Identification of two QTLs, BPH41 and BPH42, and their respective gene candidates for brown planthopper resistance in rice by a combinatorial approach of QTL mapping and RNA-seq

Abstract The brown planthopper (BPH) is the leading cause of insect damage to rice plants. It has caused profound losses in rice production since the late 1970’s and continues to be a major pest problem. Therefore, there is an urgent need to discover new BPH resistance genes to ensure the successful production of rice. Here, a new BPH resistance source provided by SeedWorks International Pvt. Ltd., SWD10, was used for this purpose. A total of 232 F2 progenies were genotyped with 216 polymorphic markers. Results revealed two dominant QTLs located on the short and long arms of chromosome 4. These QTLs are referred to as BPH41 and BPH42, respectively. BPH resistance mechanism test revealed that antibiosis and antixenosis mechanisms both play a role in BPH resistance conferred by these two QTLs. To further reduce the size of each QTL, 14,368 recombinant lines were screened, and the QTLs were delimited between markers SWRm_01617 and SWRm_01522 for BPH41, and SWRm_01695 and SWRm_00328 for BPH42. Additionally, using RNA-seq data of lines containing the QTLs, we further shortlisted four and three gene candidates for BPH41 and BPH42, respectively. Differential gene expression analysis of lines containing the QTLs suggested that SWD10 BPH resistance is contributed by the plant’s innate immunity and the candidate genes may be part of the rice innate immunity pathway. The newly identified QTLs are currently being utilized for breeding BPH resistant rice varieties and hybrids.