Genome-wide association mapping of gene loci affecting disease resistance in the rice-Fusarium fujikuroi pathosystem

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.

Transcriptome Analysis of Early Defenses in Rice against Fusarium fujikuroi

“…A susceptible rice cultivar, ZK, and a resistant rice cultivar, TNG67, were used in this study. These cultivars were selected based on resistance screening of 231 diverse rice accessions from Rice Diversity Panel 1 (RDP1) (Chen et al 2019 ). ZK was moderately susceptible and TNG67 was moderately resistant (Additional file 8 : Fig.…”

“…Plants were cultivated in the dark for the first 2 days and subsequently under a 12-h photoperiod in a walk-in chamber set at a 32 °C day/28 °C night temperature. Disease severity index (DSI) was calculated based on visual ratings of individual plants at 21 dpi using a 0–3 scale (Chen et al 2016 ; Chen et al 2019 ) as follows: .…”

“…Plants were cultivated in the dark for the first 2 days and subsequently under a 12-h photoperiod in a walk-in chamber set at a 32°C day/28°C night temperature. Disease severity index (DSI) was calculated based on visual ratings of individual plants at 21 dpi using a 0-3 scale (Chen et al 2016;Chen et al 2019 fujikuroi Ff266 was conducted as described above in two independent trials, with 6-8 plants per cultivar in each trial. The aerial and root samples were collected at 3 dpi, and the leaf, stem, and root samples were collected at 7 dpi.…”

“…Bakanae resistance has been explored by large-scale screening of rice germplasm and quantitative trait locus (QTL) mapping. Research groups in India (Fiyaz et al 2014 ), Korea (Kim et al 2014 ), and Taiwan (Chen et al 2019 ) used high-throughput inoculation methods to screen for resistant materials from 92, 500, and 231 diverse rice varieties, respectively. A total of 28 QTLs for bakanae resistance were mapped on rice chromosomes 1, 3, 4, 6, 8, 9, 10 and 11 (Volante et al 2017 ; Fiyaz et al 2016 ; Lee et al 2018 ; Cheon et al 2019 ; Ji et al 2018a ; Hur et al 2015 ; Lee et al 2019 ; Kang et al 2019 ; Yang et al 2006 ; Chen et al 2019 ).…”

“…Chromosome 1, where 13 QTLs are located, appears to be particularly important. Using four different bi-parental populations and rice diversity panel 1 (RDP1) (Cheon et al 2019 ; Ji et al 2018a ; Hur et al 2015 ; Lee et al 2019 ; Fiyaz et al 2016 ; Chen et al 2019 ), co-localized QTLs were fine-mapped to a region (21.36–24.37 Mb on chromosome 1) crucial for bakanae resistance. Although QTLs have been associated with mortality rate, disease incidence, disease severity, and F. fujikuroi colonization, no causal genes have been cloned and functionally characterized.…”