Abstract
BackgroundRice bakanae disease has emerged as a new threat to rice production. In recent years, an increase in the occurrence and severity of bakanae disease has been reported in several areas in Asia. Although bakanae disease affects rice yield and quality, little is known about the genetics of bakanae resistance in rice. The lack of large-scale screens for bakanae resistance in rice germplasm has also limited the development and deployment of resistant varieties.ResultsA genome-wide association study (GWAS) was conducted to identify genes/loci conferring bakanae resistance in rice. A total of 231 diverse accessions from Rice Diversity Panel 1 (RDP1) were inoculated with a highly virulent Taiwanese Fusarium fujikuroi isolate and assessed for resistance using two parameters: (1) disease severity index based on visual rating and (2) colonization rate determined by reisolation of F. fujikuroi from the basal stems of infected rice seedlings. We identified 14 quantitative trait loci (QTLs) (10 for disease severity and 4 for colonization rate), including 1 mapped for both parameters. A total of 206 candidate genes were identified within the 14 QTLs, including genes encoding leucine-rich repeat (LRR)-containing and NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) proteins, hormone-related genes, transcription factor genes, ubiquitination-related genes, and oxidase/oxidoreductase genes. In addition, a candidate QTL (qBK1.7) that co-localized with the previously identified QTLs qBK1 and qFfR1, was verified by linkage analysis using a population of 132 recombinant inbred lines derived from IR64 x Nipponbare. GWAS delineated qBK1.7 to a region of 8239 bp containing three genes. Full-length sequencing across qBK1.7 in 20 rice accessions revealed that the coding regions of two LRR-containing genes Os01g0601625 and Os01g0601675 may be associated with bakanae resistance.ConclusionsThis study facilitates the exploitation of bakanae resistance resources in RDP1. The information on the resistance performance of 231 rice accessions and 14 candidate QTLs will aid efforts to breed resistance to bakanae and uncover resistance mechanisms. Quantification of the level of F. fujikuroi colonization in addition to the conventional rating of visual symptoms offers new insights into the genetics of bakanae resistance.
Highlights
Rice bakanae disease has emerged as a new threat to rice production
Rice Diversity Panel 1 (RDP1) was provided by the Genetics Stocks Oryza (GSOR) germplasm collection (Agricultural Research Service, US Department of Agriculture) and the recombinant inbred lines (RILs) were provided by Dr Susan McCouch from Cornell University
Disease severity index ranged from − 0.18 to 1.04 and colonization rate ranged from − 0.21 to 0.86
Summary
Rice bakanae disease has emerged as a new threat to rice production. An increase in the occurrence and severity of bakanae disease has been reported in several areas in Asia. Rice bakanae disease caused by Fusarium fujikuroi is widely distributed in rice growing areas, causing reduced grain quality and yield loss up to 40% (Takahashi et al 1991). The disease has become a new threat to rice production. Increasing severity of the disease has been reported in many Asian countries such as Pakistan, Bangladesh, northern India, south Korea, and Taiwan (Khan et al 2000; Chu et al 2010; Haq et al 2011; Gupta et al 2014; Kim et al 2015). Fungicide-resistant strains have emerged in China, Korea, and Taiwan. Benzimidazoleresistant isolates were found in Jiangsu, China (Chen et al 2014), prochloraz-resistant isolates were discovered in Korea and Taiwan (Kim et al 2010; Chen et al 2016), and a few tebuconazole-resistant isolates were found in Taiwan (Chen et al 2016)
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