Sheath Blight Resistance In Rice Research Articles

Sugar competition is important for sheath blight resistance in rice towards climate adaptation

Sheath blight (ShB) caused by Rhizoctonia solani Kühn is one of the most serious diseases in rice and is highly susceptible to climate and environmental influences, high humidity climate conditions combined with higher temperatures often lead to more severe occurrences of ShB. The heterotrophic R. solani and rice might compete for sugar at the border of interaction; however, the underlying mechanism remains unclear. In this study, we demonstrated that the expression level of Sugar will eventually be exported transporters (SWEETs) induction was higher in ShB susceptible varieties than in ShB resistant varieties by R. solani inoculation. Inoculation of R. solani revealed that most sweet mutants were less susceptible to ShB than the wild-type. Also, sugar transporters (STPs) gene expression was sensitive to R. solani infection. STPs were localized at the plasma membrane and transported hexose in yeast. Knockdown of STP4 increased the susceptibility of rice to ShB. Interestingly, sequence analysis identified two monosaccharide transporter genes (hereafter named RsMST). RsMSTs transported 2-deoxyglucose, a toxic glucose analog in yeast, suggesting their role as glucose transporter. Spray-induced gene silencing of RsMST1 or RsMST2 dramatically suppressed their expression level and reduced virulence of R. solani. These data suggested that R. solani might induce SWEETs to efflux sugar from the cytosol to apoplast, and STP and RsMSTs compete for sugar at the apoplast for host defense and pathogen virulence. This study provided important insights for ShB-resistant breeding in rice.

Evaluation of Sheath Blight Resistance in Diverse Rice Varieties Under Artificial Inoculation and Field Conditions

Rice (Oryza sativa L.) a vital food crop for nearly half of the global population, facing significant threats from various biotic and abiotic stresses. Among biotic stresses, diseases pose the most common challenge. Sheath blight, caused by soil-borne fungal pathogen Rhizoctonia Solani Kühn (R. solani), is a major concern, leading to substantial damage to rice and cereal crops worldwide. This study evaluated sheath blight resistance across diverse rice varieties, including short grain, long grain, aromatic, hybrid, and wild types, under both artificial inoculation and field conditions. Ten host plant species were assessed for resistance to sheath blight caused by Rhizoctonia Solani, using physiological screening one-week post-inoculation. The highly virulent R. solani isolate (AG-1 IA anastomosis group) was cultured on PDA media, covering the entire plate 3 to 5 days. Screening of cultivated rice varieties, was conducted using field conditions and humidified chamber methods, with results confirmed through molecular characterization. Among the ten cultivated rice varieties, Arize 6444 and Dhanya 748 exhibited the lowest disease index, classifying them as moderately resistant. In contrast, Kalanamak and Pusa Basmati were highly susceptible, displaying high disease indices. Among wild rice accessions, Oryza rufipogon showed a disease index of five or less. Visual ratings indicated the highest susceptibility in Kalanamak, followed by Pusa Basmati and Swarna sub-1, while the lowest visual ratings were observed in wild rice accessions Oryza australiensis and Oryza rufipogon across all tested hosts. The findings underscore the importance of identifying resistant rice varieties to manage sheath blight effectively. The moderately resistant cultivars and wild rice accessions identified in this study offer valuable genetic resources for breeding programs aimed at enhancing sheath blight resistance in rice.

Comparative Field Evaluation and Transcriptome Analysis Reveals that Chromosome Doubling Enhances Sheath Blight Resistance in Rice

Rice sheath blight, caused by Rhizoctonia solani Kihn (R. solani), poses a significant threat to rice production and quality. Autotetraploid rice, developed through chromosome doubling of diploid rice, holds great potential for enhancing biological and yield traits. However, its resistance to sheath blight in the field has remained unclear. In this study, the field resistance of 35 autotetraploid genotypes and corresponding diploids was evaluated across three environments from 2020 to 2021. The booting stage was optimal for inoculating period based on the inoculation and analysis of R. solani at five rice growth stages. We found autotetraploids generally exhibited lower disease scores than diploids, indicating enhanced resistance after chromosome doubling. Among the 35 genotypes, 16 (45.71%) displayed increased resistance, 2 (5.71%) showed decreased resistance, and 17 (48.57%) displayed unstable resistance in different sowing dates. All combinations of the genotype, environment and ploidy, including the genotype-environment-ploidy interaction, contributed significantly to field resistance. Chromosome doubling increased sheath blight resistance in most genotypes, but was also dependent on the genotype-environment interaction. To elucidate the enhanced resistance mechanism, RNA-seq revealed autotetraploid recruited more down-regulated differentially expressed genes (DEGs), additionally, more resistance-related DEGs, were down-regulated at 24 h post inoculation in autotetraploid versus diploid. The ubiquinone/terpenoid quinone and diterpenoid biosynthesis pathways may play key roles in ploidy-specific resistance mechanisms. In summary, our findings shed light on the understanding of sheath blight resistance mechanisms in autotetraploid rice.

Overexpression of Calcineurin B-like Interacting Protein Kinase 31 Promotes Lodging and Sheath Blight Resistance in Rice.

A breakthrough "Green Revolution" in rice enhanced lodging resistance by using gibberellin-deficient semi-dwarf varieties. However, the gibberellic acid (GA) signaling regulation on rice disease resistance remains unclear. The resistance test showed that a positive GA signaling regulator DWARF1 mutant d1 was more susceptible while a negative GA signaling regulator Slender rice 1 (SLR1) mutant was less susceptible to sheath blight (ShB), one of the major rice diseases, suggesting that GA signaling positively regulates ShB resistance. To isolate the regulator, which simultaneously regulates rice lodging and ShB resistance, SLR1 interactors were isolated. Yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), and Co-IP assay results indicate that SLR1 interacts with Calcineurin B-like-interacting protein kinase 31 (CIPK31). cipk31 mutants exhibited normal plant height, but CIPK31 OXs showed semi-dwarfism. In addition, the SLR1 level was much higher in CIPK31 OXs than in the wild-type, suggesting that CIPK31 OX might accumulate SLR1 to inhibit GA signaling and thus regulate its semi-dwarfism. Recently, we demonstrated that CIPK31 interacts and inhibits Catalase C (CatC) to accumulate ROS, which promotes rice disease resistance. Interestingly, CIPK31 interacts with Vascular Plant One Zinc Finger 2 (VOZ2) in the nucleus, and expression of CIPK31 accumulated VOZ2. Inoculation of Rhizoctonia solani AG1-IA revealed that the voz2 mutant was more susceptible to ShB. Thus, these data prove that CIPK31 promotes lodging and ShB resistance by regulating GA signaling and VOZ2 in rice. This study provides a valuable reference for rice ShB-resistant breeding.

Development of activation-tagged gain-of-functional mutants in indica rice line (BPT 5204) for sheath blight resistance.

The development of sheath blight (ShB) resistance varieties has been a challenge for scientists for long time in rice. Activation tagging is an efficient gain-of-function mutation approach to create novel phenotypes and to identify their underlying genes. In this study, a mutant population was developed employing activation tagging in the recalcitrant indica rice (Oryza sativa L.) cv. BPT 5204 (Samba Mahsuri) through activation tagging. In this study, we have generated more than 1000 activation tagged lines in indica rice, from these mutant population 38 (GFP- RFP+) stable Ds plants were generated through germinal transposition at T2 generation based on molecular analysis and seeds selected on hygromycin (50mg/L) containing medium segregation analyses confirmed that the transgene inherited as mendelian segregation ratio of 3:1 (3 resistant: 1 susceptible). Of them, five stable activation tagged Ds lines (M-Ds-1, M-Ds-2, M-Ds-3, M-Ds-4 and M-Ds-5) were selected based on phenotypic observation through screening for sheath blight (ShB) resistance caused by fungal pathogen Rhizoctonia solani (R. solani),. Among them, M-Ds-3 and M-Ds-5 lines showed significant resistance for ShB over other tagged lines and wild type (WT) plants. Furthermore, analysed for launch pad insertion through TAIL-PCR results and mapped on corresponding rice chromosomes. Flanking sequence and gene expression analysis revealed that the upregulation of glycoside hydrolase-OsGH or similar to Class III chitinase homologue (LOC_Os08g40680) in M-Ds-3 and a hypothetical protein gene (LOC_Os01g55000) in M-Ds-5 are potential candidate genes for sheath blight resistance in rice. In the present study, we developed Ac-Ds based ShB resistance gain-of-functional mutants through activation tagging in rice. These activation tagged mutant lines can be excellent sources for the development of ShB resistant cultivars in rice.

Identification of NADPH Oxidase Genes Crucial for Rice Multiple Disease Resistance and Yield Traits

Reactive oxygen species (ROS) act as a group of signaling molecules in rice functioning in regulation of development and stress responses. Respiratory burst oxidase homologues (Rbohs) are key enzymes in generation of ROS. However, the role of the nine Rboh family members was not fully understood in rice multiple disease resistance and yield traits. In this study, we constructed mutants of each Rboh genes and detected their requirement in rice multiple disease resistance and yield traits. Our results revealed that mutations of five Rboh genes (RbohA, RbohB, RbohE, RbohH, and RbohI) lead to compromised rice blast disease resistance in a disease nursery and lab conditions; mutations of five Rbohs (RbohA, RbohB, RbohC, RbohE, and RbohH) result in suppressed rice sheath blight resistance in a disease nursery and lab conditions; mutations of six Rbohs (RbohA, RbohB, RbohC, RbohE, RbohH and RbohI) lead to decreased rice leaf blight resistance in a paddy yard and ROS production induced by PAMPs and pathogen. Moreover, all Rboh genes participate in the regulation of rice yield traits, for all rboh mutants display one or more compromised yield traits, such as panicle number, grain number per panicle, seed setting rate, and grain weight, resulting in reduced yield per plant except rbohb and rbohf. Our results identified the Rboh family members involved in the regulation of rice resistance against multiple pathogens that caused the most serious diseases worldwide and provide theoretical supporting for breeding application of these Rbohs to coordinate rice disease resistance and yield traits.

Lanthanum Silicate Nanomaterials Enhance Sheath Blight Resistance in Rice: Mechanisms of Action and Soil Health Evaluation.

In the current study, foliar spray with lanthanum (La) based nanomaterials (La10Si6O27 nanorods, La10Si6O27 nanoparticle, La(OH)3 nanorods, and La2O3 nanoparticle) suppressed the occurrence of sheath blight (Rhizoctonia solani) in rice. The beneficial effects were morphology-, composition-, and concentration-dependent. Foliar application of La10Si6O27 nanorods (100 mg/L) yielded the greatest disease suppression, significantly decreasing the disease severity by 62.4% compared with infected controls; this level of control was 2.7-fold greater than the commercially available pesticide (Thifluzamide). The order of efficacy was as follows: La10Si6O27 nanorods > La10Si6O27 nanoparticle > La(OH)3 nanorods > La2O3 nanoparticle. Mechanistically, (1) La10Si6O27 nanorods had greater bioavailability, slower dissolution, and simultaneous Si nutrient benefits; (2) transcriptomic and metabolomic analyses revealed that La10Si6O27 nanorods simultaneously strengthened rice systemic acquired resistance, physical barrier formation, and antioxidative systems. Additionally, La10Si6O27 nanorods improved rice yield by 35.4% and promoted the nutritional quality of the seeds as compared with the Thifluzamide treatment. A two-year La10Si6O27 nanorod exposure had no effect on soil health based on the evaluated chemical, physical, and biological soil properties. These findings demonstrate that La based nanomaterials can serve as an effective and sustainable strategy to safeguard crops and highlight the importance of nanomaterial composition and morphology in terms of optimizing benefit.

β-Glucanase Family Genes Promote Resistance to Sheath Blight in Rice by Inhibiting the Permeability of Plasmodesmata.

Rice sheath blight (ShB) caused by Rhizoctonia solani is one of the most serious diseases that threatens rice (Oryza sativa) production. However, the mechanisms of defense against ShB in rice remain largely unknown. In this study, we identified that the expression levels of β-glucanase (OsBGL) family genes sensitively respond to infection by R. solani, and OsBGLs positively regulate rice resistance to ShB. In addition, OsBGL2 colocalized with AtPDCB1 at the plasmodesmata (PD) and limited the PD permeability. The level of callose accumulation in osbgls mutants and overexpressors was examined, and OsBGLs were found contribute to callose accumulation. Taken together, these data suggest that OsBGLs can regulate the deposition of callose at the PD to reduce its permeability to defend itself against ShB. Through the identification of these genes and the elucidation of their functions, this research fills the gap in the mechanism of PD permeability in rice ShB resistance.

Progress in rice sheath blight resistance research.

Rice sheath blight (ShB) disease poses a major threat to rice yield throughout the world. However, the defense mechanisms against ShB in rice remain largely unknown. ShB resistance is a typical quantitative trait controlled by multiple genes. With the rapid development of molecular methods, many quantitative trait loci (QTLs) related to agronomic traits, biotic and abiotic stresses, and yield have been identified by genome-wide association studies. The interactions between plants and pathogens are controlled by various plant hormone signaling pathways, and the pathways synergistically or antagonistically interact with each other, regulating plant growth and development as well as the defense response. This review summarizes the regulatory effects of hormones including auxin, ethylene, salicylic acid, jasmonic acid, brassinosteroids, gibberellin, abscisic acid, strigolactone, and cytokinin on ShB and the crosstalk between the various hormones. Furthermore, the effects of sugar and nitrogen on rice ShB resistance, as well as information on genes related to ShB resistance in rice and their effects on ShB are also discussed. In summary, this review is a comprehensive description of the QTLs, hormones, nutrition, and other defense-related genes related to ShB in rice. The prospects of targeting the resistance mechanism as a strategy for controlling ShB in rice are also discussed.

Introgression of the QTL qSB11-1TT conferring sheath blight resistance in rice (Oryza sativa) into an elite variety, UKMRC 2, and evaluation of its backcross-derived plants.

Sheath blight (SB) is the most damaging fungal disease in rice caused by a soil-borne pathogenic fungus, Rhizoctonia solani Kuhn (R. solani). The disease resistance in rice is a complex quantitative trait controlled by a few major genes. UKMRC2 is a newly developed elite rice variety that possesses high yield potential but is susceptible to sheath blight disease indicating a huge risk of varietal promotion, mass cultivation, and large-scale adoption. The aim of our present study was the development of varietal resistance against R. solani in UKMRC2 to enhance its stability and durability in a wide range of environments and to validate the effects of an SB-resistance QTL on the new genetic background. In our study, we developed 290 BC1F1 backcross progenies from a cross between UKMRC2 and Tetep to introgress the QTL qSBR11-1TT into the UKMRC2 genetic background. Validation of the introgressed QTL region was performed via QTL analysis based on QTL-linked SSR marker genotyping and phenotyping against R. solani artificial field inoculation techniques. The QTL qSBR11-1TT was then authenticated with the results of LOD score (3.25) derived from composite interval mapping, percent phenotypic variance explained (14.6%), and additive effect (1.1) of the QTLs. The QTL region was accurately defined by a pair of flanking markers K39512 and RM7443 with a peak marker RM27360. We found that the presence of combination of alleles, RM224, RM27360 and K39512 demonstrate an improved resistance against the disease rather than any of the single allele. Thus, the presence of the QTL qSBR11-1TT has been validated and confirmed in the URMRC2 genetic background which reveals an opportunity to use the QTL linked with these resistance alleles opens an avenue to resume sheath blight resistance breeding in the future with marker-assisted selection program to boost up resistance in rice varieties.

Malectin Domain Protein Kinase (MDPK) Promotes Rice Resistance to Sheath Blight via IDD12, IDD13, and IDD14.

Sheath blight (ShB) caused by Rhizoctonia solani is a major disease of rice, seriously affecting yield; however, the molecular defense mechanism against ShB remains unclear. A previous transcriptome analysis of rice identified that R. solani inoculation significantly induced MDPK. Genetic studies using MDPK RNAi and overexpressing plants identified that MDPK positively regulates ShB resistance. This MDPK protein was found localized in the endoplasmic reticulum (ER) and Golgi apparatus. Yeast one-hybrid assay, electrophoresis mobility shift assay (EMSA), and chromatin immunoprecipitation (ChIP) showed that the intermediate domain proteins IDD12, IDD13, and IDD14 bind to the MDPK promoter. Moreover, IDD14 was found to interact with IDD12 and IDD13 to form a transcription complex to activate MDPK expression. The three IDDs demonstrated an additive effect on MDPK activation. Further genetic studies showed that the IDD13 and IDD14 single mutants were more susceptible to ShB but not IDD12, while IDD12, IDD13, and IDD14 overexpressing plants were less susceptible than the wild-type plants. The IDD12, IDD13, and IDD14 mutants also proved the additive effect of the three IDDs on MDPK expression, which regulates ShB resistance in rice. Notably, MDPK overexpression maintained normal yield levels in rice. Thus, our study proves that IDD12, IDD13, and IDD14 activate MDPK to enhance ShB resistance in rice. These results improve our knowledge of rice defense mechanisms and provide a valuable marker for resistance breeding.

OsMATE6 gene putatively involved in host defense response toward susceptibility against Rhizoctonia solani in rice

ABSTRACT Sheath blight caused by Rhizoctonia solani AG1-IA is the second most serious disease of rice worldwide. Elucidating the role of multi-drug and toxic compound extrusion (MATE) gene family in host-pathogens interactions may uncover a new possible way to comprehend the mechanism of sheath blight resistance in rice. We foremost explored the role of OsMATE genes against R. solani resistance through comparative transcriptomics in PR114 (susceptible) and ShB-8 (moderately resistant) at 24 and 48 hpi (hours post-inoculation) of R. solani infection, respectively. Six OsMATE genes were differentially expressed and further validated through qRT-PCR. OsMATE6 gene was identified as a potential candidate for sheath blight susceptibility as it was significantly up-regulated in PR114. OsMATE6 is conserved within the wild relatives and might be translocated from Oryza nivara during the domestication of rice. Further studies are focused to verify its role by overexpression and protein interactions to understand the molecular mechanism of sheath blight resistance.

Study of association between morphological traits and QTLs governing sheath blight resistance in rice (Oryza sativa L.)

Rice sheath blight is one of the most serious diseases of rice. In the current study, the relationship between morphological traits and sheath blight resistance was investigated by using 1545 recombinant inbred lines. Correlation analysis showed that culm angle, flag leaf angle, flag leaf length and plant height were significantly correlated with sheath blight resistance. Genome-wide association studies revealed that a gene controlling culm angle (TAC1), three quantitative trait loci (QTL) governing plant height (qPHT1-1), penultimate leaf angle (qPLA-1) and days to 50% flowering (qDFF-7) were found to be adjacent to the regions of qSB9, qSBR1-1 and qSB7, the QTLs conferring sheath blight resistance. Except for these cases, no QTL underlying other traits was detected near the chromosomal region associated with sheath blight resistance. The results concluded that the morphological traits were not the main factors responsible for the sheath blight resistance but had some indirect influence to evade infection of the pathogen. An efficient approach in resistance breeding for sheath blight would be to pyramid major QTLs for sheath blight resistance and select those morphological traits that favour resistant reaction. Keywords: QTL, morphological characters, correlation, GWAS, sheath blight resistance &nbsp

Assessment of Rice Sheath Blight Resistance Including Associations with Plant Architecture, as Revealed by Genome-Wide Association Studies

BackgroundSheath blight (ShB) disease caused by Rhizoctonia solani Kühn, is one of the most economically damaging rice (Oryza sativa L.) diseases worldwide. There are no known major resistance genes, leaving only partial resistance from small-effect QTL to deploy for cultivar improvement. Many ShB-QTL are associated with plant architectural traits detrimental to yield, including tall plants, late maturity, or open canopy from few or procumbent tillers, which confound detection of physiological resistance.ResultsTo identify QTL for ShB resistance, 417 accessions from the Rice Diversity Panel 1 (RDP1), developed for association mapping studies, were evaluated for ShB resistance, plant height and days to heading in inoculated field plots in Arkansas, USA (AR) and Nanning, China (NC). Inoculated greenhouse-grown plants were used to evaluate ShB using a seedling-stage method to eliminate effects from height or maturity, and tiller (TN) and panicle number (PN) per plant. Potted plants were used to evaluate the RDP1 for TN and PN. Genome-wide association (GWA) mapping with over 3.4 million SNPs identified 21 targeted SNP markers associated with ShB which tagged 18 ShB-QTL not associated with undesirable plant architecture traits. Ten SNPs were associated with ShB among accessions of the Indica subspecies, ten among Japonica subspecies accessions, and one among all RDP1 accessions. Across the 18 ShB QTL, only qShB4-1 was not previously reported in biparental mapping studies and qShB9 was not reported in the GWA ShB studies. All 14 PN QTL overlapped with TN QTL, with 15 total TN QTL identified. Allele effects at the five TN QTL co-located with ShB QTL indicated that increased TN does not inevitably increase disease development; in fact, for four ShB QTL that overlapped TN QTL, the alleles increasing resistance were associated with increased TN and PN, suggesting a desirable coupling of alleles at linked genes.ConclusionsNineteen accessions identified as containing the most SNP alleles associated with ShB resistance for each subpopulation were resistant in both AR and NC field trials. Rice breeders can utilize these accessions and SNPs to develop cultivars with enhanced ShB resistance along with increased TN and PN for improved yield potential.

Analysis of the Efficiency of Genomic Selection Models for Predicting Sheath Blight Resistance in Rice (Oryza sativa L.,)

The research was undertaken during June-October 2020 at Seethanagaram and Draksharam villages of East Godavari district, Andhra Pradesh, India with an objective to evaluate efficiency of genomic selection models involving 1545 recombinant inbred lines (RILs) derived from eleven bi-parental populations in Rice. During June-October 2020, the F7 RILs were screened in two hot spot locations. The genotyping was done with Infinium platform having 6564 SNP markers. Five models were used rrBLUP, BayesA, BayesB, BayesCPi and GBLUP to train the statistical model for calculation of marker effects and genomic estimated breeding values (GEBVs). The prediction accuracy (data fit) of training set across models ranged 0.63–0.72, lowest and highest prediction accuracies were observed with rrBLUP and GBLUP models respectively. Tenfold cross validation with different approaches, the average prediction accuracy ranged from 0.60 (rrBLUP, BayesA, BayesB and BayesCPi) –0.72 (GBLUP). BayesB and GBLUP models exhibit higher prediction accuracies compared to other models studied. The predictive ability increased dramatically with more SNPs included in analysis until 2000 markers with average prediction accuracy of 0.681, no significant improvement beyond this was observed. The results are lucrative, all in all, high prediction accuracies observed in this study suggest genomic selection as a very promising strategy while breeding for sheath blight resistance in rice to increase genetic gain.

Effects of marker density and training set size on the genomic selection accuracy for predicting sheathblight resistance in rice (Oryza sativa L.)

The success of genomic selection mainly depends on the extent of linkage disequilibrium between markers and quantitative trait loci, size of training set, heritability of the trait etc. The extent of linkage disequilibrium depends on the genetic structure of the population and marker density. This study was conducted to determine the effects of marker density and size of training set on prediction accuracy using 1545 recombinant inbred lines derived from eleven bi-parental rice populations. All RILs were genotyped with 6564 SNPs and screened in two hot spot locations to assess reaction against sheath blight.Bayesian B model was used to train the statistical model for calculation of marker effects and genomic estimated breeding values. To evaluate the genomic prediction accuracy, various levels of training set size (300, 500, 700, 900 and 1200 lines) and marker density (500, 800, 1100, 1400, 1700, 2000, 4000 and 6000 markers) were considered. In our study, the prediction accuracy increased with increase in training set size, however, average prediction accuracy of 0.717 was obtained for the training set comprising of 900 lines before reaching plateau with marginal increase in prediction accuracy with higher training set sizes. The predictive ability increased dramatically with more SNPs included in the analysis until 2000 markers with average prediction accuracy of 0.681, no significant improvement beyond this was observed. The results indicate that training set with approximately 900 lines and 2000 uniformly distributed SNP markers with good amount of polymorphism across populations would be enough to reach achievable accuracy to predict sheath blight resistance in rice.

EVALUATION OF THE EFFICIENCY OF GENOMIC SELECTION APPROACH FOR PREDICTING SHEATH BLIGHT RESISTANCE IN RICE (ORYZA SATIVA L.) USING BAYESIAN MODELS

sheath blight (ShB) is one of the most serious fungal diseases caused by Rhizoctonia solani, instigating significant yield losses in many rice-growing regions of the world. Intensive studies indicated that resistance for sheath blight is controlled possibly by polygenes. Because of complex inheritance, it’s very difficult to exploit and tap all the genomic regions conferring resistance using classical approaches of quantitative trait loci (QTL) mapping, it’s very important to have a planned strategy to harness such resistance mechanism. One of the most promising approach is genomic selection (GS). The research was undertaken with an objective to validate genomic selection approach for predicting sheath blight resistance involving 1545 Recombinant inbred lines (RILs) derived from eleven bi-parental populations from crosses between resistant and susceptible parents. Where, Jasmine 85, Tetep and MTU 9992 were resistant parents and TN1, Swarna Sub1, II32B, IR54 and IRBB4 were susceptible parents. During rainy season (2020) the F7 recombinant inbred lines (RIL) were screened for their reaction to sheath blight in two hot spot locations. The genotyping was done with Illumina platform having 6564 SNP markers. Three Bayesian models were used, Bayesian A, Bayesian B and Bayesian CPi to train the statistical model for calculation of marker effects and genomic estimated breeding values (GEBV). The prediction accuracy of training set across models ranged from 0.69 to 0.72, lowest and highest prediction accuracies were observed with Bayesian A and Bayesian B models respectively and the average prediction accuracy of tenfold cross validation with different models was 0.60. Bayesian B model exhibited higher prediction accuracies compared to other models studied. The results are lucrative, all in all, higher prediction accuracies across the models studied suggest genomic selection as a promising breeding strategy for predicting sheath blight resistance in Rice.

Validation of Genomic Selection Approach for Predicting Sheath Blight Resistance in Rice (Oryza sativa L.,)

Rice sheath blight (ShB) is one of the most serious fungal diseases caused by Rhizoctonia solani, instigating significant yield losses in many rice-growing regions of the world. Intensive studies indicated that resistance for sheath blight is controlled possibly by polygenes. Because of complex inheritance, it’s very difficult to exploit and tap all the genomic regions conferring resistance using classical approaches of QTL mapping, it’s very important to have a different strategy to harness such resistance mechanism. One promising approach that can potentially provide accurate predictions of the resistance phenotypes is genomic selection (GS). The research was undertaken with an objective to validate genomic selection approach for predicting sheath blight resistance involving 1545 Recombinant inbred lines (RILs) derived from eleven crosses between resistant and susceptible parents (Jasmine 85XTN1, Jasmine 85XSwarnaSub1, Jasmine 85XII32B, Jasmine 85XIR54, TetepXTN1, TetepXSwarna Sub1, TetepXII32B, TetepXIR54, MTU 9992XTN1, MTU 9992XII32B and MTU 9992XIRBB4). Where, Jasmine 85, Tetep & MTU 9992 were resistant parents and TN1, Swarna Sub1, II32B, IR54 & IRBB4 were susceptible parents. During rainy season (2020) the F7 RILs were screened for their reaction to sheath blight in two hot spot locations. The genotyping was done with Illumina platform having 6564 SNP markers. Bayesian B approach was used to train the statistical model for calculation of marker effects and GEBVs. The prediction accuracy of training set (data fit analysis) obtained was 0.70 and random cross validation with different approaches, the prediction accuracy ranged from 0.67 to 0.74. The results are lucrative, all in all, high prediction accuracies observed in this study suggest genomic selection as a very promising breeding strategy for predicting sheath blight resistance in Rice.

Genome Wide Association Studies to Dissect Genetic Factors Conferring Sheath Blight Resistance in Rice (Oryza sativa L.)

Rice Sheath blight (ShB) is one of the most serious fungal diseases caused by Rhizoctonia solani. Breeding for sheath blight resistance has been ineffective exercise so far, mainly because of lack of good number of reliable sources of resistance in rice germplasm. In this context our studies indicated that the lines Tetep, Jasmine 85 and MTU 9992 confer resistant to moderately resistant reaction against the pathogen. The current investigation was carried out to dissect the genetic factors governing resistance to sheath blight through genome wide association study (GWAS) from the mapping populations developed by design where in, each of the resistant parents were crossed to three to four highly susceptible parents to generate eleven populations (Jasmine 85XTN1, Jasmine 85XSwarnaSub1, Jasmine 85XII32B, Jasmine 85XIR54, TetepXTN1, TetepXSwarnaSub1, TetepXII32B, TetepXIR54, MTU 9992XTN1, MTU 9992XII32B and MTU 9992XIRBB4). A total of 1545 Recombinant inbred lines (RILs) derived from eleven crosses were used for the study. During rainy 2020 the F7 RILs were screened for their reaction to Sheath blight in two hot spot locations. The genotyping was done with Illumina platform having 6564 SNP markers. Genome wide association study was done with two models Generalized Linear Model (GLM) and Mixed Linear Model (MLM). Results clearly indicate the superiority of MLM over GLM in correcting the population structure. With MLM model, in Jasmine 85 half-sib populations with 565 RILs analyzed, five QTLs (Quantitative Trait Loci) were detected on Chr1, Chr3, Chr9, Chr10 and Chr11 with –log10 (P-Value) more than 3. In TETEP half-sib populations with 714 RILs examined, seven QTLs were observed on Chr1, Chr2, Chr5, Chr6, Chr7, Chr8, and Chr11 with –log10 (P-Value) more than 4. Whereas in MTU 9992 half-sib populations with 266 RILs studied, three novel QTLs were identified on Chr2, Chr6 and Chr11 with –log10 (P-Value) more than 3. Some of these QTLs were reported by researches earlier. In the current research, some novel QTLs were detected in Jasmine 85 (Chr10) and Tetep (Chr2, Chr5 and Chr6) apart from three new QTLs discovered in MTU 9992. The results facilitated to have better understanding of the genetic basis for sheath blight resistance in rice. Pyramiding all the QTL identified so far into a susceptible varieties is complicated affair as resistance is governed by not only several large effect QTLs but also medium to small effect QTLs as well, hence genomic selection approach could be rewarding for breeding for sheath blight resistance.

Sheath blight resistance in rice is negatively regulated by WRKY53 via SWEET2a activation

Sheath blight (ShB) is one of the most common diseases in rice that significantly affects yield production. However, the underlying mechanisms of rice defense remain largely unknown. Our previous transcriptome analysis identified that infection with Rhizoctonia solani significantly induced the expression level of SWEET2a, a member of the SWEET sugar transporter. The sweet2a genome-editing mutants were less susceptible to ShB. Further yeast-one hybrid, ChIP, and transient assays demonstrated that WRKY53 binds to the SWEET2a promoter to activate its expression. WRKY53 is a key brassinosteroid (BR) signaling transcription factor. Similar to the BR receptor gene BRI1 and biosynthetic gene D2 mutants, the WRKY53 mutant and overexpressor were less and more susceptible to ShB compared to wild-type, respectively. Inoculation with R. solani induced expression of BRI1, D2, and WRKY53, but inhibited MPK6 (a BR-signaling regulator) activity. Also, MPK6 is known to phosphorylate WRKY53 to enhance its transcription activation activity. Transient assay results indicated that co-expression of MPK6 and WRKY53 enhanced WRKY53 trans-activation activity to SWEET2a. Furthermore, expression of WRKY53 SD (the active phosphorylated forms of WRKY53) but not WRKY53 SA (the inactive phosphorylated forms of WRKY53), enhanced WRKY53-mediated activation of SWEET2a compared to expression of WRKY53 alone. Taken together, our analyses showed that R. solani infection may activate BR signaling to induce SWEET2a expression via WRKY53 through negative regulation of ShB resistance in rice.