additionally, C. lupini DNA could be detected in infected lupin shoots and close to the infection site, thereby allowing us to study the disease cycle of this hemibiotrophic pathogen. This qPCR assay provides a useful diagnostic tool to determine anthracnose infection levels of white lupin seeds and will facilitate the use of seed health assessments as a strategy to reduce the primary infection source and spread of this disease.

Lupin cultivation worldwide is threatened by anthracnose, a destructive disease caused by the seed- and air-borne fungal pathogen Colletotrichum lupini. In this study we explored the intraspecific diversity of 39 C. lupini isolates collected from different lupin cultivating regions around the world, and representative isolates were screened for their pathogenicity and virulence on white and Andean lupin. Multi-locus phylogeny and morphological characterizations showed intraspecific diversity to be greater than previously shown, distinguishing a total of six genetic groups and ten distinct morphotypes. Highest diversity was found across South America, indicating it as the center of origin of C. lupini. The isolates that correspond to the current pandemic belong to a genetic and morphological uniform group, were globally widespread, and showed high virulence on tested white and Andean lupin accessions. Isolates belonging to the other five genetic groups were mostly found locally and showed distinct virulence patterns. Two highly virulent strains were shown to overcome resistance of advanced white lupin breeding material. This stresses the need to be careful with international seed transports in order to prevent spread of currently confined but potentially highly virulent strains. This study improves our understanding of the diversity, phylogeography and pathogenicity of a member of one of the world's top 10 plant pathogen genera, providing valuable information for breeding programs and future disease management.

White lupin (Lupinus albus) is a valuable grain legume with a high protein content and quality, contributing to soil fertility (Monteiro et al., 2014, Lambers et al., 2013). Its high yield potential could make it a sustainable alternative for imported soybean in Europe (Lucas et al., 2015). However, lupin anthracnose, caused by the air- and soilborne fungus Colletotrichum lupini severely limits cultivation as low levels of seed infestation can already cause total yield loss (Talhinhas et al., 2016). Host resistance is crucial for managing anthracnose but a better insight into the genetic basis is required. We developed a high-throughput phenotyping tool that identifies field-relevant anthracnose resistance under controlled conditions. For inoculation, we identified a local, highly virulent C. lupini strain. Phylogenetic analyses revealed that the strain belongs to a globally dispersed genetic group corresponding to Dubrulle et al.’s (2020) C. lupini group II. Using the developed tool we phenotyped a diverse collection of 200 white lupin accessions, revealing a strong segregation between susceptible and resistant plants, potentially holding novel sources of resistance. Genotyping-bysequencing was performed and the generated single-nucleotide polymorphic markers (SNPs) are currently being used for genetic mapping. Quantitative trait loci (QTLs) for anthracnose resistance will be presented aiding to improve and speed up white lupin breeding programs.

The seed- and air-borne pathogen Colletotrichum lupini, the causal agent of lupin anthracnose, is the most important disease in white lupin (Lupinus albus) worldwide and can cause total yield loss. The aims of this study were to establish a reliable high-throughput phenotyping tool to identify anthracnose resistance in white lupin germplasm and to evaluate a genomic prediction model, accounting for previously reported resistance quantitative trait loci, on a set of independent lupin genotypes. Phenotyping under controlled conditions, performing stem inoculation on seedlings, showed to be applicable for high throughput, and its disease score strongly correlated with field plot disease assessments (r = 0.95, P < 0.0001) and yield (r = -0.64, P = 0.035). Traditional one-row field disease phenotyping showed no significant correlation with field plot disease assessments (r = 0.31, P = 0.34) and yield (r = -0.45, P = 0.17). Genomically predicted resistance values showed no correlation with values observed under controlled or field conditions, and the parental lines of the recombinant inbred line population used for constructing the prediction model exhibited a resistance pattern opposite to that displayed in the original (Australian) environment used for model construction. Differing environmental conditions, inoculation procedures, or population structure may account for this result. Phenotyping a diverse set of 40 white lupin accessions under controlled conditions revealed eight accessions with improved resistance to anthracnose. The standardized area under the disease progress curves (sAUDPC) ranged from 2.1 to 2.8, compared with the susceptible reference accession with a sAUDPC of 3.85. These accessions can be incorporated into white lupin breeding programs. In conclusion, our data support stem inoculation-based disease phenotyping under controlled conditions as a time-effective approach to identify field-relevant resistance, which can now be applied to further identify sources of resistance and their underlying genetics.

In this video, interested researchers can find an explanation on how the seed borne fungal pathogen Anthracnose affects lupin crops, and a description of FiBL’s project for screening under controlled conditions, aimed at identifying resistance to Anthracnose (Colletotrichum lupini) in seed as a basis for breeding resistance programmes.

White lupin (Lupinus albus) is a grain legume known for its high protein content and quality, efficient nutrient acquisition and health benefits (Lambers et al., 2013, Arnoldi et al., 2015). Its high yield potential could make it a sustainable alternative to soybean in cooler regions (Lucas et al., 2015). However, since the 1980s anthracnose disease, caused by the air- and seed-borne fungal disease Colletotrichum lupini, threatens lupin cultivations worldwide (Nirenberg et al., 2002, Damm et al., 2012, Talhinhas et al., 2016). Even low levels of seed infestation can lead up to total yield loss (Thomas 2004, Diggle 2002). To assist white lupin breeding programs, we analyzed the genetic diversity of globally collected lupin-infecting Colletotrichum isolates by multi-locus sequencing (Pecchia et al., 2019, Dubrulle et al., 2019). First analyses indicate that all isolates belong to the species C. lupini and that the genetic diversity of isolates collected from Europe and Australia is lower compared with isolates collected from South America, showing different genetic groups. Pathogenicity tests with isolates representing the different genetic groups were performed on two white lupin cultivars, the susceptible variety Feodora and the tolerant breeding line Blu-25 from Erik von Baer. Combining the outcome of the genetic diversity analysis with virulence and morphological data, at least five different strains could be distinguished. The most widespread strain is also the most aggressive and is the cause of the current anthracnose epidemic in (white) lupin cultivation.

Currently Europe imports large amounts of unsustainably produced soy to meet the plant-based protein demand of the feed and food industry. The high protein content and low nutrient requirements of white lupins make them a sustainable local alternative. However, lupin cultivation is severely impaired by anthracnose disease, caused by the seed- and air-borne fungus Colletotrichum lupini. Low levels of seed infestation can already lead to complete yield loss. Understanding the pathogen’s lifestyle and identifying sources of resistance are therefore of major importance to make the re-introduction of white lupin a success. Resistance screening was performed under controlled conditions. Disease severity was scored visually and qPCR was performed on inoculated and freshly unfolding leaves. Lifestyle was monitored by performing qPCR on drop-inoculated leaves and plants grown from naturally-infected seeds.

Ubersicht - Strategien und Ansatze der okologischen Pflanzenzuchtung - Zuchtung weisser Lupinen auf Anthraknosetoleranz - Selektion des Holobionts (Pflanze + Mikroorganismen): Erforschung der Beziehung zwischen Erbsenmikrobiom und Toleranz gegenuber Bodenmudigkeit - Zuchtung fur Mischkulturen: Erbsen & Gerste - Zuchtung der Soja auf Unkrautunterdruckung - Partizipative Zuchtungsansatze bei Soja