Parallel GWAS of Brown and White-Backed Planthopper Resistance in Rice

The brown planthopper (BPH, Nilaparvata lugens) and white-backed planthopper (WBPH, Sogatella furcifera) are major rice pests, yet WBPH resistance and its overlap with BPH resistance remain poorly defined. Using the Rice Diversity Panel 1 (RDP1), screened against laboratory colonies, we mapped resistance to both pests across three panels and three models (MLM, FarmCPU, BLINK), examined leading loci with the High-Density Rice Array, and mined 3000-genome candidate-gene haplotypes. Resistance correlated weakly between pests (r = 0.26). We identified six BPH and five WBPH candidate loci, all ≥2.38 Mb from cloned Bph genes; correspondence with uncloned QTL cannot be excluded, and the WBPH chromosome 9 locus is the strongest novel candidate. Top signals did not co-locate and candidates shared most defense modules, but neither pattern exceeded chance in permutation testing, and the cross-trait genomic correlation was non-significant (rg = 0.38, SE ≈ 0.33). These loci sit on a background of low genomic heritability; we can neither demonstrate pest-specificity nor exclude a shared polygenic background. Resistance-allele sources were subspecies-differentiated but locus-specific. This is the first parallel diversity-panel genome-wide association study of the two planthoppers and the first for WBPH host resistance. It provides positional candidates and candidate donor haplotypes as a validation-pending breeding resource.