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Background  Brown planthopper (BPH,  Nilaparvata lugens  Stål), is the most destructive phloem-feeding insect pest of rice ( Oryza sativa ). The BPH-resistance gene  BPH15  has been proved to be effective in controlling the pest and widely applied in rice breeding programs. Nevertheless, molecular mechanism of the resistance remain unclear. In this study, we narrowed down the position of  BPH15  on chromosome 4 and investigated the transcriptome of  BPH15  rice after BPH attacked.    Results  We analyzed 13,000 BC 2 F 2  plants of cross between susceptible rice TN1 and the recombinant inbred line RI93 that carrying the  BPH15  gene from original resistant donor B5.  BPH15  was mapped to a 0.0269 cM region on chromosome 4, which is 210-kb in the reference genome of Nipponbare. Sequencing bacterial artificial chromosome (BAC) clones that span the  BPH15  region revealed that the physical size of  BPH15  region in resistant rice B5 is 580-kb, much bigger than the corresponding region in the reference genome of Nipponbare. There were 87 predicted genes in the  BPH15  region in resistant rice. The expression profiles of predicted genes were analyzed. Four jacalin-related lectin proteins genes and one LRR protein gene were found constitutively expressed in resistant parent and considered the candidate genes of  BPH15 . The transcriptomes of resistant  BPH15  introgression line and the susceptible recipient line were analyzed using high-throughput RNA sequencing. In total, 2,914 differentially expressed genes (DEGs) were identified. BPH-responsive transcript profiles were distinct between resistant and susceptible plants and between the early stage (6 h after infestation, HAI) and late stage (48 HAI). The key defense mechanism was related to jasmonate signaling, ethylene signaling, receptor kinase, MAPK cascades, Ca 2+  signaling, PR genes, transcription factors, and protein posttranslational modifications.    Conclusions  Our work combined BAC and RNA sequencing to identify candidate genes of  BPH15  and revealed the resistance mechanism that it mediated. These results increase our understanding of plant–insect interactions and can be used to protect against this destructive agricultural pest.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-674) contains supplementary material, which is available to authorized users.

BAC and RNA sequencing reveal the brown planthopper resistance gene BPH15 in a recombination cold spot that mediates a unique defense mechanism