Analysis of differentially expressed rice genes reveals the ATP-Binding Cassette (ABC) transporters as a candidate gene against the sheath blight pathogen, rhizoctonia solani

Authors: OH, YOUNGJAE - University Of Florida; LEE, SEONGHEE - University Of Florida; RIOUX, RENEE - University Of Florida; SINGH, PRATIBHA - Australian Centre For International Agricultural Research; Jia, Melissa; Jia, Yulin; MYSORE, KIRNKUMAR - Noble Research Institute

Submitted to: Rice
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/30/2021
Publication Date: 5/16/2022
Citation: Oh, Y., Lee, S., Rioux, R., Singh, P., Jia, M.H., Jia, Y., Mysore, K.S. 2022. Analysis of differentially expressed rice genes reveals the ATP-Binding Cassette (ABC) transporters as a candidate gene against the sheath blight pathogen, rhizoctonia solani. Rice. https://doi.org/10.1094/PHYTOFR-05-21-0035-R.
DOI: https://doi.org/10.1094/PHYTOFR-05-21-0035-R

Interpretive Summary: Sheath blight disease caused by Rhizoctonia solani is one of the most devastating diseases of rice worldwide. The US adapted indica rice cultivar Jasmine 85 has been used as a breeding parent for resistance to R. solani however, the molecular mechanisms for resistance are not understood. In this study, we identified 105 differentially expressed genes in Jasmine 85 after infection with R. solani. These induced genes are mainly involved in strengthening cell walls and production and movement of nutrients in response to sheath blight infection. Pleiotropic drug resistance (PDR)-like ATP binding cassette (ABC) transporters are known to transport molecules inside plant cells. We verified that products of three pleiotropic drug resistance (PDR)-like ATP binding cassette (ABC) transporter (OsABC1, OsABC9 and OsABC12) in Jasmine 85 rapidly accumulated to restrict the pathogen. We then sequenced each allele in Jasmine 85 and a susceptible rice variety, Lemont, and developed a gene-specific functional marker for each. The role of one ABC transporter, OsABC9, in resistance to sheath blight was validated using 86 recombinant inbred lines derived from the cross of Jasmine 85 and Lemont. OsABC9 was found at the border of the major sheath blight resistance QTL qShB9-2. Taken together, these findings shed light on the molecular mechanism of sheath blight resistance at early interphase of pathogen infection and should benefit molecular marker-assisted breeding for sheath blight resistance.

Technical Abstract: Sheath blight disease, caused by the fungus Rhizoctonia solani (R. solani) is one of the most devastating diseases of rice worldwide, and genes closely linked to the resistance for sheath blight are not characterized. The US-adapted indica rice cultivar Jasmine 85 was determined to contain several sheath blight resistance QTLs in our previous studies. In the present study, differentially expressed genes were identified from a suppression subtractive cDNA library constructed using RNA isolated 16 h after inoculation of detached leaves of Jasmine 85 with a virulent field isolate of Rhizoctonia solani (RR0102). A total of 159 unique expressed sequences tags were identified, including 105 from rice with enrichment in categories related to cellular response, molecular signaling, and host defense. Combined with our previous gene expression studies using DNA microarray, 27 highly induced genes involved in signal transduction and defense responses were identified within 16 h post inoculation (hpi) with RR0102. 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 with a time-course experiment following R. solani inoculation. Three high resolution melting (HRM) markers were developed from these ABC gene family members to distinguish alleles in the sheath blight susceptible cultivar, Lemont, and resistant cultivar, Jasmine 85. Correlation of sheath blight resistance to these HRM markers was examined in 86 recombinant inbred lines derived from the cross of Jasmine 85 with Lemont. The OsABC9 gene located in the major sheath blight resistance QTL qShB9-2 showed major contribution (R = 0.34) to sheath blight resistance. These results suggest that the ABC gene on chromosome 9 plays an important role in preventing sheath blight disease in rice.