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Rice blast, caused by Magnaporthe oryzae (M. oryzae), is one of the most destructive diseases in cultivated rice. The Wuling Mountain Area is marked as the key area for the national prevention and control of rice blast disease in China and is the ideal area for M. oryzae research according to its unique natural condition. In this study, a simple, low-cost and effective marker system including RAPD, REMAP, rep-PCR and Avr genes was developed for genetic diversity analysis of 108 M. oryzae isolates collected from the Wuling Mountain Area during 2012–2014. The results showed significant changes in the genetic structures of M. oryzae populations over the 3 years. However, there was no remarkably simple relationship between the genetic lineages and pathotypes (physiological races) of M. oryzae. The main mechanisms of M. oryzae to overcome host genes in the natural conditions of the Wuling Mountain Area might be point mutations or small deletions of gene sequences.

Due to its unique natural conditions, the Wuling Mountain region is a key area of prevention and control of rice blast disease in China and an ideal area for investigation of its causal fungus, Magnaporthe oryzae (M. oryzae) research. A total of 237 M. oryzae isolates collected from the Wuling Mountain region in 2017–2018 were used for the study of genetic diversity and pathogenicity dynamics. A set of differential varieties (DVs), including 7 Chinese DVs, 12 Japanese DVs and 21 monogenic lines, were established, which differentiate the 237 isolates in this study into different physiological races. Cluster analysis of the combined molecular marker system (RAPD, REMAP, rep-PCR and the avirulence (Avr) gene) results showed that Baiyang and Jianshi had the greatest genetic diversity, which is consistent with the pathogenic results. The proportion of the two mating types was roughly equal each year; however, the dominance of the mating type between the two years was opposite. Furthermore, four isolates contained both mating types, which were assumed to be dual maters. Isolates with amplified bands of Avr genes (Avr-Pizt and Avr-Pita) and corresponding pathogenicity were selected for Sanger sequencing. The result showed that point mutations and small indels resulted in the loss of avirulence function, indicating that mutations are potential mechanism for the rich pathogenic and genetic diversity of M. oryzae in the Wuling Mountain region.

In vitroembryogenic callus is a critical factor for genetic transformation of rice, especially for indica varieties. In this study, we investigated the relationship between polyamines, including putrescine (Put), spermidine (Spd) and spermine (Spm), and callus browning, and we studied the effect of exogenous Put on callus regeneration and on the content of endogenous polyamines. In addition, the expression levels of arginine decarboxylase gene (Adc1) and S-adenosylmethionine decarboxylase gene (Samdc) in embryogenic callus were studied by quantitative Real-time PCR analysis. The results showed that the contents of endogenous Put and Spd in the browning callus were significantly lower than those in normal callus. Exogenous Put could effectively improve the growing state of callus of indica rice and enhance the development of embryogenic callus. The content of endogenous polyamines in embryogenic callus, especially Spd and Spm, was increased after addition of exogenous Put. Additionally, exogenous Put also had an obvious impact on the expression levels ofAdc1but partial effect on the expression levels ofSamdcgene. This study could increase the knowledge of both embryogenic callus induction and polyamine catabolism in callus in indica rice.

Rice blast resistance (R) genes-mediated resistance response depends on various resistance-related genes involved in incompatible interactions. In this work, the expression profiles of innate rice immunity related genes were examined in the mediated resistance response of true/field resistance genes. Three sets of rice near-isogenic lines (NILs) were used: the resistant NILs carrying true resistance genes in the genetic background of the susceptible cultivar Nipponbare (NB), NB-Pib, NB-Pizt, NB-Pik and NB-Pita2; NILs bearing field resistance genes pi21 in the susceptible cultivar Aichiasahi (AA) AA-pi21, Kahei (KHR). The marker gene OsWRKY45 of salicylic acid (SA) signalling was upregulated in all tested cultivars. And, JAmyb (marker gene of jasmonic acid signalling) showed higher upregulation in the resistance lines with nucleotide-binding sites and leucine-rich repeat (NBS-LRR) R genes Pib, Pizt, Pik, Pita2 and Pikahei than in NB and KHS. SalT of abscisic acid (ABA) signalling may be involved in the R/Avr interaction, including Pizt, Pik, pi21 and Pikahei. However, SalT was shown to negatively regulate Pib/AvrPib interaction. OsPR1b and PBZ1 were differentially expressed and strongly activated at a later stage by 48 h post-inoculation. Interestingly, there was evidence that OsPR1b and PBZ1 played an important role in the pi21-mediated response. It was shown that OsRAR1 could be upregulated in the true resistance line NB-Pita2 and the field resistance line KHR, while OsSGT1 and OsHSP90 could be upregulated in all tested lines. The involvement of these genes illustrated the complexity of the downstream signalling pathways in the mediated resistance response of true/field resistance genes.

Rice blast is one of the most serious diseases of cultivated rice. We characterize here the nucleotide variation present at nine blast resistance (R) genes within a collection of 13 indica and 13 japonica rice cultivars, along with 12 accessions of wild rice (Oryza rufipogon). Compared with other functional genes, high genetic diversity has been observed in blast R genes (mean nucleotide diversity of 3.2%), which might be the most important characteristics of blast R genes. Even if the overall diversity in R genes is high, the genes can also be divided into three types according to different degrees of conservation by principal component analysis: relative conservation (Pita, Pit, Pi5-1, and Pid-2), intermediate diversity (Pi37, Pib, and Pi9), and high diversity (Pi36 and Pikm-2), suggesting that these types of R genes might recognize different categories of molecules released by rice blast pathogens. Our data also revealed that a significant regression was observed between the wild and the cultivated acc...

The resistance gene Pi36 confers a stable and high level of resistance against Chinese isolates of the rice blast pathogen Magnaporthe oryzae. Quantitative real time RT-PCR was used to investigate the expression profiles of various resistance-related genes in both the Pi36/AvPi36 incompatible interactions. Among 17 members of the OsMAPK family, OsMAPK2, OsMAPK4, OsMAPK8 and OsMAPK15 were differentially expressed, as were OsWRKY30, OsWRKY32, OsWRKY64 and OsWRKY67 among the 13 OsWRKY members studied. The induction of the expression of genes from both of these families suggests that both the JA and SA pathways are involved in Pi36-mediated defence. Other genes differentially expressed included the OsbZIP transcription factors, OsNIF1 and OsNIF2, and the NPR1 homologue OsNH2, all of which were reported in the rice blast pathosystem. The involvement of these genes illustrates the complexity of the downstream signalling pathways involved in the Pi36/AvrPi36 interaction.

The single‐locus rice blast resistance gene Pi36 is of the coiled‐coil NBS‐LRR (nucleotide binding site–leucine‐rich repeat) type. We have investigated its evolution by resequencing a set of haplotypes (six ssp. indica and four ssp. japonica cultivars and three wild rice accessions) both within and outside the gene’s coding region. It was found that the average nucleotide diversity was ∼4.5%, characteristic of an intermediately diversified pattern. The Ka/Ks ratio and Tajima’s D test were used to show that the gene’s evolution reflects a mixture of purifying and balancing selection. In all, 186 significant gene conversion events were identified across the full coding region, suggesting that gene conversion has also been an important driver of sequence diversification.

Blast, caused by the ascomycete fungus Magnaporthe oryzae, is one of the most devastating diseases of rice worldwide. The Chinese native cultivar (cv.) Q15 expresses the broad-spectrum resistance to most of the isolates collected from China. To effectively utilize the resistance, three rounds of linkage analysis were performed in an F2 population derived from a cross of Q15 and a susceptible cv. Tsuyuake, which segregated into 3:1 (resistant/susceptible) ratio. The first round of linkage analysis employing simple sequence repeat (SSR) markers was carried out in the F2 population through bulked-segregant assay. A total of 180 SSR markers selected from each chromosome equally were surveyed. The results revealed that only two polymorphic markers, RM247 and RM463, located on chromosome 12, were linked to the resistance (R) gene. To further define the chromosomal location of the R gene locus, the second round of linkage analysis was performed using additional five SSR markers, which located in the region anchored by markers RM247 and RM463. The locus was further mapped to a 0.27 cM region bounded by markers RM27933 and RM27940 in the pericentromeric region towards the short arm. For fine mapping of the R locus, seven new markers were developed in the smaller region for the third round of linkage analysis, based on the reference sequences. The R locus was further mapped to a 0.18 cM region flanked by marker clusters 39M11 and 39M22, which is closest to, but away from the Pita/Pita 2 locus by 0.09 cM. To physically map the locus, all the linked markers were landed on the respective bacterial artificial chromosome clones of the reference cv. Nipponbare. Sequence information of these clones was used to construct a physical map of the locus, in silico, by bioinformatics analysis. The locus was physically defined to an interval of ≈37 kb. To further characterize the R gene, five R genes mapped near the locus, as well as 10 main R genes those might be exploited in the resistance breeding programs, were selected for differential tests with 475 Chinese isolates. The R gene carrier Q15 conveys resistances distinct from those conditioned by the carriers of the 15 R genes. Together, this valuable R gene was, therefore, designated as Pi39(t). The sequence information of the R gene locus could be used for further marker-based selection and cloning.