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Background  The development of rice varieties with broad-spectrum resistance to insect pests is the most promising approach for controlling a fast evolving insect pest such as the brown planthopper (BPH). To cope with rapid evolution, discovering new sources of broad-spectrum resistance genes is the ultimate goal.    Results  We used a forward genetics approach to identify BPH resistance genes in rice ( Oryza sativa  L.) using double digest restriction site-associated DNA sequencing (ddRADseq) for quantitative trait loci (QTL)-seq of the backcross inbred lines (BILs) derived from a cross between the BPH-susceptible cultivar KDML105 and BPH-resistant cultivar Rathu Heenati (RH). Two major genomic regions, located between 5.78–7.78 Mb (QBPH4.1) and 15.22–17.22 Mb (QBPH4.2) on rice chromosome 4, showed association with BPH resistance in both pooled BILs and individual highly resistant and susceptible BILs. The two most significant candidate resistance genes located within the QBPH4.1 and QBPH4.2 windows were lectin receptor kinase 3 ( OsLecRK3 ) and sesquiterpene synthase 2 ( OsSTPS2 ), respectively. Functional markers identified in these two genes were used for reverse screening 9323 lines of the fast neutron (FN)-mutagenized population developed from the BPH-susceptible, purple-pigmented,  indica  cultivar Jao Hom Nin (JHN). Nineteen FN-mutagenized lines (0.24%) carried mutations in the  OsLecRK3  and/or  OsSTPS2  gene. Among these mutant lines, only one highly resistant line (JHN4) and three moderately resistant lines (JHN09962, JHN12005, and JHN19525) were identified using three active, local BPH populations. The 19 mutant lines together with three randomly selected mutant lines, which did not harbor mutations in the two target genes, were screened further for mutations in six known BPH resistance genes including  BPH9 ,  BPH14 ,  BPH18 ,  BPH26 ,  BPH29 , and  BPH32 . Multiple single nucleotide polymorphisms (SNPs) and insertion-deletion (Indel) mutations were identified, which formed gene-specific haplotype patterns (HPs) essential for broad-spectrum resistance to BPH in both BILs and JHN mutant populations.    Conclusion  On the one hand, HPs of  OsLekRK2–3 ,  OsSTPS2 , and  BPH32  determined broad-spectrum resistance to BPH among RH-derived BILs. On the other hand, in the JHN mutant population,  BPH9  together with seven significant genes on chromosome 4 played a crucial role in BPH resistance.    Electronic supplementary material  The online version of this article (10.1186/s12284-019-0274-1) contains supplementary material, which is available to authorized users.

Identification of spontaneous mutation for broad-spectrum brown planthopper resistance in a large, long-term fast neutron mutagenized rice population