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.

Analysis of Differentially Expressed Rice Genes Reveals the ATP-Binding Cassette (ABC) Transporters as a Candidate Gene Against the Sheath Blight Pathogen, Rhizoctonia solani

Sheath blight is a serious rice disease worldwide and genes involved in resistance remain unclear. In the present study, a virulent field isolate of Rhizoctonia solani was used to inoculate detached leaves of a sheath blight resistant rice cultivar ‘Jasmine 85’, a suppression subtractive cDNA library was constructed using RNA isolated 16 hours post inoculation (hpi), and differentially expressed genes were identified from the cDNA library. A total of 159 uniquely expressed sequence tags were identified, including 105 from rice with enrichment in categories related to cellular response, molecular signaling and host defense. Coupled with gene expression studies by DNA microarray, 27 highly induced genes involved in signal transduction and defense responses were identified within 16 hpi. Three members of the ABC transporter gene family (OsABC1, OsABC9 and OsABC12) encoding pleiotropic drug resistance (PDR)-like ATP binding cassette (ABC) transporters were mapped to different sheath blight resistance QTL and their differential expressions were validated. Three high-resolution melting (HRM) markers were developed from these ABC gene family members to distinguish alleles between sheath blight susceptible cultivar ‘Lemont’ and resistant cultivar ‘Jasmine 85’. Association of sheath blight resistance to these HRM markers was examined in 77 recombinant inbred lines derived from the cross between ‘Jasmine 85’ and “Lemont”. The OsABC9 gene located in a major sheath blight resistance QTL qShB9-2 showed a major contribution to sheath blight resistance. These results are useful for marker assisted section and functional validation of the ABC genes in sheath blight disease resistance.

Strategies to Manage Rice Sheath Blight: Lessons from Interactions between Rice and Rhizoctonia solani

Rhizoctonia solani is an important phytopathogenic fungus with a wide host range and worldwide distribution. The anastomosis group AG1 IA of R. solani has been identified as the predominant causal agent of rice sheath blight, one of the most devastating diseases of crop plants. As a necrotrophic pathogen, R. solani exhibits many characteristics different from biotrophic and hemi-biotrophic pathogens during co-evolutionary interaction with host plants. Various types of secondary metabolites, carbohydrate-active enzymes, secreted proteins and effectors have been revealed to be essential pathogenicity factors in R. solani. Meanwhile, reactive oxygen species, phytohormone signaling, transcription factors and many other defense-associated genes have been identified to contribute to sheath blight resistance in rice. Here, we summarize the recent advances in studies on molecular interactions between rice and R. solani. Based on knowledge of rice-R. solani interactions and sheath blight resistance QTLs, multiple effective strategies have been developed to generate rice cultivars with enhanced sheath blight resistance.