Blast resistance in Indian rice landraces: Genetic dissection by gene specific markers

Dissecting genomic regions and underlying sheath blight resistance traits in rice (Oryza sativa L.) using a genome-wide association study

The productivity of rice is greatly affected by the infection of the plant pathogenic fungus Rhizoctonia solani, which causes a significant grain yield reduction globally. There exist a limited number of rice accessions that are available to develop sheath blight resistance (ShB). Our objective was to identify a good source of the ShB resistance, understand the heritability, and trait interactions, and identify the genomic regions for ShB resistance traits by genome-wide association studies (GWAS). In the present study, a set of 330 traditional landraces and improved rice varieties were evaluated for ShB resistance and created a core panel of 192 accessions used in the GWAS. This panel provides a more considerable amount of genetic variance and found a significant phenotypic variation among the panel of rice accessions for all the agro-morphological and disease-resistance traits over the seasons. The infection rate of ShB and disease reaction were calculated as percent disease index (PDI) and area under the disease progress curve (AUDPC). The correlation analysis showed a significant positive association between PDIs and AUPDC and a negative association between PDI and plant height, flag leaf length, and grain yield. The panel was genotyped with 133 SSR microsatellite markers, resulting in a genome coverage of 314.83 Mb, and the average distance between markers is 2.53 Mb. By employing GLM and MLM (Q + K) models, 30 marker-trait associations (MTAs) were identified with targeted traits over the seasons. Among these QTLs, eight were found to be novel and located on 2, 4, 8, 10, and 12 chromosomes, which explained the phenotypic variation ranging from 5% to 15%. With the GWAS approach, six candidate genes were identified. Os05t0566400, Os08t0155900, and Os09t0567300 were found to be associated with defense mechanisms against ShB. These findings provided insights into the novel donors of IC283139, IC 277248, Sivappuchithirai Kar, and Bowalia. The promising genomic regions on 10 of 12 chromosomes associated with ShB would be useful in developing rice varieties with durable disease resistance.

Phenotypic and Genotypic screening of fifty-two rice (Oryza sativa L.) genotypes for desirable cultivars against blast disease

Magnaporthe oryzae, the rice blast fungus, is one of the most dangerous rice pathogens, causing considerable crop losses around the world. In order to explore the rice blast-resistant sources, initially performed a large-scale screening of 277 rice accessions. In parallel with field evaluations, fifty-two rice accessions were genotyped for 25 major blast resistance genes utilizing functional/gene-based markers based on their reactivity against rice blast disease. According to the phenotypic examination, 29 (58%) and 22 (42%) entries were found to be highly resistant, 18 (36%) and 29 (57%) showed moderate resistance, and 05 (6%) and 01 (1%), respectively, were highly susceptible to leaf and neck blast. The genetic frequency of 25 major blast resistance genes ranged from 32 to 60%, with two genotypes having a maximum of 16 R-genes each. The 52 rice accessions were divided into two groups based on cluster and population structure analysis. The highly resistant and moderately resistant accessions are divided into different groups using the principal coordinate analysis. According to the analysis of molecular variance, the maximum diversity was found within the population, while the minimum diversity was found between the populations. Two markers (RM5647 and K39512), which correspond to the blast-resistant genes Pi36 and Pik, respectively, showed a significant association to the neck blast disease, whereas three markers (Pi2-i, Pita3, and k2167), which correspond to the blast-resistant genes Pi2, Pita/Pita2, and Pikm, respectively, showed a significant association to the leaf blast disease. The associated R-genes might be utilized in rice breeding programmes through marker-assisted breeding, and the identified resistant rice accessions could be used as prospective donors for the production of new resistant varieties in India and around the world.

Deciphering environmental factors and defense response of rice genotypes against sheath blight disease

Sheath blight (ShB) is one of the most serious diseases in rice, leading to severe yield losses globally. In our study, we evaluated a total of 63 rice genotypes for resistance against sheath blight disease by artificial inoculation over two seasons under field conditions and studied the weather parameters associated with disease incidence. Based on two years of testing, 23 genotypes were found moderately resistant, 38 were moderately susceptible, and 2 exhibited a susceptible reaction to sheath blight disease. Among the specific four genotypes (IC283139, IC283041, IC283038, and IC283023) of the moderately resistant group exhibited less disease reaction in comparison with check variety Tetep. Further, the correlation of percent disease index (PDI) with weather parameters revealed negative associations between PDI and maximum temperature, minimum temperature, low rainfall and the positive association with maximum relative humidity (RH) suggest that very low temperature or high precipitation might have a negative impact on pathogen establishment. In addition, the sheath blight-linked SSRs were assessed using distance and model-based approaches, results of both the models revealed that genotypes distinguished the resistant population from the susceptible one. From the output of two years of principal component analysis, two genotypes from each group of moderately resistant, moderately susceptible and susceptible were studied for their biochemical reaction against the sheath blight pathogen. The biochemical study revealed that the accumulation of defense and antioxidant enzymes, namely, polyphenol oxidase, peroxidase, total phenol, phenylalanine ammonia-lyase, catalase, and superoxide dismutase, were higher in moderately resistant genotypes, but was observed to be lower in moderately susceptible and susceptible genotypes. The statistical analysis revealed the enzyme activities (defense and antioxidant) exhibited a strong negative correlation with area under the disease progress curve (AUDPC) and influence of weather parameter RH. This demonstrates that the environment factor RH plays a major role in imparting the resistance mechanism by decreasing the enzymes activities and increasing PDI. This study found that the identified novel resistant genotype (IC283139) with purple stem base demonstrated improved resistance against sheath blight infection through a defense response and the use of antioxidant machinery.

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.

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.

Optimisation of a rapid and efficient transformation protocol for fungal blast-susceptible indica rice cultivars HR-12 and CO-39

Rice is an important staple crop and fungal blast disease destroys about 10-30% of its global produce, annually. Although genetic manipulation has largely been employed in crop-improvement programmes and agricultural biotechnology, the ease of transformation of several recalcitrant indica cultivars continues to be a challenge. HR-12 and CO-39 are two indica cultivars that are commonly used in breeding programmes, but are susceptible to biotic threats like fungal blast and sheath blight disease. Here in this study, we have optimised a rapid and reproducible transformation protocol for the said cultivars, having compared both the tissue-culture and in-planta methods of transformation. Murashige & Skoog basal media supplemented with maltose and 2.5 mg l^-1 2,4-D induced efficient callogenesis in HR-12, while maltose with 3 mg l^-1 2,4-D gave optimum results in case of CO-39. The media containing 0.5 mg l^-1 NAA, 3 mg l^-1 BAP, and 1 mg l^-1 kinetin yielded a maximum regeneration efficiency of 62% and 65% in HR-12 and CO-39, respectively. The studies with Agrobacterium tumefaciens, LBA4404 strain harbouring pCAMBIA1303 suggested that although these cultivars demonstrated successful gene-transfer, they failed to regenerate efficiently, post-transformation. Alternatively, our modified in-planta piercing and vacuum infiltration-based protocol resulted in 33-35% transformation efficiency in less than half the time required for tissue-culture based transformation method. As per our knowledge, it is among the highest obtained from existing piercing-based direct transformation protocols in rice, and can also be implemented in genetically manipulating other recalcitrant varieties of rice.

In silico molecular and morphological analysis of rice blast resistant gene Pi-ta in Sri Lankan rice germplasm

Background

Pi-ta is a major blast resistant gene, introgressed from indica rice varieties. In this study, diversity of the Pi-ta gene of 47 Sri Lankan rice accessions was studied by bioinformatics, and the results were validated with molecular and disease reaction assays. Sequences of rice accessions at the locus Os12g0281300 were retrieved from Rice SNP-Seek Database, and the coding sequence of reference Pi-ta gene of cultivar Tetep (accession no. GQ918486.1) was obtained from GenBank. Comparisons were made at nucleotide, amino acid, and protein structure level, and the 3D models predicted using Phyre2 software were superimposed using TM-align software.

Results

In silico analysis revealed that 10 accessions possessed resistant allele of the Pi-ta gene. The remaining accessions recorded high polymorphism in the leucine-rich domain resulting in 9 allele types, leading to single–amino acid substitutions at 27 different positions including a functional mutation of alanine to serine at the 918th amino acid position. None of the genotypes led to truncations in the amino acid sequence. The in silico analysis results were validated on 23 accessions comprising resistant and susceptible genotypes and another 25 cultivars from Northern Sri Lanka, by molecular assay using YL183/YL87 and YL155/YL87 resistant and susceptible allele-specific markers. Resistance of Pi-ta gene for the causal fungus, Magnaporthe oryzae, was further validated through pathogenicity assay.

Conclusion

The Pi-ta gene, especially the LRD region, revealed significant variations within Sri Lankan rice cultivars leading to high levels of resistance against blast. This information would be highly useful in breeding programmes for resistance against rice blast.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-021-00239-7.

Cataloguing of blast resistance genes in landraces and breeding lines of rice from India

The rice blast caused by the fungus Magnaporthe oryzae is one of the most devastating diseases of rice and can lead to complete failure of the crop under severe cases. The first step in breeding for blast resistance in rice is therefore to identify the novel sources of resistance and cataloguing different blast resistant genes in these genotypes. In the present study, a set of 37 rice genotypes comprising of landraces, advanced breeding lines and released varieties were first characterized for blast resistance under epiphytotic conditions and subsequently different blast resistant genes were catalogued with the help of markers tightly linked to these genes. A total of 22 different blast resistant genes were catalogued in these genotypes. Lot of diversity was found to be present for different genes in the rice genotypes studied. In addition, a set of 2-3 markers were identified which could distinguish genotypes of a particular geographic area from each other.The results are useful for identifying the right combination of genotypes in the resistance breeding programme.

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.