Population structure of Magnaporthe oryzae from different geographic regions and interaction transcriptomes with rice genotypes at high temperature | Genomic studies on rice-rice blast fungus interaction in different climatic scenarios

It is currently hypothesized that climate change may lead to global warming, and temperatures might increase by 2-5°C at the end of the twenty-first century. However, the consequences of the expected temperature elevation on pathogen biology, epidemiology and plant host resistance have continued to provide conflicting results due to several interacting factors. Magnaporthe oryzae is conceivably the most important pathogen in global rice production. Although the rice-M. oryzae pathosystem is well-studied at both the phenotypic and genomic level, the effect of elevated temperatures on Rice-M. oryzae interaction is presently less studied. In the first part of this study, we analyzed the host phenotypic reactions and RNA-seq genome-wide transcript profiles of two genetic rice backgrounds, CO (O. sativa indica; Co39) and LT (O. sativa japonica; LTH), carrying the same R gene (Pi54), and exposed to M. oryzae infection, after exposure to 28°C and 35°C. Both backgrounds were more resistant at 35°C compared to 28°C. Moreover, callose deposits and cell wall fluorescence of the attacked epidermal cells were more intense at 35oC than at 28oC. However, CO had a more severe disease phenotype compared to LT at 28°C. The differential reaction of Pi54 in the two backgrounds suggests that genetic factors other than Pi54 determine the resistance response, and further indicates that the genetic background of japonica rice facilitates the function of Pi54 more than the background of indica rice. Gene expression analysis further revealed substantial background transcriptional profile variation, and demonstrated that LT and CO exhibit differences in genes expressed in response to high temperature and M. oryzae. Hydrogen peroxide (H2O2) production and abscisic acid (ABA) responsive genes were more pronounced in LT compared to CO, whereas SA levels were higher in CO than LT. Both genotypes showed a high induction of OsBISAMT1, which converts SA to MeSA. Conversely, only LT showed a significant induction of jasmonate O-methyltransferase and JA induced jacalin-like lectin (LOC_Os12g14440) that mediates broad spectrum resistance. Thus, the nature, timing and magnitude of ROS and hormone signaling pathways in response to both high temperature and M. oryzae infection may be largely controlled by the genetic backgrounds. In the second study, we analyzed the effect of temperature on the transcriptomes of the rice cultivar Nipponbare and its pathogen M. oryzae simultaneously at 35°C and 28°C using RNA-seq. Our results showed that plants exposed to 35°C and inoculated with M. oryzae had increased number and expression levels of M. oryzae putative effectors compared to plants grown and inoculated at 28°C. Genes involved in secondary metabolism, transport, lipid metabolism and carbohydrate metabolism also showed increased transcription during M. oryzae infection at 35°C compared to 28°C. These transcription changes likely facilitated host colonization and adaptation by the pathogen. Certainly, plants exposed to 35°C followed by inoculation with M. oryzae had a more severe disease phenotype than plants inoculated at 28°C. Moreover, in planta fungal biomass was significantly higher in Nip35i than Nip28i, suggesting rapid colonization of the host tissues by the pathogen at 35°C. Considering that a stronger induction of expansins, pectin methylesterase and von Willebrand factor type A was observed in plants exposed to 35°C, it is possible that these enzymes could have compromised the plant cell wall, probably facilitating rapid colonization and delivery of several proteins able to promptly manipulate the plant defense by the pathogen. Several genes, including Avr genes also appeared to be indispensable for M. oryzae infection at high temperature, given their high expression levels at 35°C compared to 28°C. It could be argued that plants introgressed with the cognate R gene may probably detect easily the pathogen effectors and subsequently evoke ETI, even at reduced expression levels induced by high temperature treatment. Thus, it is likely that despite the lowered expression of Pi54 in CO and LT at 35°C, this R gene was able to detect M. oryzae effectors, e.g., AvrPik/km/kp, in the backgrounds of these ecotypes. The expression level of an avr gene therefore determines the plant capacity to detect the pathogen under abiotic stresses that tend to reduce transcript levels of the R gene. Thus, R gene-mediated resistance at high temperature may depend on the avr gene dosage effect. Because the Pik/km/kp alleles, which correspond with a AvrPik/km/kp like gene in M. oryzae are redundant or missing in Nipponbare, it is likely that the high temperature effect on plant cell wall and membrane permeability provided a direct pass for the pathogen effectors. Taken together, the inability of the plant to defend itself when exposed to both abiotic and biotic stresses is correlated with the absence or the degree at which abiotic stress alters both specific and general defense responses. On the other hand, temperature effect on both R gene mediated resistance and partial resistance is likely more variable than earlier envisaged, and will require intensive screening efforts to identify stable resistant gene combinations. Thus, it may be too soon to generalize the effect of the changing temperature on host resistance beyond the current study because of the significant differences in defense responses among host genotypes studied so far. The likely scenario is that some cultivars may have a more stable resistance against M. oryzae than others despite increasing temperatures, and research efforts to identify such stable genotypes will need to be raised. In the third part of this study, we analyzed the genetic diversity and population structure of 88 isolates of M. oryzae from East Africa and representative isolates from West Africa and the Philippines using amplified fragment length polymorphism (AFLP) markers. Our results indicate low genetic differentiation in East African populations, suggesting that the populations are relatively homogeneous. It appears that selection pressures have played a weak role in altering allele frequencies on the East African populations. It is also tempting to suggest that any selection pressures that exist to influence allele frequencies are not confined to a particular geographic area, and most likely the pathogen is exposed to lowly variable climatic conditions, hosts and cropping systems. On the other hand, a strong indication of gene flow was detected among East African populations. Although this tends to reduce genetic differentiation among populations, if local selection and genetic drift within populations is sufficiently high it may permit emergence and spread of highly advantageous alleles. Thus, regional efforts to limit informal movement of planting materials may need to be raised to prevent epidemics associated with exotic strains. The presence of two mating types in some locations indicates past signatures of evolution which may need further examination to understand. Being the first study on M. oryzae on rice in East Africa, the effect of the predicted climate change on M. oryzae epidemics and variability will have to be carefully considered, considering the homogeneity of the populations studied, so far.