Identification and Functional Characterization of Two Major Loci Associated with Resistance against Brown Planthoppers () Derived from .

The brown planthopper (BPH) is a highly destructive pest of rice, causing significant economic losses in various regions of South and Southeast Asia. Researchers have made promising strides in developing resistance against BPH in rice. Introgression line RPBio4918-230S, derived from , has shown consistent resistance to BPH at both the seedling and adult stages of rice plants. Segregation analysis has revealed that this resistance is governed by two recessive loci, known as and , contributing to 21% and 22% of the phenotypic variance, respectively. We later mapped the genes using a backcross population derived from a cross between Swarna and RPBio4918-230S. We identified specific marker loci, namely RM8213, RM5953, and R4M17, on chromosome 4, flanking the and loci. Furthermore, quantitative expression analysis of candidate genes situated between the RM8213 and R4M17 markers was conducted. It was observed that eight genes exhibited up-regulation in RPBio4918-230S and down-regulation in Swarna after BPH infestation. One gene of particular interest, a serine/threonine-protein kinase receptor (), showed significant up-regulation in RPBio4918-230S. In-depth sequencing of the susceptible and resistant alleles of from Swarna and RPBio4918-230S, respectively, revealed numerous single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) mutations, both in the coding and regulatory regions of the gene. Notably, six of these mutations resulted in amino acid substitutions in the coding region of (R5K, I38L, S120N, T319A, T320S, and F348S) when compared to Swarna and the reference sequence of . Further validation of these mutations in a set of highly resistant and susceptible backcross inbred lines confirmed the candidacy of the gene with respect to BPH resistance controlled by and . Functional markers specific for have been developed and validated and can be used for accelerated transfer of the resistant locus to elite rice cultivars.