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Background   Bph3 , a major brown planthopper (BPH) resistance locus derived from the rice cultivar Rathu Heenati (RH), has been used as a stable donor of traits that improve highly susceptible aromatic rice varieties in Thailand. Map-based cloning was initiated using a set of isogenic lines (ILs) harboring the major  Bph3  locus on chromosome 6. IL genomes were scanned with a 57 K Affymetrix Rice GeneChip to identify the gene responsible for  Bph3 .    Findings  Single-feature polymorphism (SFP) mapping was used to localize 84 candidate genes. An expression analysis of 15 selected candidate genes in the aromatic rice cultivar KDML105 (KD) and the ILs under normal conditions revealed two differentially expressed sequences. Following hopper feeding, only one candidate gene, Os04g27430, was differentially expressed. Os04g27430 encodes a putative  sesquiterpene synthase  ( STPS ) gene that was induced by BPH feeding in ILs. An antixenosis test in three selected ILs revealed a major role for  STPS  in insect preference during the first 120 hours of the rice-insect interaction. Functional SNPs in exon 5 that resulted in the deletion of seven amino acids in the susceptible rice line were identified. Moreover, three additional SNPs associated with three transcription binding sites were also identified, which might explain the differential response of Os04g27430 during the anti-feeding test.    Conclusion  Os04g27430 is the second known rice  STPS  induced by BPH. The gene may involve an antixenosis BPH resistance mechanism. The combination of the  STPS  and the  Bph3  locus was more effective than  Bph3  alone in the tested ILs.    Electronic supplementary material  The online version of this article (doi:10.1186/1939-8433-6-18) contains supplementary material, which is available to authorized users.

Single-feature polymorphism mapping of isogenic rice lines identifies the influence of terpene synthase on brown planthopper feeding preferences