▪ Abstract We hypothesize that the evolutionary potential of a pathogen population is reflected in its population genetic structure. Pathogen populations with a high evolutionary potential are more likely to overcome genetic resistance than pathogen populations with a low evolutionary potential. We propose a flexible framework to predict the evolutionary potential of pathogen populations based on analysis of their genetic structure. According to this framework, pathogens that pose the greatest risk of breaking down resistance genes have a mixed reproduction system, a high potential for genotype flow, large effective population sizes, and high mutation rates. The lowest risk pathogens are those with strict asexual reproduction, low potential for gene flow, small effective population sizes, and low mutation rates. We present examples of high-risk and low-risk pathogens. We propose general guidelines for a rational approach to breed durable resistance according to the evolutionary potential of the pathogen.

Pathogen population genetics, evolutionary potential, and durable resistance

The current rate of biodiversity loss threatens to disrupt greatly the functioning of ecosystems, with potentially significant consequences for humanity. The magnitude of the loss is generally measured with the use of species extinction rates, an approach that understates the severity of the problem and masks some of its most important consequences. Here, we propose a major expansion of this focus to include population diversity: considering changes in the size, number, distribution and genetic composition of populations and the implications of those changes for the functioning of ecosystems and the provision of ecosystem services. We also outline the key components of population diversity and describe a new approach to delineating a population unit that explicitly links it to the services that it provides

http://max2.ese.u-psud.fr/epc/conservation/PDFs/luck.pdf

Population diversity and ecosystem services

Phylogenetic and population genetic methods that compare nucleic acid variation are being used to identify species and populations of pathogenic fungi and determine how they reproduce in nature. These studies show that asexual or sexual reproductive morphology does not necessarily correlate with clonal or recombining reproductive behavior, and that fungi with all types of reproductive morphologies and behaviors can be accommodated by a phylogenetic species concept. Although approximately one fifth of described fungi have been thought to be asexual and clonal, recent studies have shown that they are also recombining. Whether a particular pathogen reproduces clonally or by recombination depends on factors relating to its biology and its distribution in space and time. Knowing the identity of species and populations and their reproductive modes, while taking a broad view of pathogen behavior in space and time, should enhance the ability of pathologists to control pathogens and even predict their behavior.

THE EVOLUTION OF ASEXUAL FUNGI: Reproduction, Speciation and Classification

Rice, as a widely and intensively cultivated crop, should be a target for parasite host shifts and a source for shifts to co-occurring weeds. Magnaporthe oryzae, of the M. grisea species complex, is the most important fungal pathogen of rice, with a high degree of host specificity. On the basis of 10 loci from six of its seven linkage groups, 37 multilocus haplotypes among 497 isolates of M. oryzae from rice and other grasses were identified. Phylogenetic relationships among isolates from rice (Oryza sativa), millet (Setaria spp.), cutgrass (Leersia hexandra), and torpedo grass (Panicum repens) were predominantly tree like, consistent with a lack of recombination, but from other hosts were reticulate, consistent with recombination. The single origin of rice-infecting M. oryzae followed a host shift from a Setaria millet and was closely followed by additional shifts to weeds of rice, cutgrass, and torpedo grass. Two independent estimators of divergence time indicate that these host shifts predate the Green Revolution and could be associated with rice domestication. The rice-infecting lineage is characterized by high copy number of the transposable element MGR586 (Pot3) and, except in two haplotypes, by a loss of AVR-Co39. Both mating types have been retained in ancestral, well-distributed rice-infecting haplotypes 10 (mainly temperate) and 14 (mainly tropical), but only one mating type was recovered from several derived, geographically restricted haplotypes. There is evidence of a common origin of both ACE1 virulence genotypes in haplotype 14. Host-haplotype association is evidenced by low pathogenicity on hosts associated with other haplotypes.

https://www.genetics.org/content/genetics/early/2005/03/31/genetics.105.041780.full.pdf

Origins of host-specific populations of the blast pathogen, Magnaporthe oryzae, in crop domestication with subsequent expansion of pandemic clones on rice and weeds of rice

Rice blast, caused by the fungus Pyricularia grisea (Cooke) Sacc., is a serious rice (Oryza sativa L.)disease causing considerable economic damage worldwide. DNA markers for rice blast resistance have been developed, but most are not suitable for routine use in a marker-assisted selection breeding program involving large numbers of progeny. After identifying candidate microsatellite markers from public database sources, we have mapped these markers near the blast resistance genes Pi-b, Pi-k, and Pi-ta 2 on rice chromosomes 2, 11, and 12, respectively, using segregation information from hundreds of progeny in several crosses. Two microsatellite markers, RM208 and RM224, were found to cosegregate with the Pi-b and Pi-k genes, respectively, while additional microsatellites were found to closely flank these two genes and the Pi-ta 2 gene. The new markers are polymorphic in the narrow crosses characteristic of applied breeding programs and appear to be ideally suited for marker assisted selection for blast resistance in rice because of their tight linkage with resistance genes and ease of use through analysis of amplification products. A dominant marker indicating the presence of the Pi-b gene, Pibdom, has also been developed on the basis of the sequence of the cloned Pi-b gene. These markers should facilitate the introgression and pyramiding of these three blast resistance genes into new rice cultivars and elite lines.

Development of DNA Markers Suitable for Marker Assisted Selection of Three Pi Genes Conferring Resistance to Multiple Pyricularia grisea Pathotypes

DNA fingerprinting was used to analyze microgeographic variation in the Magnaporthe grisea population in Arkansas. One hundred and thirteen isolates were collected from two commercial rice fields (cv. Newbonnet) in 1991. In addition, several reference isolates representing the predominant pathotypes in Arkansas were examined. Total DNA of each isolate was restricted with EcoR1 and probed with a dispersed repeated MGR586 DNA probe. MGR586 DNA fingerprint groups were identified based on DNA restriction fragment length polymorphism similarities. Seven distinct fingerprint groups (designated A through G) were identified among the field and reference isolates. These seven fingerprint groups were very similar to seven of the eight fingerprint groups (lineages) previously reported for M. grisea [...]

DNA fingerprinting to examine microgeographic variation in the Magnaporthe grisea (Pyricularia grisea) population in two rice fields in Arkansas

MGR586 DNA fingerprinting has been widely used to characterize population diversity of the rice blast pathogen, Pyricularia grisea. However, the frequency and distribution of particular haplotypes (individuals) within MGR-delimited lineages has not been examined in the United States. MGR586 DNA fingerprinting, mitochondrial DNA (mtDNA) restriction fragment length polymorphism (RFLPs), and virulence phenotyping were used to examine genetic diversity of P. grisea in Arkansas. A total of 470 monoconidial isolates were recovered from eight rice cultivars in 18 commercial fields in nine counties in Arkansas. All isolates were examined for nuclear DNA RFLPs with the MGR586 DNA fingerprint probe, and both the MGR lineage (isolates with >80% similarity) and the haplotype frequencies were determined. Four distinct MGR586 DNA fingerprint lineages (designated A, B, C, and D) were identified among the 470 field isolates. All four lineages were found in 9 of the 18 locations. Three lineages were found in four...

/pdf/regional-population-diversity-of-pyricularia-grisea-in-56kaxq2ehr.pdf

J. Q. Xia

Papers

DNA fingerprinting to examine microgeographic variation in the Magnaporthe grisea (Pyricularia grisea) population in two rice fields in Arkansas

Regional Population Diversity of Pyricularia grisea in Arkansas and the Influence of Host Selection.