A New Recessive Gene Conferring Resistance Against Rice Blast

Gene Genealogy-Based Mutation Analysis Reveals Emergence of Aus, Tropical japonica, and Aromatic of Oryza sativa during the Later Stage of Rice Domestication

Asian rice (Oryza sativa L.) has become a model for understanding gene functions and domestication in recent decades; however, its own diversification is still controversial. Although the division of indica and japonica and five subgroups (aus, indica (sensu stricto), japonica (sensu stricto), tropical japonica, and aromatic) are broadly accepted, how they are phylogenetically related is not transparent. To clarify their relationships, a sample of 121 diverse genes was chosen here from 12 Oryza genomes (two parental and ten O. sativa (Os)) in parallel to allow gene genealogy-based mutation (GGM) analysis. From the sample, 361 Os mutations were shared by two or more subgroups (referred to here as trans mutations) from 549 mutations identified at 51 Os loci. The GGM analysis and related tests indicates that aus diverged from indica at a time significantly earlier than when tropical japonica split from japonica. The results also indicate that aromatic was selected from hybrid progeny of aus and tropical japonica and that all five subgroups share a significant number of the early mutations identified previously. The results suggest that aus, tropical japonica, and aromatic emerged sequentially within the most recent 4-5 millennia of rice domestication after the split of indica and japonica.

Advancement in the Breeding, Biotechnological and Genomic Tools towards Development of Durable Genetic Resistance against the Rice Blast Disease

Rice production needs to be sustained in the coming decades, as the changeable climatic conditions are becoming more conducive to disease outbreaks. The majority of rice diseases cause enormous economic damage and yield instability. Among them, rice blast caused by Magnaportheoryzae is a serious fungal disease and is considered one of the major threats to world rice production. This pathogen can infect the above-ground tissues of rice plants at any growth stage and causes complete crop failure under favorable conditions. Therefore, management of blast disease is essentially required to sustain global food production. When looking at the drawback of chemical management strategy, the development of durable, resistant varieties is one of the most sustainable, economic, and environment-friendly approaches to counter the outbreaks of rice blasts. Interestingly, several blast-resistant rice cultivars have been developed with the help of breeding and biotechnological methods. In addition, 146 R genes have been identified, and 37 among them have been molecularly characterized to date. Further, more than 500 loci have been identified for blast resistance which enhances the resources for developing blast resistance through marker-assisted selection (MAS), marker-assisted backcross breeding (MABB), and genome editing tools. Apart from these, a better understanding of rice blast pathogens, the infection process of the pathogen, and the genetics of the immune response of the host plant are very important for the effective management of the blast disease. Further, high throughput phenotyping and disease screening protocols have played significant roles in easy comprehension of the mechanism of disease spread. The present review critically emphasizes the pathogenesis, pathogenomics, screening techniques, traditional and molecular breeding approaches, and transgenic and genome editing tools to develop a broad spectrum and durable resistance against blast disease in rice. The updated and comprehensive information presented in this review would be definitely helpful for the researchers, breeders, and students in the planning and execution of a resistance breeding program in rice against this pathogen.

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.

Linkage of SSR markers with rice blast resistance and development of partial resistant advanced lines of rice (Oryza sativa) through marker-assisted selection

Rice blast disease is one of the major bottlenecks of rice production in the world including Bangladesh. To develop blast resistant lines, a cross was made between a high yielding but blast susceptible variety MR263 and a blast resistant variety Pongsu seribu 2. Marker-assisted backcross breeding was followed to develop F₁, BC₁F₁, BC₂F₁, BC₂F₂, BC₂F_3, BC₂F₄ and BC₂F₅ population. DNA markers i.e., RM206, RM1359 and RM8225 closely linked to Pb1, pi21 and Piz blast resistant genes, respectively and marker RM276 linked to panicle blast resistant QTL (qPbj-6.1) were used in foreground selection. Calculated chi-square (χ²) value of phenotypic and genotypic segregation data of BC₂F₁ population followed goodness of fit to the expected ratio (1:1) (phenotypic data χ² = 1.08, p = 0.701; genotypic data χ² = range from 0.33 to 3.00, p = 0.08-0.56) and it indicates that the inheritance pattern of blast resistance was followed by a single gene model. Eighty-nine advanced lines of BC₂F₅ population were developed and out of them, 58 lines contained Piz, Pb1, pi21, and qPbj-6.1 while 31 lines contained Piz, Pb1, and QTL qPbj-6.1. Marker-trait association analysis revealed that molecular markers i.e., RM206, RM276, and RM8225 were tightly linked with blast resistance, and each marker was explained by 33.33% phenotypic variation (resistance reaction). Morphological and pathogenicity performance of advanced lines was better compared to the recurrent parent. Developed blast resistance advanced lines could be used as donors or blast resistant variety for the management of devastating rice blast disease.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01141-3.

Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management

Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.

Integrated Strategies for Durable Rice Blast Resistance in Sub-Saharan Africa

Rice is a key food security crop in Africa. The importance of rice has led to increasing country-specific, regional, and multinational efforts to develop germplasm and policy initiatives to boost production for a more food-secure continent. Currently, this critically important cereal crop is predominantly cultivated by small-scale farmers under suboptimal conditions in most parts of sub-Saharan Africa (SSA). Rice blast disease, caused by the fungus Magnaporthe oryzae, represents one of the major biotic constraints to rice production under small-scale farming systems of Africa, and developing durable disease resistance is therefore of critical importance. In this review, we provide an overview of the major advances by a multinational collaborative research effort to enhance sustainable rice production across SSA and how it is affected by advances in regional policy. As part of the multinational effort, we highlight the importance of joint international partnerships in tackling multiple crop production constraints through integrated research and outreach programs. More specifically, we highlight recent progress in establishing international networks for rice blast disease surveillance, farmer engagement, monitoring pathogen virulence spectra, and the establishment of regionally based blast resistance breeding programs. To develop blast-resistant, high yielding rice varieties for Africa, we have established a breeding pipeline that utilizes real-time data of pathogen diversity and virulence spectra, to identify major and minor blast resistance genes for introgression into locally adapted rice cultivars. In addition, the project has developed a package to support sustainable rice production through regular stakeholder engagement, training of agricultural extension officers, and establishment of plant clinics.

Identification and Characterization of a Large Effect QTL from Oryza glumaepatula Revealed Pi68(t) as Putative Candidate Gene for Rice Blast Resistance

BACKGROUND

Field resistance is often effective and durable as compared to vertical resistance. The introgression line (INGR15002) derived from O. glumaepatula has proven broad spectrum field resistance for both leaf and neck blast.

RESULTS

Quantitative Trait Loci (QTL) analysis of INGR15002, led to the identification of two major QTL - qBL3 contributing about 34% and 32% phenotypic variance towards leaf and neck blast resistance, respectively and qBL7 contributing about 25% of phenotypic variance for leaf blast. Further, qBL3 was fine mapped, narrowed down to 300 kb region and a linked SNP maker was identified. By combining mapping with microarray analysis, a candidate gene, Os03g0281466 (malectin-serine threonine kinase), was identified in the fine mapped region and named as Pi68(t). The nucleotide variations in the coding as well as upstream region of the gene was identified through cloning and sequence analysis of Pi68(t) alleles. These significant variations led to the non-synonymous changes in the protein as well as variations (presence/absence) in four important motifs (W-box element; MYC element; TCP element; BIHD1OS) at promoter region those are associated with resistance and susceptible reactions. The effect of qBL3 was validated by its introgression into BPT5204 (susceptible variety) through marker-assisted selection and progeny exhibiting resistance to both leaf and neck blast was identified. Further, the utility of linked markers of Pi68(t) in the blast breeding programs was demonstrated in elite germplasm lines.

CONCLUSIONS

This is the first report on the identification and characterization of major effect QTL from O. glumaepatula, which led to the identification of a putative candidate gene, Pi68(t), which confers field resistance to leaf as well as neck blast in rice.

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.

Candidate screening of blast resistance donors for rice breeding

Rice blast is one of the most serious diseases in the world. The use of resistant cultivars is the most preferred means to control this disease. Resistance often breaks down due to emergence of new races; hence identification of novel resistance donors is indispensable. In this study, a panel of 80 released varieties from National Rice Research Institute, Cuttack was genotyped with 36 molecular markers that were linked to 36 different blast resistance genes, to investigate the varietal genetic diversity and molecular marker-trait association with blast resistance. The polymorphism information content of 36 loci varied from 0.11 to 0.37 with an average of 0.34. The cluster analysis and population structure categorized the 80 National Rice Research Institute released varieties (NRVs) into three major genetic groups. The principal co-ordinate analysis displays the distribution of resistant and moderately resistant NRVs into different groups. Analysis of molecular variance result demonstrated maximum (97%) diversity within populations and minimum (3%) diversity between populations. Among tested markers, two markers (RM7364 and pi21_79-3) corresponding to the blast resistance genes (Pi56(t) and pi21) were significantly associated and explained a phenotypic variance of 4.9 to 5.1% with the blast resistance. These associated genes could be introgressed through marker-assisted to develop durable blast resistant rice varieties. The selected resistant NRVs could be good donors for the blast resistance in rice crop improvement research.

Current status on mapping of genes for resistance to leaf- and neck-blast disease in rice

Blast disease caused by fungal pathogen Pyricularia oryzae is a major threat to rice productivity worldwide. The rice-blast pathogen can infect both leaves and panicle neck nodes. Nearly, 118 genes for resistance to leaf blast have been identified and 25 of these have been molecularly characterized. A great majority of these genes encode nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins and are organized into clusters as allelic or tightly linked genes. Compared to ever expanding list of leaf-blast-resistance genes, a few major genes mediating protection to neck blast have been identified. A great majority of the genetic studies conducted with the genotypes differing in the degree of susceptibility/resistance to neck blast have suggested quantitative inheritance for the trait. Several reports on co-localization of gene/QTLs for leaf- and neck-blast resistance in rice genome have suggested the existence of common genes for resistance to both phases of the disease albeit inconsistencies in the genomic positions leaf- and neck-blast-resistance genes in some instances have presented the contrasting scenario. There is a strong evidence to suggest that developmentally regulated expression of many blast-resistance genes is a key determinant deciding their effectiveness against leaf or neck blast. Testing of currently characterized leaf-blast-resistance genes for their reaction to neck blast is required to expand the existing repertoire resistance genes against neck blast. Current developments in the understanding of molecular basis of host-pathogen interactions in rice-blast pathosystem offer novel possibilities for achieving durable resistance to blast through exploitation of natural or genetically engineered loss-of-function alleles of host susceptibility genes.

Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice

Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.

Proteomics of Rice-Magnaporthe oryzae Interaction: What Have We Learned So Far?

Rice blast disease, caused by Magnaporthe oryzae, is one of the major constraints to rice production, which feeds half of the world's population. Proteomic technologies have been used as effective tools in plant-pathogen interactions to study the biological pathways involved in pathogen infection, plant response, and disease progression. Advancements in mass spectrometry (MS) and apoplastic and plasma membrane protein isolation methods facilitated the identification and quantification of subcellular proteomes during plant-pathogen interaction. Proteomic studies conducted during rice-M. oryzae interaction have led to the identification of several proteins eminently involved in pathogen perception, signal transduction, and the adjustment of metabolism to prevent plant disease. Some of these proteins include receptor-like kinases (RLKs), mitogen-activated protein kinases (MAPKs), and proteins related to reactive oxygen species (ROS) signaling and scavenging, hormone signaling, photosynthesis, secondary metabolism, protein degradation, and other defense responses. Moreover, post-translational modifications (PTMs), such as phosphoproteomics and ubiquitin proteomics, during rice-M. oryzae interaction are also summarized in this review. In essence, proteomic studies carried out to date delineated the molecular mechanisms underlying rice-M. oryzae interactions and provided candidate proteins for the breeding of rice blast resistant cultivars.

Prospects of Understanding the Molecular Biology of Disease Resistance in Rice

Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host-pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs) and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice.

Fine mapping of Pi57(t) conferring broad spectrum resistance against Magnaporthe oryzae in introgression line IL-E1454 derived from Oryza longistaminata

Wild species of the genus Oryza are excellent gene pools for improvement of agronomic traits of Asian cultivated rice. The blast resistance gene Pi57(t) in the introgression line IL-E1454 derived from Oryza longistaminata was previously mapped on rice chromosome 12. Inoculation with 322 Magnaporthe oryzae isolates collected from 6 countries indicated that Pi57(t) conferred broad spectrum resistance against M. oryzae. Two mapping populations consisting of 29070 and 10375 F2 plants derived from the crosses of resistant donor IL-E1454 with susceptible parents RD23 and Lijiangxintuanheigu respectively, were used for fine mapping of Pi57(t) locus. Based on genotyping and phenotyping results of recombinants screened from the two crosses, Pi57(t) was finally mapped to a 51.7-kb region flanked by two molecular markers (STS57-320 and STS57-372) on the short arm and close to the centromere of chromosome 12. Six candidate resistance genes were predicted in the target region according to the reference sequence of Nipponbare. These results could facilitate both marker-assisted selection for disease-resistant breeding and gene cloning.

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.