Pathotypes of Pyricularia grisea in Rice Fields of Central and Southern China

Genome-Wide Association Study Identifies Rice Panicle Blast-Resistant Gene Pb4 Encoding a Wall-Associated Kinase

Rice blast is one of the most devastating diseases, causing a significant reduction in global rice production. Developing and utilizing resistant varieties has proven to be the most efficient and cost-effective approach to control blasts. However, due to environmental pressure and intense pathogenic selection, resistance has rapidly broken down, and more durable resistance genes are being discovered. In this paper, a novel wall-associated kinase (WAK) gene, Pb4, which confers resistance to rice blast, was identified through a genome-wide association study (GWAS) utilizing 249 rice accessions. Pb4 comprises an N-terminal signal peptide, extracellular GUB domain, EGF domain, EGF-Ca2+ domain, and intracellular Ser/Thr protein kinase domain. The extracellular domain (GUB domain, EGF domain, and EGF-Ca2+ domain) of Pb4 can interact with the extracellular domain of CEBiP. Additionally, its expression is induced by chitin and polygalacturonic acid. Furthermore, transgenic plants overexpressing Pb4 enhance resistance to rice blast. In summary, this study identified a novel rice blast-resistant gene, Pb4, and provides a theoretical basis for understanding the role of WAKs in mediating rice resistance against rice blast disease.

Development of a molecular marker for the Pi1 gene based on the association of the SNAP protocol with the touch-up gradient amplification method

Genetic resistance is the most effective and eco-friendly approach to combat rice blast. The application of resistance genes may be facilitated by the availability of molecular markers that allow marker-assisted selection during the breeding process. The Pi1 gene, considered to be a broad-spectrum resistance gene, might contribute to enhancing resistance to rice blast, but it lacks a suitable marker that can be used. In this study, we investigated nucleotide polymorphism in the Pik locus and combined the SNAP protocol with the touch-up gradient amplification method to develop a SNAP marker. The Pi1 SNAP marker could distinguish Pi1 from Pik alleles, and when used for screening a germplasm bank and an F2 population, it consistently identified germplasms carrying the Pi1 gene. The P1 SNAP marker offers as advantages to involve only the presence/absence analysis of PCR amplicons resolved on an agarose gel.

Approaches to Reduce Rice Blast Disease Using Knowledge from Host Resistance and Pathogen Pathogenicity

Rice is one of the staple foods for the majority of the global population that depends directly or indirectly on it. The yield of this important crop is constantly challenged by various biotic stresses. Rice blast, caused by Magnaporthe oryzae (M. oryzae), is a devastating rice disease causing severe yield losses annually and threatening rice production globally. The development of a resistant variety is one of the most effective and economical approaches to control rice blast. Researchers in the past few decades have witnessed the characterization of several qualitative resistance (R) and quantitative resistance (qR) genes to blast disease as well as several avirulence (Avr) genes from the pathogen. These provide great help for either breeders to develop a resistant variety or pathologists to monitor the dynamics of pathogenic isolates, and ultimately to control the disease. Here, we summarize the current status of the isolation of R, qR and Avr genes in the rice-M. oryzae interaction system, and review the progresses and problems of these genes utilized in practice for reducing rice blast disease. Research perspectives towards better managing blast disease by developing a broad-spectrum and durable blast resistance variety and new fungicides are also discussed.

Frequencies and Variations of Magnaporthe oryzae Avirulence Genes in Hunan Province, China

Rice blast caused by Magnaporthe oryzae poses significant threaten to rice production. For breeding and deploying resistant rice varieties, it is essential to understand the frequencies and genetic variations of avirulence (AVR) genes in the pathogen populations. In this study, 444 isolates were collected from Hunan Province, China in 2012, 2015, and 2016, and their pathogenicity was evaluated by testing them on monogenic rice lines carrying resistance genes Pita, Pizt, Pikm, Pib, or Pi9. The frequencies of corresponding AVR genes AVRPizt, AVRPikm, AVRPib, AVRPi9, and AVRPita were characterized by amplification and sequencing these genes in the isolates. Both Pi9 and Pikm conferred resistance to >75% of the tested isolates, while Pizt, Pita, and Pib were effective against 55.63, 15.31, and 3.15% of the isolates, respectively. AVRPikm and AVRPi9 were detected in 90% of the isolates and AVRPita, AVRPizt, and AVRPib were present in 26.12, 66.22, and 79% of the isolates, respectively. Sequencing of AVR genes showed that most mutations were single nucleotide polymorphisms, transposon insertions, and insertion mutations. The variable sites of AVRPikm and AVRPita were mainly located in the coding sequence regions (CDS), and most were synonymous mutations. A 494-bp Pot2 transposon sequence insertion was found at the 87 bp position upstream of the start codon in AVRPib. Noteworthy, although no mutations were found in CDS of AVRPi9, a GC-rich inserted sequence of ∼200 bp was found at the 1,272 bp position upstream of the start codon in three virulent isolates. As AVRPikm and AVRPi9 were widely distributed with low genetic variation in the pathogen population, Pikm and Pi9 should be promising genes for breeding rice cultivars with blast resistance in Hunan.

Dynamics of the Rice Blast Fungal Population in the Field After Deployment of an Improved Rice Variety Containing Known Resistance Genes

Rice blast, caused by the fungus Magnaporthe oryzae, is one of the most destructive diseases of rice worldwide. Management through the deployment of host resistance genes would be facilitated by understanding the dynamics of the pathogen's population in the field. Here, to investigate the mechanism underlying the breakdown of disease resistance, we conducted a six-year field experiment to monitor the evolution of M. oryzae populations in Qujiang from Guangdong. The new variety of Xin-Yin-Zhan (XYZ) carrying R genes Pi50 and Pib was developed using the susceptible elite variety, Ma-Ba-Yin-Zhan (MBYZ), as the recurrent line. Field trials of disease resistance assessment revealed that the disease indices of XYZ in 2012, 2013, 2016, and 2017 were 0.19, 0.39, 0.70, and 0.90, respectively, indicating that XYZ displayed a very rapid increase of disease severity in the field. To investigate the mechanism underlying the quick erosion of resistance of XYZ, we collected isolates from both XYZ and MBYZ for pathogenicity testing against six different isogenic lines. The isolates collected from XYZ showed a similar virulence spectrum across four different years whereas those from MBYZ showed increasing virulence to the Pi50 and Pib isogenic lines from 2012 to 2017. Molecular analysis of AvrPib in the isolates from MBYZ identified four different AvrPib haplotypes, i.e., AvrPib-AP1-1, AvrPib-AP1-2, avrPib-AP2, and avrPib-AP3, verified by sequencing. AvrPib-AP1-1 and AvrPib-AP1-2 are avirulent to Pib whereas avrPib-AP2 and avrPib-AP3 are virulent. Insertions of a Pot3 and an Mg-SINE were identified in avrPib-AP2 and avrPib-AP3, respectively. Two major lineages based on rep-PCR analysis were further deduced in the field population, implying that the field population is composed of genetically related isolates. Our data suggest that clonal propagation and quick dominance of virulent isolates against the previously resistant variety could be the major genetic events contributing to the loss of varietal resistance against rice blast in the field.

Dynamics of Race Structures of Pyricularia oryzae Populations Across 18 Seasons in Guangdong Province, China

Rice blast, caused by Pyricularia oryzae, is one of the most damaging fungal diseases affecting rice. Understanding how the pathogen's race structure varies over time supports the efforts of rice breeders to develop improved cultivars. Here, the race structure of P. oryzae in Guangdong province, China, where rice is cropped twice per year, was assessed over 18 seasons from 1999 through 2008. The analysis was based on the reactions of a panel of seven differential Chinese cultivars to inoculation with a set of 1,248 isolates of P. oryzae in the province. The "total race frequency" parameter ranged from 14.7 to 39.7%, and the "race diversity index" ranged from 0.63 to 0.93. Twelve (ZA63, ZA31, ZA29, ZA21, ZA13, ZA9, ZB30, ZB17, ZB8, ZB2, ZC14, and ZC8) and two (ZD8 and ZD3) races were recognized as specific to indica and japonica rice types, respectively. Of the 59 distinct races identified, only two indica type races (ZC13 and ZC15) were identified as population-common, and nine indica type races (ZB1, ZB5, ZB6, ZB7, ZB13, ZB15, ZC5, ZC13, and ZC15) and one japonica type race (ZG1) were deemed to be population-dominant; the "total top two race isolate frequency" parameter ranged from 29.8 to 74.5%. On the host side, dynamics of resistance structures of the differential set were divided into three patterns: Both Tetep and Kanto 51 expressed the highest and most stable resistance, both Sifeng 43 and Lijiangxintuanheigu conveyed much lower and unstable resistance, and Zhenlong 13, Dongnong 363, and Heijiang 18 performed intermediate and seasonally dynamic resistance. Three interesting points distinguishing race structures of P. oryzae populations in southern and northeastern China were also discussed.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Elucidation of genetic relatedness of Magnaporthe grisea, an incitent of pearl millet blast disease by molecular markers associated with virulence of host differential cultivars

In recent years, blast disease caused by Magnaporthe grisea, an ascomycete fungus is becoming a serious threat to pearl millet crop in India and worldwide. Due to the increase in virulent races of pathogen, blast disease management strategies seemed to be very limited. Hence, unraveling the occurrence of blast isolates across India and understanding their virulence and genetic relatedness using molecular markers are the key objectives of this study. From Farmer's field survey we have evidenced variability in blast pathogen across India by recording 10.6 to 7.9 disease severities. A fair to good variation in cultural and conidial characters were also noticed for 17 field isolates. The identity of 17 isolates was confirmed as Magnaporthe grisea by internal transcribed spacer (ITS) region. Based on 12 host differential virulence reactions, five isolates BgKMg1, BdmMg2, MtgMg11, JprMg16 and JmnMg17 recorded highly susceptible (>5 grade) to nine differentials used in the study. While, host differentials ICMB95444, ICMR06222, ICMR11003, IP21187 and ICMV155 found effective for screening virulence of blast disease. Furthermore, genetic relatedness assessed by ITS, inter simple sequence repeats (ISSR) and simple sequence repeats (SSR) markers produced high degree of polymorphism and was able to distinguish the virulence pattern of 17 isolates that correlated with phenotypic screening. Among markers, clustering of isolates within groups was significantly different with remarkable genetic similarity coefficient and bootstrap values. Overall, these results confirm a significant morphological and genetic variation among 17 isolates, thereby helping to elucidate the virulence of pearl millet blast populations in India that could avoid breakdown of resistance and assist breeding improved pearl millet cultivars.

Exploring the Distribution of Blast Resistance Alleles at the Pi2/9 Locus in Major Rice-Producing Areas of China by a Novel Indel Marker

Rice blast disease caused by the fungus Magnaporthe oryzae damages cereal crops and poses a high risk to rice production around the world. Currently, planting cultivars with resistance (R) genes is still the most environment-friendly approach to control this disease. Effective identification of R genes existing in diverse rice cultivars is important for understanding the distribution of R genes and predicting their contribution to resistance against blast isolates in regional breeding. Here, we developed a new insertion/deletion (InDel) marker, Pigm/2/9InDel, that can differentiate the cloned R genes (Pigm, Pi9, and Pi2/Piz-t) at the Pi2/9 locus. Pigm/2/9InDel combined with the marker Pi2-LRR for Pi2 was applied to determine the distribution of these four R genes among 905 rice varieties, most of which were collected from the major rice-producing regions in China. In brief, nine Pigm-containing varieties from Fujian and Guangdong provinces were identified. All of the 62 Pi2-containing varieties were collected from Guangdong, and 60 varieties containing Piz-t were from seven provinces. However, Pi9 was not found in any of the Chinese varieties. The newly identified varieties carrying the Pi2/9 alleles were further subjected to inoculation tests with regional blast isolates and field trials. Our results indicate that Pigm and Pi2 alleles have been introgressed for blast resistance breeding mainly in the Fujian and Guangdong region, and Pi9 is a valuable blast resistance resource to be introduced into China.

Pathogenicities of Rice Blast (Pyricularia oryzae Cavara) Isolates From Kenya

A total of 99 isolates of rice blast (Pyricularia oryzae Cavara) were collected from 2010 to 2015 from four regions in Kenya: Kirinyaga County and Embu County, Kisumu County, Tana River County, and Mombasa County. The pathogenicities of these isolates were clarified based on the reaction patterns of Lijiangxintuanheigu and differential varieties (DVs) targeting 23 resistance genes. The frequency of virulent isolates was high for DVs for Pib, Pia, Pii, Pi3, Pi5(t), Pik-s, Pik-m, Pi1, Pik-h, Pik, Pik-p, Pi7(t), Pi19(t), and Pi20(t); low for DVs for Pish, Pi9(t), Piz-5, and Piz-t; and intermediate for the remaining DVs for Pit, Piz, Pita-2, Pita, and Pi12(t). These blast isolates were classified into three cluster groups: Ia, Ib, and II. The frequencies of virulent isolates to DVs for Pit, Pii, Pik-m, Pi1, Pik-h, Pik, Pik-p, Pi7(t), Piz, and Pi12(t) differed markedly between clusters I and II, and those of DVs for Pib, Pit, Pia, Pi3, Pita-2, Pita, and Pi20(t) differed between Ia and Ib. The frequencies of cluster groups in the four geographical regions were different. A total of 62 races were found, with 19 blast isolates categorized into one race (U63-i7-k177-z00-ta003), whereas the other races included only some isolates in each.

Dynamics of Race Structures of the Rice Blast Pathogen Population in Heilongjiang Province, China From 2006 Through 2015

Rice blast caused by the fungus Magnaporthe oryzae is one of the most destructive diseases of rice. Its control through the deployment of host resistance genes would be facilitated by understanding the pathogen's race structure. Here, dynamics of race structures in this decade in Heilongjiang province were characterized by Chinese differential cultivars. Two patterns of dynamics of the race structures emerged: both race diversity and population-specific races increased gradually between 2006 and 2011, but they increased much more sharply between 2011 and 2015, with concomitant falls in both the population-common races and dominant races. Four races (ZD1, ZD3, ZD5, and ZE1) were among the top three dominant races over the whole period, indicating that the core of the race structure remained stable through this decade. On the host side, the composition of resistance in the cultivar differential set could be divided in two: the three indica-type entries of the differential set expressed a higher level of resistance to the population of M. oryzae isolates tested than did the four japonica-type entries. The cultivars Tetep and Zhenlong 13 as well as two additional resistance genes α and ε were confirmed as the most promising donors of blast resistance for the local rice improvement programs.[Formula: see text]Copyright © 2019 The Author(s). This is an open-access article distributed under the CC BY-NC-ND 4.0 International license.

Comprehensive evaluation of resistance effects of pyramiding lines with different broad-spectrum resistance genes against Magnaporthe oryzae in rice (Oryza sativa L.)

BACKGROUND

Broad-spectrum resistance gene pyramiding helps the development of varieties with broad-spectrum and durable resistance to M. oryzae. However, detailed information about how these different sources of broad-spectrum resistance genes act together or what are the best combinations to achieve broad-spectrum and durable resistance is limited.

RESULTS

Here a set of fifteen different polygene pyramiding lines (PPLs) were constructed using marker-assisted selection (MAS). Using artificial inoculation assays at seedling and heading stage, combined with natural induction identification under multiple field environments, we evaluated systematically the resistance effects of different alleles of Piz locus (Pigm, Pi40, Pi9, Pi2 and Piz) combined with Pi1, Pi33 and Pi54, respectively, and the interaction effects between different R genes. The results showed that the seedling blast and panicle blast resistance levels of PPLs were significantly higher than that of monogenic lines. The main reason was that most of the gene combinations produced transgressive heterosis, and the transgressive heterosis for panicle blast resistance produced by most of PPLs was higher than that of seedling blast resistance. Different gene pyramiding with broad-spectrum R gene produced different interaction effects, among them, the overlapping effect (OE) between R genes could significantly improve the seedling blast resistance level of PPLs, while the panicle blast resistance of PPLs were remarkably correlated with OE and complementary effect (CE). In addition, we found that gene combinations, Pigm/Pi1, Pigm/Pi54 and Pigm/Pi33 displayed broad-spectrum resistance in artificial inoculation at seedling and heading stage, and displayed stable broad-spectrum resistance under different disease nursery. Besides, agronomic traits evaluation also showed PPLs with these three gene combinations were at par to the recurrent parent. Therefore, it would provide elite gene combination model and germplasms for rice blast resistance breeding program.

CONCLUSIONS

The development of PPLs and interaction effect analysis in this study provides valuable theoretical foundation and innovative resources for breeding broad-spectrum and durable resistant varieties.

The Race Structure of the Rice Blast Pathogen Across Southern and Northeastern China

BACKGROUND

Rice blast, caused by the ascomycete Magnaporthe oryzae (Mo), imposes a major constraint on rice productivity. Managing the disease through the deployment of host resistance requires a close understanding of race structure of the pathogen population.

RESULTS

The host/pathogen interaction between isolates sampled from four Mo populations collected across the rice-producing regions of China was tested using two established panels of differential cultivars. The clearest picture was obtained from the Chinese cultivar panel, for which the frequency of the various races, the race diversity index, the specific race isolate frequency, and the frequency of the three predominant races gave a consistent result, from which it was concluded that the pathogen population present in the southern production region was more diverse than that in the northeastern region. The four blast resistance genes Pi1, Pik, Pik-m, and Piz all still remain effective in the southern China rice production area, as does Pi1 in the northeastern region. The effectiveness of Pita, Pik-p, Piz, and Pib is restricted to single provinces. The distinctive resistance profile shown by the Chinese differential cultivar set implied the presence of at least five as yet unidentified blast resistance genes.

CONCLUSIONS

The Chinese differential cultivar set proved to be more informative than the Japanese one for characterizing the race structure of the rice blast pathogen in China. A number of well characterized host resistance genes, in addition to some as yet uncharacterized ones, remain effective across the major rice production regions in China.

Characterization of Molecular Identity and Pathogenicity of Rice Blast Fungus in Hunan Province of China

The blast (Magnaporthe oryzae) resistance (R) gene is the most economical and environmental method to control rice blast disease. Characterization of molecular identity and pathogenicity of M. oryzae benefits the deployment of effective blast R genes. In order to identify blast R genes that would be effective in Hunan Province,182 M. oryzae strains were analyzed with a Chinese differential system (CDS), repetitive element-based polymerase chain reaction (rep-PCR), and the presence and absence of avirulence (AVR) genes by PCR amplification with gene-specific primers. Identified blast R genes were validated with 24 monogenic lines (ML) carrying 24 major R genes. In total, 28 races (isolates) of M. oryzae was identified with CDS, and classified into 20 distinct groups with rep-PCR. Interestingly, AVR-Pia, AVR-Pik, AVR-Pizt, AVR-Pib, and AVR-Pi9 were detected in more than 86.8% of the isolates; AVR-Pita1 was in 51.3% and AVR-Pii was in only 2.5%. In contrast, pathogenicity assays on 24 ML demonstrated that Pi9, Piz5, Pikh, and Pikm were more effective, with resistant frequencies of 91.6, 91, 87.9, and 87.3%, respectively; Pia, Piks, Pit, Pi12, and Pib were less than 15%. These findings revealed the complexity of a genetic basis of rice blast resistance, and shed light on useful blast R genes in Hunan Province.

Diversity and Distribution of Rice Blast (Pyricularia oryzae Cavara) Races in Bangladesh

The pathogenicity of 331 blast isolates (Pyricularia oryzae Cavara) collected from different regions and ecosystems for rice cultivation in Bangladesh was evaluated by compatibility on 23 differential varieties (DV), each harboring a single blast resistance gene, and susceptible 'Lijiangxintuanheigu' (LTH). A wide variation in virulence was found among the isolates, and 267 races were classified using a new designation system. Virulence of blast isolates against DV carrying the resistance genes Pia, Pib, Pit, Pik-s, Piz-t, Pi12(t), Pi19(t), and Pi20(t), as well as avirulence against those carrying Pish, Pi9, Pita-2, and Pita, was distributed widely in Bangladesh. Cluster analysis of the compatibility data on the DV initially classified the isolates into groups I and II. The virulence spectra of the two groups differed mainly according to the reactions of the DV to Pii, Pi3, Pi5(t), Pik-m, Pi1, Pik-h, Pik, Pik-p, and Pi7(t). Group I isolates were distributed mainly in rainfed lowlands, whereas group II isolates were found mainly in irrigated lowlands; however, there were no critical differences in geographic distribution of the blast isolates. In total, 26 isolates, which could be used to identify the 23 resistance genes of the DV on the basis of their reaction patterns, were selected as a set of standard differential blast isolates. To our knowledge, this is the first clear demonstration of the diversity and differentiation of blast races in Bangladesh. This information will be used to develop a durable blast protection system in that country.

Identification of rice blast resistance genes in the elite hybrid rice restorer line Yahui2115

Rice blast, caused by the ascomycete fungus Magnaporthe oryzae, is one of the most serious rice diseases worldwide. We previously developed an elite hybrid rice restorer line with high resistance to rice blast, Yahui2115 (YH2115). To identify the blast resistance genes in YH2115, we first performed expression profiling on previously reported blast resistance genes and disease assay on monogenic lines, and we found that Pi2, Pi9, and Pikm were the most likely resistance candidates in YH2115. Furthermore, RNA interference and linkage analysis demonstrated that silencing of Pi2 reduced the blast resistance of YH2115 and a Pi2 linkage marker was closely associated with blast resistance in an F2 population generated from YH2115. These data suggest that the broad-spectrum blast resistance gene Pi2 contributes greatly to the blast resistance of YH2115. Thus, YH2115 could be used as a new germplasm to facilitate rice blast resistance breeding in hybrid rice breeding programs.

Diversity and Distribution of Rice Blast (Pyricularia oryzae Cavara) Races in Japan

In total, 310 rice blast (Pyricularia oryzae Cavara) isolates from Japan showed wide variation in virulence. Virulence on rice (Oryza sativa L.) differential varieties (DV) harboring resistance genes Pish, Pia, Pii, Pi3, Pi5(t), Pik-s, and Pi19(t) ranged from 82.9 to 100.0%. In contrast, virulence on DV possessing Pib, Pit, Pik-m, Pi1, Pik-h, Pik, Pik-p, Pi7(t), Pi9(t), Piz, Piz-5, Piz-t, Pita-2, Pita, Pi12(t), and Pi20(t) ranged from 0 to 21.6%. Cluster analysis using the reaction patterns of the DV classified isolates into three groups: I, virulent to Pik, Pik-h, Pik-p, Pik-m, Pi1, and Pi7(t); IIa, avirulent to the preceding 6 genes and virulent to Pia, Pii, Pi3, and Pi5(t); and IIb, avirulent to all 10 genes. Group I was limited to northern Japan and group IIb to central Japan, while group IIa was distributed throughout Japan. We estimate that group IIa represents the original population and that groups I and IIb arose from it through minor changes in pathogenicity. We classified these isolates into 123 races by a new designation system and conclude that the rice blast races in Japan are less diverse than previously thought.

Function and evolution of Magnaporthe oryzae avirulence gene AvrPib responding to the rice blast resistance gene Pib

Magnaporthe oryzae (Mo) is the causative pathogen of the damaging disease rice blast. The effector gene AvrPib, which confers avirulence to host carrying resistance gene Pib, was isolated via map-based cloning. The gene encodes a 75-residue protein, which includes a signal peptide. Phenotyping and genotyping of 60 isolates from each of five geographically distinct Mo populations revealed that the frequency of virulent isolates, as well as the sequence diversity within the AvrPib gene increased from a low level in the far northeastern region of China to a much higher one in the southern region, indicating a process of host-driven selection. Resequencing of the AvrPiballele harbored by a set of 108 diverse isolates revealed that there were four pathoways, transposable element (TE) insertion (frequency 81.7%), segmental deletion (11.1%), complete absence (6.7%), and point mutation (0.6%), leading to loss of the avirulence function. The lack of any TE insertion in a sample of non-rice infecting Moisolates suggested that it occurred after the host specialization of Mo. Both the deletions and the functional point mutation were confined to the signal peptide. The reconstruction of 16 alleles confirmed seven functional nucleotide polymorphisms for the AvrPiballeles, which generated three distinct expression profiles.

A paralog of the MtN3/saliva family recessively confers race-specific resistance to Xanthomonas oryzae in rice

Approximately one third of the identified 34 rice major disease resistance (R) genes conferring race-specific resistance to different strains of Xanthomonas oryzae pv. oryzae (Xoo), which causes rice bacterial blight disease, are recessive genes. However, only two of the recessive resistance genes have been characterized thus far. Here we report the characterization of another recessive resistance gene, xa25, for Xoo resistance. The xa25, localized in the centromeric region of chromosome 12, mediates race-specific resistance to Xoo strain PXO339 at both seedling and adult stages by inhibiting Xoo growth. It encodes a protein of the MtN3/saliva family, which is prevalent in eukaryotes, including mammals. Transformation of the dominant Xa25 into a resistant rice line carrying the recessive xa25 abolished its resistance to PXO339. The encoding proteins of recessive xa25 and its dominant allele Xa25 have eight amino acid differences. The expression of dominant Xa25 but not recessive xa25 was rapidly induced by PXO339 but not other Xoo strain infections. The nature of xa25-encoding protein and its expression pattern in comparison with its susceptible allele in rice-Xoo interaction indicate that the mechanism of xa25-mediated resistance appears to be different from that conferred by most of the characterized R proteins.

Strategies for developing Green Super Rice

From a global viewpoint, a number of challenges need to be met for sustainable rice production: (i) increasingly severe occurrence of insects and diseases and indiscriminate pesticide applications; (ii) high pressure for yield increase and overuse of fertilizers; (iii) water shortage and increasingly frequent occurrence of drought; and (iv) extensive cultivation in marginal lands. A combination of approaches based on the recent advances in genomic research has been formulated to address these challenges, with the long-term goal to develop rice cultivars referred to as Green Super Rice. On the premise of continued yield increase and quality improvement, Green Super Rice should possess resistances to multiple insects and diseases, high nutrient efficiency, and drought resistance, promising to greatly reduce the consumption of pesticides, chemical fertilizers, and water. Large efforts have been focused on identifying germplasms and discovering genes for resistance to diseases and insects, N- and P-use efficiency, drought resistance, grain quality, and yield. The approaches adopted include screening of germplasm collections and mutant libraries, gene discovery and identification, microarray analysis of differentially regulated genes under stressed conditions, and functional test of candidate genes by transgenic analysis. Genes for almost all of the traits have now been isolated in a global perspective and are gradually incorporated into genetic backgrounds of elite cultivars by molecular marker-assisted selection or transformation. It is anticipated that such strategies and efforts would eventually lead to the development of Green Super Rice.

OsWRKY13 mediates rice disease resistance by regulating defense-related genes in salicylate- and jasmonate-dependent signaling

Although 109 WRKY genes have been identified in the rice genome, the functions of most are unknown. Here, we show that OsWRKY13 plays a pivotal role in rice disease resistance. Overexpression of OsWRKY13 can enhance rice resistance to bacterial blight and fungal blast, two of the most devastating diseases of rice worldwide, at both the seedling and adult stages, and shows no influence on the fertility. This overexpression was accompanied by the activation of salicylic acid (SA) synthesis-related genes and SA-responsive genes and the suppression of jasmonic acid (JA) synthesis-related genes and JA-responsive genes. OsWRKY13 bound to the promoters of its own and at least three other genes in SA- and JA-dependent signaling pathways. Its DNA-binding activity was influenced by pathogen infection. These results suggest that OsWRKY13, as an activator of the SA-dependent pathway and a suppressor of JA-dependent pathways, mediates rice resistance by directly or indirectly regulating the expression of a subset of genes acting both upstream and downstream of SA and JA. Furthermore, OsWRKY13 will provide a transgenic tool for engineering wider-spectrum and whole-growth-stage resistance rice in breeding programs.

Dual function of rice OsDR8 gene in disease resistance and thiamine accumulation

The function of OsDR8, a rice disease resistance-responsive gene, was studied. Silencing of OsDR8 using an RNA interference approach resulted in phenotypic alteration of the plants. The transgenic plants with repressed expression of OsDR8 showed reduced resistance or susceptibility to Xanthomonas oryzae pv. oryzae and Magnaporthe grisea causing bacterial blight and blast, which are two of the most devastating diseases in rice worldwide, respectively. The putative product of OsDR8 was highly homologous to an enzyme involved in the biosynthesis of the thiazole precursor of thiamine. Transgenic plants showing repressed expression of OsDR8 and reduced resistance had significantly lower levels of thiamine than the control plants. Exogenous application of thiamine could complement the compromised defense of the OsDR8-silenced plants. The expression level of several defense-responsive genes including the earlier functional genes of defense transduction pathway, OsPOX and OsPAL, and the downstream genes of the pathway, OsPR1a, OsPR1b, OsPR4, OsPR5 and OsPR10, was also decreased in the OsDR8-silenced plants. These results suggest that the impact of OsDR8 on disease resistance in rice may be through the regulation of expression of other defense-responsive genes and the site of OsDR8 function is on the upstream of the signal transduction pathway. In addition, the accumulation of thiamine may be essential for bacterial blight resistance and blast resistance.

Features of the expressed sequences revealed by a large-scale analysis of ESTs from a normalized cDNA library of the elite indica rice cultivar Minghui 63

The indica subspecies of cultivated rice occupies the largest area of rice production in the world. However, a systematic analysis of cDNA sequences from the indica subspecies has not been performed. The aim of the present study was to collect and analyze the expressed sequence tags (ESTs) of indica rice on a large scale. A total of 39 208 raw sequences were generated from a normalized cDNA library prepared by use of 15 different tissues of the indica cultivar Minghui 63. After trimming, processing and analysis, 17 835 unique sequences were obtained, each of which presumably represents a unique gene. Of these sequences, 2663 were novel, and at least 70 were indica specific. Comparison of the Minghui 63 sequences with the ESTs/full-length cDNAs in GenBank revealed a large number of deletion/insertion/substitution (DIS) at both the inter- and intra-subspecific levels. The overall number of polymorphisms in the expressed sequences was higher in the inter-subspecific comparisons than in the intra-subspecific comparisons. However, the extent of DIS-based polymorphism was highly variable among different rice varieties. In total, 15 726 unique sequences, including 697 novel sequences, were assigned to regions where large numbers of quantitative trait loci (QTLs) for agronomic traits had been detected previously. These results may be useful for developing new molecular markers for genetic mapping, detecting allelic polymorphisms associated with phenotypic variations between rice varieties, and facilitating QTL cloning by providing the starting points for candidate-gene identification.

Pathogenicity and virulence

Invertebrate pathologists have multiple definitions for the terms pathogenicity and virulence, and these definitions vary across disciplines that focus on host-pathogen interactions. We surveyed various literatures, including plant pathology, invertebrate pathology, evolutionary biology, and medicine, and found most define pathogenicity as the broader term, which incorporates virulence. Virulence is seen as the severity of disease manifestation that can only be measured in infected individuals. These definitions readily apply to both lethal and non-lethal diseases. Invertebrate pathologists commonly use dose-response bioassays to estimate LD(50) or LC(50) (dose or concentration needed to kill 50% of hosts exposed). These bioassays measure pathogenicity if the bioassay includes a transmission component, and measure virulence if the bioassay is measured in infected individuals only. Another common bioassay estimate is LT(50) (median time to death of infected hosts), which is a measure of virulence as long as survivors are not included in its calculation.

Genome-wide analysis of defense-responsive genes in bacterial blight resistance of rice mediated by the recessive R gene xa13

Defense responses triggered by dominant and recessive disease resistance (R) genes are presumed to be regulated by different molecular mechanisms. In order to characterize the genes activated in defense responses against bacterial blight mediated by the recessive R gene xa13, two pathogen-induced subtraction cDNA libraries were constructed using the resistant rice line IRBB13--which carries xa13--and its susceptible, near-isogenic, parental line IR24. Clustering analysis of expressed sequence tags (ESTs) identified 702 unique expressed sequences as being involved in the defense responses triggered by xa13; 16% of these are new rice ESTs. These sequences define 702 genes, putatively encoding a wide range of products, including defense-responsive genes commonly involved in different host-pathogen interactions, genes that have not previously been reported to be associated with pathogen-induced defense responses, and genes (38%) with no homology to previously described functional genes. In addition, R-like genes putatively encoding nucleotide-binding site/leucine rich repeat (NBS-LRR) and LRR receptor kinase proteins were observed to be induced in the disease resistance activated by xa13. A total of 568 defense-responsive ESTs were mapped to 588 loci on the rice molecular linkage map through bioinformatic analysis. About 48% of the mapped ESTs co-localized with quantitative trait loci (QTLs) for resistance to various rice diseases, including bacterial blight, rice blast, sheath blight and yellow mottle virus. Furthermore, some defense-responsive sequences were conserved at similar locations on different chromosomes. These results reveal the complexity of xa13-mediated resistance. The information obtained in this study provides a large source of candidate genes for understanding the molecular bases of defense responses activated by recessive R genes and of quantitative disease resistance.

Three types of defense-responsive genes are involved in resistance to bacterial blight and fungal blast diseases in rice

Bacterial blight and fungal blast diseases of rice, caused by Xanthomonas oryzae pv. oryzae and Pyricularia grisea Sacc., respectively, are two of the most devastating diseases in rice worldwide. To study the defense responses to infection with each of these pathogens, expression profiling of 12 defense-responsive genes was performed using near-isogenic rice lines that are resistant or susceptible to bacterial blight and fungal blast, respectively, and rice cultivars that are resistant or susceptible to both pathogens. All 12 genes showed constitutive expression, but expression levels increased in response to infection. Based on their expression patterns in 12 host-pathogen combinations, these genes could be classified into three types, pathogen non-specific (6), pathogen specific but race non-specific (4) and race specific (2). Most of the 12 genes were only responsive during incompatible interactions. These results suggest that bacterial blight and fungal blast resistances share common pathway(s), but are also regulated by different defense pathways in rice. Activation of the corresponding R gene is the key step that initiates the action of these genes in defense responses. The chromosomal locations and pathogen specificities of seven of the 12 genes were consistent with those of previously identified quantitative trait loci for rice disease resistance, which indicates that some of the 12 genes studied may have a phenotypic impact on disease resistance in rice.

Comparative analyses of genomic locations and race specificities of loci for quantitative resistance to Pyricularia grisea in rice and barley

Comparative genomic analyses have revealed extensive colinearity in gene orders in distantly related taxa in mammals and grasses, which opened new horizons for evolutionary study. The objective of our study was to assess syntenic relationships of quantitative trait loci (QTL) for disease resistance in cereals by using a model system in which rice and barley were used as the hosts and the blast fungus Pyricularia grisea Sacc. as the pathogen. In total, 12 QTL against three isolates were identified in rice; two had effects on all three isolates, and the other 10 had effects on only one or two of the three isolates. Twelve QTL for blast resistance were identified in barley; one had effect on all three isolates, and the other 11 had effects on only one or two of the three isolates. The observed isolate specificity led to a hypothesis about the durability of quantitative resistance commonly observed in many plant host-pathogen systems. Four pairs of the QTL showed corresponding map positions between rice and barley, two of the four QTL pairs had complete conserved isolate specificity, and another two QTL pairs had partial conserved isolate specificity. Such corresponding locations and conserved specificity suggested a common origin and conserved functionality of the genes underlying the QTL for quantitative resistance and may have utility in gene discovery, understanding the function of the genomes, and identifying the evolutionary forces that structured the organization of the grass genomes.