Resistance to multiple temperate and tropical stem and sheath diseases of rice

Authors: ROSAS, JUAN - Universidad De La República; MARTINEZ, SEBASTIAN - National Agricultural Research Institute(INIA); BLANCO, PEDRO - National Agricultural Research Institute(INIA); PEREZ DE VIDA, FERNANDO - National Agricultural Research Institute(INIA); BONNECARRERE, VICTORIA - National Agricultural Research Institute(INIA); MOSQUERA, GLORIA - International Center For Tropical Agriculture (CIAT); CRUZ, MARIBEL - International Center For Tropical Agriculture (CIAT); GARAYOCHEA, SILVIA - National Agricultural Research Institute(INIA); MONTEVERDE, ELIANA - Cornell University; MCCOUCH, SUSAN - Cornell University; GERMAN, SILVIA - National Agricultural Research Institute(INIA); Jannink, Jean-Luc; GUTIERREZ, LUCIA - National Agricultural Research Institute(INIA)

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/19/2017
Publication Date: 12/14/2017
Citation: Rosas, J., Martinez, S., Blanco, P., Perez De Vida, F., Bonnecarrere, V., Mosquera, G., Cruz, M., Garayochea, S., Monteverde, E., McCouch, S., German, S., Jannink, J., Gutierrez, L. 2017. Resistance to multiple temperate and tropical stem and sheath diseases of rice. The Plant Genome. 11(1). https://doi.org/10.3835/plantgenome2017.03.0029.
DOI: https://doi.org/10.3835/plantgenome2017.03.0029

Interpretive Summary: Stem rot and aggregated sheath spot are the two major stem and sheath diseases affecting rice (Oryza sativa L.) in temperate areas. A third fungal disease, sheath blight, is a major disease in tropical areas. Resistance to these diseases is a key objective in rice breeding programs but phenotyping is challenged by the confounding effects of traits such as flowering time (FT) and plant height (PH). This study sought to identify genes for resistance to these three diseases after removing the confounding effects of FT and PH. We evaluated advanced breeding germplasm in field and greenhouse trials for resistance to the diseases. A total of 29 associations with resistance were identified. A gene with very large effect was found on chromosome 9. Incorporating the resistance allele at this locus could reduce all three diseases with little impact on FT and PH.

Technical Abstract: Stem rot and aggregated sheath spot are the two major stem and sheath diseases affecting rice (Oryza sativa L.) in temperate areas. A third fungal disease, sheath blight, is a major disease in tropical areas. Resistance to these diseases is a key objective in rice breeding programs but phenotyping is challenged by the confounding effects of phenological and morphological traits such as flowering time (FT) and plant height (PH). This study sought to identify quantitative trait loci (QTL) for resistance to these three diseases after removing the confounding effects of FT and PH. Two populations of advanced breeding germplasm, one with 316 tropical japonica and the other with 325 indica genotypes, were evaluated in field and greenhouse trials for resistance to the diseases. Phenotypic means for field and greenhouse disease resistance, adjusted by FT and PH, were analyzed for associations with 29,000 single nucleotide polymorphisms (SNPs) in tropical japonica and 50,000 SNPs in indica. A total of 29 QTL were found for resistance that were not associated with FT or PH. Multilocus models with selected resistance associated SNPs were fitted for each disease to estimate their effects on the other diseases. A QTL on chromosome 9 accounted for more than 15% of the phenotypic variance for the three diseases. When resistance-associated SNPs at this locus from both the tropical japonica and indica populations were incorporated into the model, resistance was improved for all three diseases with little impact on FT and PH.