Didier Tharreau

World population structure and migration of the rice blast fungus, #Magnaporthe oryzae#

The clonal structure of Magnaporthe oryzae populations was observed in various countries. This information was used to propose new resistance deployment strategies. However, our understanding of how new virulent races appear and spread remains limited. Population genetic analyses, with neutral and selected markers, provide tools to evaluate such events. We used microsatellite markers to study populations at the worldwide scale. We observed three major genetic groups. Two groups include isolates of only one mating each. The third group includes isolates of both mating types. During natural epidemics spores disperse over short distances (1–5 m). This is likely to cause the partial geographic structuring we observed. However, long distance migrations are possible through the transportation of infected seeds. We observed that, in some cases, one population is more closely related to populations from other continents than from a population from the same area. Long distance migration was also confirmed by studying the distribution of the genotypes of the cloned avirulence gene ACE1. Two major virulent genotypes were identified. These genotypes appeared by a complex duplication/deletion event. These two genotypes are widely distributed over different continents. Altogether, these results suggest a unique apparition event followed by long distance migrations of virulent genotypes.

ARCHIPELAGO: Towards Bridging the Gap Between Molecular and Genetic Information in Rice Blast Disease Resistance

Large amounts of major resistance genes, QTL (Quantitative Trait Locus) and expression data dealing with rice blast resistance have been described in the past. We extensively reviewed this information and inserted it into the OryGenesDB database, creating the ARCHIPELAGO resource. This represents more than 1,500 genes differentially expressed upon infection by Magnaporthe oryzae, 1,000 resistance gene analogs, 88 mapped resistance genes, 341 QTLs and 165 metaQTLs. Further analysis of the metaQTL data allowed the identification of robust or broad spectrum metaQTLs. Cross referencing defense gene expression and metaQTL information identified some candidate genes for metaQTL but does not demonstrate preferential co-localization of defense-related genes in metaQTLs. In contrast, disease regulators are statistically associated with disease QTLs. At the genomic level, we can observe that some regions of the rice genome are richer than others for defense-related genes. This resource opens new possibilities for marker-assisted selection and QTL cloning.

Sequence Variation and Recognition Specificity of the Avirulence Gene AvrPiz-T in Magnaporthe Oryzae Field Populations

Magnaporthe oryzae, the rice blast pathogen, causes significant annual yield loss of rice worldwide. Currently, the most effective disease control approach is deployment of host resistance through introduction of resistance (R) genes into elite cultivars. The function of each R gene relies on the specific recognition of an avirulence (AVR) gene of the pathogen. However, the introduced resistance can be broken down within a few years, due to mutation of the AVR genes in the field populations. It is known from a few case studies that AVR mutation patterns are different from one to another. Therefore, knowledge of AVR genes sequence diversity serves as fundamental background in introducing new resistance to control rice blast. In this study, we focused on a newly identified AVR gene AvrPiz-t. We PCR amplified open reading frames (ORFs) of AvrPiz-t as well as promoter regions to detect size variation at this locus in 711 isolates of M. oryzae collected from 38 countries and regions. Through sequencing and Southern hybridization of the amplified locus, strains with polymorphisms in the ORF were classified into groups based on mutation type and site. Natural selection intensity on this gene was calculated and pathogenicity assays were applied to evaluate the association between AvrPiz-t ORF/promoter polymorphism and virulence. In conclusion, sequences at the AvrPiz-t locus were revealed to contain variations at both promoter and ORF regions. This locus is undergoing a relatively strong positive selection. The diversity in coding sequence and the insertions of transposable elements in the promoter region enable M. oryzae to evade recognition by the cognate Piz-t R gene in the host.

Additional file 3: Table S3. of Association mapping of resistance to rice blast in upland field conditions

Blast disease scores measured on 18 differential lines in Andranomanelatra in 2011 and 2015. (XLSX 9 kb)