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Background  The brown planthopper ( Nilaparvata lugens  Stål; BPH), one of the most destructive pests of rice, has proven to be a substantial threat, conferring enormous production losses in Asia and becoming a difficult challenge to manipulate and control under field conditions. The continuous use of insecticides promotes the resurgence of BPH, which results in resistant varieties adapting through the upgrading of new BPH biotypes. To overcome resistance acquired by BPH against resistance varieties, different forms of novel resistant gene fusions act as functional domains for breeding to enhance insect resistance.    Results  The current study reports on the novel BPH resistance gene  Bph36  derived from two introgression lines (RBPH16 and RBPH17) developed from wild rice GX2183 which was previously reported to be resistant to BPH. Using two F 2  crossing populations (Kangwenqizhan × RBPH16 and Huanghuazhan × RBPH17) in a bulked segregant analysis (BSA) for identification of resistant genes and QTL analysis, two QTLs for BPH resistance were generated on the long and short arms of chromosome 4, which was further confirmed by developing BC 1 F 2:3  populations by backcrossing via marker assisted selection (MAS) approach. One BPH resistance locus on the short arm of chromosome 4 was mapped to a 38-kb interval flanked by InDel markers S13 and X48, and then was named  Bph36 , whereas another locus on the long arm of chromosome 4 was also detected in an interval flanked by RM16766 and RM17033, which was the same as that of  Bph27 . An evaluation analysis based on four parameters (BPH host selection, honeydew weight, BPH survival rate and BPH population growth rate) shows that  Bph36  conferred high levels antibiosis and antixenosis to BPH. Moreover,  Bph36  pyramided with  Bph3 ,  Bph27 , and  Bph29  through MAS into elite cultivars 9311 and MH511 (harbored  Xa23 ), creating different background breeding lines that also exhibited strong resistance to BPH in the seedling or tillering stage.    Conclusion   Bph36  can be utilized in BPH resistance breeding programs to develop high resistant rice lines and the high-resolution fine mapping will facilitate further map-based cloning and marker-assisted gene pyramiding of resistant gene. MAS exploited to pyramid with  Bph3 ,  Bph27 ,  Bph29 , and  Xa23  was confirmed the effectiveness for BPH resistance breeding in rice and provided insights into the molecular mechanism of defense to control this devastating insect.    Electronic supplementary material  The online version of this article (10.1186/s12284-019-0289-7) contains supplementary material, which is available to authorized users.

High-resolution mapping and breeding application of a novel brown planthopper resistance gene derived from wild rice (Oryza. rufipogon Griff)