Candidate genes and molecular markers associated with brown planthopper (Nilaparvata lugens Stal) resistance in rice cultivar Rathu Heenati

Brown planthopper (BPH) is a destructive insect pest of rice and causes severe yield loss. In attempts to develop a BPH-resistant rice variety, Rathu Heenati (RH), a rice cultivar with a strong BPH resistance, has been used as the donor in breeding programs. Quantitative trait loci analysis was conducted for the area under the curve of BPH damage scores of a backcross (BC3F5) population infested by six different BPH populations. Single nucleotide polymorphism (SNP) markers on chromosome 4, i.e., LecRK2-SNP and LecRK3-SNP, and markers on chromosome 6, i.e., Bph32-SNP and SSR23, were identified to be associated with resistance against five BPH populations. To identify genes on chromosome 6 that are involved in BPH resistance, expression analysis was conducted for genes located in the genomic region of Bph32-SNP and SSR23. Genes that showed differential expression ofRH at 24 h after BPH infestation, when compared to an RH control, were identified. Those that encode proteins putatively involved in the BPH resistance mechanism are LOC_Os06g03240, LOC_Os06g03380, LOC_Os06g03486, LOC_Os06g03514, LOC_Os06g03520, LOC_Os06g03610, LOC_Os06g03676, and LOC_Os06g03890. SNP markers were developed from several differentially expressed genes and were validated by genotyping in the backcross population. The SNP marker developed from LOC_Os06g03514 showed the highest association with BPH resistance and the gene may be involved in the BPH resistance mechanism. This SNP marker will be useful in breeding programs for BPH resistance.