Evaluation of Rice Responses to the Blast Fungus Magnaporthe oryzae at Different Growth Stages

Horizontal gene transfer of Cccyt contributes to virulence of mycoparasite Calcarisporium cordycipiticola by interacting with a host heat shock protein

Horizontal gene transfer (HGT) is an important driving force for virulence evolution of pathogens, however, functions of these transferred genes are still not fully investigated. Here, an HGT effector, CcCYT was reported to contribute to virulence of a mycoparasite, Calcarisporium cordycipiticola to the host Cordyceps militaris, an important mushroom. Cccyt was predicted to be horizontally transferred from Actinobacteria ancestor by phylogenetic, synteny, GC content and codon usage pattern analyses. The transcript of Cccyt was sharply up-regulated at the early stage of infecting C. militaris. This effector was localized to the cell wall and contributed to the virulence of C. cordycipiticola without affecting its morphology, mycelial growth, conidiation, and resistance to abiotic stress. CcCYT can firstly bind the septa, and finally cytoplasm of the deformed hyphal cells of C. militaris. Pull-down assay coupled mass spectrometry revealed that proteins with which CcCYT interacted were related to protein process, folding and degradation. GST-Pull down assay confirmed that C. cordycipiticola effector CcCYT can interact with host protein CmHSP90 to inhibit the immune response of host. The results provided functional evidence that HGT is an important driving force for the virulence evolution and will be helpful for revealing the interaction between mycoparasite and mushroom host.

Interactive effects of tropospheric ozone and blast disease (Magnaporthe oryzae) on different rice genotypes

Rising tropospheric ozone concentrations can cause rice yield losses and necessitate the breeding of ozone-tolerant rice varieties. However, ozone tolerance should not compromise the resistance to important biotic stresses such as the rice blast disease. Therefore, we investigated the interactive effects of ozone and rice blast disease on nine different rice varieties in an experiment testing an ozone treatment, blast inoculation, and their interaction. Plants were exposed to an ozone concentration of 100 ppb for 7 h per day or ambient air throughout the growth period. Half of the plants were simultaneously infected with rice blast inoculum. Grain yield was significantly reduced in the blast treatment (17%) and ozone treatment (37%), while the combination of both stresses did not further decrease grain yields compared to ozone alone. Similar trends occurred for physiological traits such as vegetation indices, normalized difference vegetation index (NDVI), photochemical reflectance index (PRI), Lichtenthaler index 2 (Lic2), and anthocyanin reflectance index 1 (ARI1), as well as stomatal conductance and lipid peroxidation. Ozone exposure mitigated the formation of visible blast symptoms, while blast inoculation did not significantly affect visible ozone symptoms. Although different genotypes showed contrasting responses to the two types of stresses, no systematic pattern was observed regarding synergies or trade-offs under the two types of stresses. Therefore, we conclude that despite the similarities in physiological stress responses to ozone and blast, the tolerance to these stresses does not appear to be genetically linked in rice.

Mapping Blast Resistance Genes in Rice Varieties 'Minghui 63' and 'M-202'

Rice blast caused by the fungus Magnaporthe oryzae (syn. Magnaporthe grisea) is one of the most lethal diseases for sustainable rice production worldwide. Blast resistance mediated by major resistance genes is often broken down after a short period of deployment, while minor blast resistance genes, each providing a small effect on disease reactions, are more durable. In the present study, we first evaluated disease reactions of two rice breeding parents 'Minghui 63' and 'M-202' with 11 blast races, IA45, IB1, IB45, IB49, IB54, IC1, IC17, ID1, IE1, IG1, and IH1, commonly present in the United States, under greenhouse conditions using a category disease rating resembling infection types under field conditions. 'Minghui 63' exhibited differential resistance responses in comparison with those of 'M-202' to the tested blast races. A recombinant inbred line (RIL) population of 275 lines from a cross between 'Minghui 63' and 'M-202' was also evaluated with the above-mentioned blast races. The population was genotyped with 156 simple sequence repeat (SSR) and insertion and deletion (Indel) markers. A linkage map with a genetic distance of 1,022.84 cM was constructed using inclusive composite interval mapping (ICIM) software. A total of 10 resistance QTLs, eight from 'Minghui 63' and two from 'M-202', were identified. One major QTL, qBLAST2 on chromosome 2, was identified by seven races/isolates. The remaining nine minor resistance QTLs were mapped on chromosomes 1, 3, 6, 9, 10, 11, and 12. These findings provide useful genetic markers and resources to tag minor blast resistance genes for marker-assisted selection in rice breeding program and for further studies of underlying genes.

Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution

BACKGROUND

Taichung Native 1 (TN1) is the first semidwarf rice cultivar that initiated the Green Revolution. As TN1 is a direct descendant of the Dee-geo-woo-gen cultivar, the source of the sd1 semidwarf gene, the sd1 gene can be defined through TN1. Also, TN1 is susceptible to the blast disease and is described as being drought-tolerant. However, genes related to these characteristics of TN1 are unknown. Our aim was to identify and characterize TN1 genes related to these traits.

RESULTS

Aligning the sd1 of TN1 to Nipponbare sd1, we found a 382-bp deletion including a frameshift mutation. Sanger sequencing validated this deleted region in sd1, and we proposed a model of the sd1 gene that corrects errors in the literature. We also predicted the blast disease resistant (R) genes of TN1. Orthologues of the R genes in Tetep, a well-known resistant cultivar that is commonly used as a donor for breeding new blast resistant cultivars, were then sought in TN1, and if they were present, we looked for mutations. The absence of Pi54, a well-known R gene, in TN1 partially explains why TN1 is more susceptible to blast than Tetep. We also scanned the TN1 genome using the PosiGene software and identified 11 genes deemed to have undergone positive selection. Some of them are associated with drought-resistance and stress response.

CONCLUSIONS

We have redefined the deletion of the sd1 gene in TN1, a direct descendant of the Dee-geo-woo-gen cultivar, and have corrected some literature errors. Moreover, we have identified blast resistant genes and positively selected genes, including genes that characterize TN1's blast susceptibility and abiotic stress response. These new findings increase the potential of using TN1 to breed new rice cultivars.

Acid Rain Increases Impact of Rice Blast on Crop Health via Inhibition of Resistance Enzymes

Worldwide, rice blast (Pyricularia oryzae) causes more rice crop loss than other diseases. Acid rain has reduced crop yields globally for nearly a century. However, the effects of acid rain on rice-Pyricularia oryzae systems are still far from fully understood. In this study, we conducted a lab cultivation experiment of P. oryzae under a series of acidity conditions as well as a glasshouse cultivation experiment of rice that was inoculated with P. oryzae either before (P. + SAR) or after (SAR + P.) simulated acid rain (SAR) at pH 5.0, 4.0, 3.0 and 2.0. Our results showed that the growth and pathogenicity of P. oryzae was significantly inhibited with decreasing pH treatments in vitro culture. The SAR + P. treatment with a pH of 4.0 was associated with the highest inhibition of P. oryzae expansion. However, regardless of the inoculation time, higher-acidity rain treatments showed a decreased inhibition of P. oryzae via disease-resistance related enzymes and metabolites in rice leaves, thus increasing disease index. The combined effects of high acidity and fungal inoculation were more serious than that of either alone. This study provides novel insights into the effects of acid rain on the plant-pathogen interaction and may also serve as a guide for evaluating disease control and crop health in the context of acid rain.

A Rapid Survey of Avirulence Genes in Field Isolates of Magnaporthe oryzae

Magnaporthe oryzae is the causal agent for the devastating disease rice blast. The avirulence (AVR) genes in M. oryzae are required to initiate robust disease resistance mediated by the corresponding resistance (R) genes in rice. Therefore, monitoring pathogen AVR genes is important to predict the stability of R gene-mediated blast resistance. In the present study, we analyzed the DNA sequence dynamics of five AVR genes, namely, AVR-Pita1, AVR-Pik, AVR-Pizt, AVR-Pia, and AVR-Pii, in field isolates of M. oryzae in order to understand the effectiveness of the R genes, Pi-ta, Pi-k, Pi-zt, Pia, and Pii in the Southern U.S. rice growing region. Genomic DNA of 258 blast isolates collected from commercial fields of the Southern UNITED STATES during 1975-2009 were subjected to PCR amplification with AVR gene-specific PCR markers. PCR products were obtained from 232 isolates. The absence of PCR products in the remaining 26 isolates suggests that these isolates do not contain the tested AVR genes. Amplified PCR products were subsequently gel purified and sequenced. Based on the presence or absence of the five AVR genes, 232 field isolates were classified into 10 haplotype groups. The results revealed that 174 isolates of M. oryzae carried AVR-Pita1, 225 isolates carried AVR-Pizt, 44 isolates carried AVR-Pik, 3 isolates carried AVR-Pia, and one isolate carried AVR-Pii. AVR-Pita1 was highly variable, and 40 AVR-Pita1 haplotypes were identified in avirulent isolates. AVR-Pik had four nucleotide sequence site changes resulting in amino acid substitutions, whereas three other AVR genes, AVR-Pizt, AVR-Pia, and AVR-Pii, were relatively stable. Two AVR genes, AVR-Pik and AVR-Pizt, were found to exist in relatively larger proportions of the tested field isolates, which suggested that their corresponding R genes Pi-k and Pi-zt can be deployed in preventing blast disease in the Southern UNITED STATES in addition to Pi-ta. This study demonstrates that continued AVR gene monitoring in the pathogen population is critical for ensuring the effectiveness of deployed blast R genes in commercial rice fields.

Deciphering signalling network in broad spectrum Near Isogenic Lines of rice resistant to Magnaporthe oryzae

Disease resistance (R) genes like Pi9, Pita, Pi21, Pi54 are playing important role for broad spectrum blast resistance in rice. Development of near isogenic lines (NILs) using these type of broad spectrum genes and understanding their signalling networks is essential to cope up with highly evolving Magnaporthe oryzae strains for longer duration. Here, transcriptional-level changes were studied in three near-isogenic lines (PB1 + Pi1, PB1 + Pi9 and PB1 + Pi54) of rice resistant to blast infection, to find the loci that are unique to resistant lines developed in the background of Pusa Basmati 1 (PB1). The pathway analysis of loci, unique to resistant NILs compared to susceptible control revealed that plant secondary metabolite synthesis was the common mechanism among all NILs to counter against M. oryzae infection. Comparative transcriptome analysis helped to find out common clusters of co-expressed significant differentially expressed loci (SDEL) in both PB1 + Pi9 and PB1 + Pi54 NILs. SDELs from these clusters were involved in the synthesis and degradation of starch; synthesis and elongation of fatty acids; hydrolysis of phospholipids; synthesis of phenylpropanoid; and metabolism of ethylene and jasmonic acid. Through detailed analysis of loci specific to each resistant NIL, we identified a network of signalling pathways mediated by each blast resistance gene. The study also offers insights into transcriptomic dynamics, points to a set of important candidate genes that serve as module to regulate the changes in resistant NILs. We suggest that pyramiding of the blast resistance gene Pi9 with Pi54 will lead to maximum broad spectrum resistance to M. oryzae.