Biology subjects

Bourras, S.

Publications and source records attributed to Bourras, S..

8 recordsLinked to original sources

bioRxiv2025

Transcriptome analysis of the response of domesticated emmer wheat (Triticum turgidum subsp. dicoccum) to single vs. mixed infections with Zymosptoria tritici and Puccinia graminis

Tetraploid emmer Triticum turgidum subsp. dicoccum is one of the first wheat species to be domesticated. Emmer shares many pathogen species with modern durum wheat (Triticum turgidum subsp. durum) and hexaploid bread wheat (Triticum aestivum L.). Domesticated emmer is considered a highly valuable source of potentially novel disease resistance genes that can be introduced into modern wheat varieties, however, large gaps remain in our understanding of the basic immune responses of emmer to the most common wheat pathogens. In this work we describe the transcriptional response of emmer to single and mixed pathogen species infections with the ascomycete Zymoseptoria tritici, and the basidiomycete Puccinia graminis. In doing so, we here uncover unique patterns in the response of emmer to a more complex pathogen population with mixed species infections.

plant biology↗

bioRxiv2024

Interactions of sequence diverse effector proteins of wheat powdery mildew control recognition specificity by the corresponding immune receptor

To successfully colonize the living tissue of its host, the fungal wheat powdery mildew pathogen produces diverse effector proteins that are suggested to reprogram host defense responses and physiology. When recognized by host immune receptors, these proteins become avirulence (AVR) effectors. Several sequence-diverse AVRPM3 effectors and the suppressor of AVRPM3-PM3 recognition (SVRPM3a1/f1) are involved in triggering allele-specific, Pm3-mediated resistance, but the molecular mechanisms controlling their function in the host cell remain unknown. Here, we describe that AVRPM3b2/c2, AVRPM3a2/f2 and SVRPM3a1/f1 form homo- and heteromeric complexes with each other, suggesting they are present as dimers in the host cell. Alphafold2 modelling substantiated previous predictions that AVRPM3b2/c2, AVRPM3a2/f2 and SVRPM3a1/f1 all adopt a core RNase-like fold. We found that a single amino acid mutation in a predicted surface exposed region of AVRPM3a2/f2 resulted in recognition by the PM3b immune receptor, which does not recognize wildtype AVRPM3a2/f2. This indicates that differential AVRPM3 recognition by variants of the highly related PM3 immune receptors is due to subtle differences in similar protein surfaces of sequence-diverse AVRs. Based on our findings, we propose a model in which homodimers of AVRPM3s are recognized by their corresponding PM3 variants and that heterodimer formation with SVRPM3a1/f1 allows for evasion of recognition.

plant biology↗

bioRxiv2024

Population genomics and molecular epidemiology of wheat powdery mildew in Europe

Agricultural diseases are a major threat to sustainable food production. Yet, for many pathogens we know exceptionally little about their epidemiological and population dynamics, and this knowledge gap is slowing the development of efficient control strategies. Here we study the population genomics and molecular epidemiology of wheat powdery mildew, a disease caused by the biotrophic fungus Blumeria graminis forma specialis tritici (Bgt). We sampled Bgt for two consecutive years, 2022 and 2023, from 22 countries in Europe and surrounding regions, and compiled a genomic dataset of 415 Bgt isolates. We found one single epidemic unit in the north of Europe, consisting of a highly homogeneous population. Conversely, the south of Europe hosts smaller local populations which are less interconnected. In addition, we show that the population structure can be largely predicted by the prevalent wind patterns. We identified several loci that were under selection in the recent past, including fungicide targets and avirulence genes. Some of these loci are common between populations, while others are not, suggesting different local selective pressures. We reconstructed the evolutionary history of one of these loci, AvrPm17, coding for an effector recognized by the wheat receptor Pm17. We found evidence for a soft sweep on standing genetic variation. Multiple AvrPm17 haplotypes, which can partially escape recognition by Pm17, spread rapidly throughout the continent upon its introduction in the early 2000s. We also identified a new virulent variant, which emerged more recently and can evade Pm17 resistance altogether. Overall, we highlight the potential of genomic surveillance in resolving the evolutionary and epidemiological dynamics of agricultural pathogens, as well as in guiding control strategies.

evolutionary biology↗

bioRxiv2024

An experimental approach to study multi-species diseases interactions in wheat using machine learning-aided image analysis

Fusarium Head Blight (FHB) is a major disease of cereal crops present everywhere where wheat is produced. A complex of several, distinctly different, species from the genus Fusarium are responsible for causing the disease, with important taxa being F. graminearum, F. culmorum, and F. avenaceum. FHB is an adult stage, late season disease affecting wheat at anthesis. However, recent discoveries are now challenging the basic assumption that anthers and spikes are the only ecological niches relevant for resistance to FHB. Most prominently, it has been established that pathogens typically occurring earlier in the season, such as Zymoseptoria tritici, induce strong systemic changes in the plant immune system, that expand way beyond their primary ecological niche. Furthermore, taxa implicated in FHB can be isolated from virtually all wheat tissues, including typical blotch symptoms on wheat leaves. Strikingly, such important biological observations about the complex lifestyle of FHB causing taxa are overlooked as potential targets in resistance breeding. In this work we present a simplified approach allowing the dissection of the intricate lifestyles of the FHB causing Fusarium taxa. In doing so, we provide an experimental proof-of-concept that systemic signals from Z. tritici can affect the basic response of wheat to F. graminearum. We further demonstrate that differences in Fusarium species composition affect the outcome of the interaction in a genotype-specific manner. We argue that efforts to study hidden layers of the biology of FHB associated taxa are crucial to developing new resistance breeding strategies, based on a better understanding of the genetic drivers of the disease.

plant biology↗

bioRxiv2024

Genome sequence resources from three isolates of the apple canker pathogen Neonectria ditissima infecting forest trees.

Neonectria ditissima is a generalist ascomycete plant pathogen causing canker diseases on a variety of hardwood tree species and can cross-infect many of them. The fungus enters the plants through wounds throughout the year. N. ditissima is considered a major threat to apple production responsible for the fruit tree canker disease which damages trees and causes rotting of fruits in storage. Nearby forests and shelter belts can serve as source of inoculum for well-managed apple orchards. Thus, knowledge about the N. ditissima isolates infecting different host species is essential for designing integrated pest management strategies. Here, we describe the genomes of three N. ditissima isolates, Nd_iso34, Nd_iso35, and Nd_iso36, infecting European beech, American tulip tree, and American beech, respectively. We obtained genome assemblies of ca. 45 megabases for all isolates, covering 94% of the N. ditissima reference annotation, and 97% of the universal single-copy orthologs (BUSCOs). We conclude that these genome assemblies are a highly relevant resource considering the scarcity of genomic data available for N. ditissima.

genomics↗

bioRxiv2024

Survey of the wheat mycobiome associated with leaf blotch and head blight diseases in Sweden

Increasing the durability of crop resistance to plant pathogens has become a major concern in plant pathology. There are 32 diseases of agronomical importance in wheat, which makes disease management in this crop of worldwide importance extremely challenging. Two important groups of wheat pathogens driving the consumption of chemical fungicides in Sweden and worldwide are those causing head blight diseases and leaf blotch diseases. Swedish fields are regularly infested with head blight diseases typically driven by a complex of Fusarium and non-fusarium taxa including F. graminearum, F. culmorum, while leaf blotches are typically caused by Zymoseptoria tritici, Pyrenophora tritici-repentis, and Parastagonospora nodorum. In this work, we present a survey of the larger diversity of taxa associated with head blight and leaf blotch diseases in Sweden, with the primary aim to assess the usefulness of such an approach to develop new understanding and tools for disease diagnostics and management sensu lato. Here, we analyze nearly a thousand isolates collected from wheat fields across eight counties in Sweden and report the identification of pathogenic and non-pathogenic taxa as well as candidate biological control agents associated with head blight and leaf blotch diseases. We argue that such surveys represent an important tool for improving disease diagnostics, disease forecasting, and integrated management in wheat.

plant biology↗

bioRxiv2021

NRPS-gene disruption in the apple-pathogen, Neonectria ditissima

Apple production in Sweden and elsewhere is being threaten by the fungus, Neonectria ditissima, which causes a disease known as Fruit Tree Canker. The disease can cause extensive damages and the removal of diseased-wood and heavily infected trees can be laborious and expensive. Currently, there is no way to eradicate the fungus from infected trees and our knowledge of the infection process is limited. Thus, in order to target and modify genes efficiently, the genetic transformation technique developed for N. ditissima back in 2003 was modified. We report on the upgraded protocol and show that protoplasts were viable, able to uptake foreign DNA, and able to regenerate back into a mycelial colony, either as targeted gene-disruption mutants or as ectopic mutants expressing GFP.

molecular biology↗

bioRxiv2021

Standing genetic variation of the AvrPm17 avirulence gene in powdery mildew limits the effectiveness of an introgressed rye resistance gene in wheat

Introgressions of chromosomal segments from related species into wheat are important sources of resistance against fungal diseases. The durability and effectiveness of introgressed resistance genes upon agricultural deployment is highly variable - a phenomenon that remains poorly understood as the corresponding fungal avirulence genes are largely unknown. Until its breakdown, the Pm17 resistance gene introgressed from rye to wheat provided broad resistance against powdery mildew (Blumeria graminis). Here, we used QTL mapping to identify the corresponding wheat mildew avirulence effector AvrPm17. It is encoded by two paralogous genes that exhibit signatures of re-occurring gene conversion events and are members of a mildew sub-lineage specific effector cluster. Extensive haplovariant mining in wheat mildew and related sub-lineages identified several ancient virulent AvrPm17 variants that were present as standing genetic variation in wheat powdery mildew prior to the Pm17 introgression, thereby paving the way for the rapid breakdown of the Pm17 resistance. QTL mapping in mildew identified a second genetic component likely corresponding to an additional resistance gene present on the 1AL.1RS translocation carrying Pm17. This gene remained previously undetected due to suppressed recombination within the introgressed rye chromosomal segment. We conclude that the initial effectiveness of 1AL.1RS was based on simultaneous introgression of two genetically linked resistance genes. Our results demonstrate the relevance of pathogen-based genetic approaches to disentangle complex resistance loci in wheat. We propose that identification and monitoring of avirulence gene diversity in pathogen populations becomes an integral part of introgression breeding to ensure effective and durable resistance in wheat. Significance StatementDomesticated and wild wheat relatives provide an important source of new immune receptors for wheat resistance breeding against fungal pathogens. The durability of these resistance genes is variable and difficult to predict, yet it is crucial for effective resistance breeding. We identified a fungal effector protein recognised by an immune receptor introgressed from rye to wheat. We found that variants of the effector allowing the fungus to overcome the resistance are ancient. They were already present in the wheat powdery mildew gene pool before the introgression of the immune receptor and are therefore responsible for the rapid resistance breakdown. Our study demonstrates that the effort to identify new resistance genes should be accompanied by studies of avirulence genes on the pathogen side.

plant biology↗