Genome-wide association mapping of resistance to stem and sheath diseases in advanced rice germplasm

Doctoral thesis abstract

Abstract

Fungicides are sprayed over almost 100% of the Uruguayan rice crop area, mostly due to susceptibility of local cultivars to stem and sheath diseases caused by Nakataea oryzae (NO) and Rhizoctonia oryzae sativae (ROS). To breed new resistant cultivars, more efficient selection methods are required. Five greenhouse methods for greenhouse evaluation of resistance to NO and ROS were compared. A population of 641 indica and tropical japonica type advanced breeding lines were phenotyped for resistance to NO and ROS in greenhouse and in field trials. A genome-wide association study (GWAS) was performed to analyze the association between single nucleotide polymorphisms (SNPs) and the field and greenhouse phenotypic means, adjusted by plant height and flowering time. GWAS analysis detected 29 QTL for resistance to the studied diseases, independent of plant height and flowering time, explaining up to 43% and 21% of the phenotypic variance observed in field and greenhouse trials, respectively. A region on chromosome 9 explained more than 15% of the phenotypic variance of studied diseases. The identified QTL are useful for assisted selection of resistance to NO and ROS in INIA’s rice breeding program, without effects in plant height and flowering time, and with an efficiency comparable to that of the currently used field trials.