To characterize the genetic basis for ShB resistance in rice, we conducted association studies for traits related to ShB resistance, namely culm length (CL), lesion height (LH), and relative lesion height (RLH). Combined a single locus genome-wide scan and a multi-locus method using 2,977,750 single-nucleotide polymorphisms to analyse 563 rice accessions, we detected 134, 562, and 75 suggestive associations with CL, LH, and RLH, respectively. The adjacent signals associated with RLH were merged into 27 suggestively associated loci (SALs) based on the estimated linkage disequilibrium blocks. More than 44% of detected RLH-SALs harboured multiple QTLs/genes associated with ShB resistance, while the other RLH-SALs were putative novel ShB resistance loci. A total of 261 ShB resistance putative functional genes were screened from 23 RLH-SALs according to bioinformatics and haplotype analyses. Some of the annotated genes were previously reported to encode defence-related and pathogenesis-related proteins, suggesting that quantitative resistance to ShB in rice is mediated by SA- and JA-dependent signalling pathways.
Our findings may improve the application of germplasm resources as well as knowledge-based ShB management and the breeding of ShB-resistant rice cultivars.
Fig. 3 Manhattan and quantile-quantile plots for relative lesion height (RLH) for the whole, Xian, Geng, and Aus association panels based on the multi-locus GWAS method of FarmCPU. a, e Whole association panel. b, f Xian association panel. c, g Geng association panel. d, h Aus association panel. The strength of the associations for the RLH is indicated as the negative logarithm of the P value. Horizontal blue lines in the Manhattan plots indicate the following genome-wide suggestive thresholds (P values adjusted by a Bonferroni correction based on the effective number of independent markers calculated using GEC software): 2.16 × 10− 6 , 3.28 × 10− 6 , 6.57 × 10− 6 , and 5.34 × 10− 6 for the whole, Xian, Geng, and Aus association panels, respectively. Horizontal red lines in the Manhattan plots indicate the following genome-wide significance thresholds (P < 0.05): 1.08 × 10− 7 , 1.64 × 10− 7 , 6.57 × 10− 6 , and 2.67 × 10− 7 for the whole, Xian, Geng, and Aus association panels, respectively.