Exploring genetic resistance to brown planthopper, Nilaparvata lugens (Stål) biotype-4 in rice germplasm

Abstract

Brown planthopper, Nilaparvata lugens (Stål) is a major rice pest, with infestations increasing in India in recent decades. While various control methods exist, deploying resistant rice varieties is economical. Among the four known N. lugens biotypes in the world, biotype-4 predominates in India, overcoming plant resistance through biochemical and molecular adaptations. Molecular markers, particularly DNA-based markers, were employed to characterise resistance-associated loci, enabling precise screening and selection of resistant genotypes. Hence, in this study, 22 previously reported resistant rice germplasms carrying different resistant QTLs/genes, along with resistant check (Salkathi), susceptible check (TN-1) and four popular varieties, were used for both phenotypic and genotypic studies. A phenotypic screening over three years identified two highly resistant genotypes (Dhobanumberi & Salkathi with score 1) and eight resistant genotypes (score 3). Additionally, resistance genotypes exhibited lower plant damage (4%–23%), reduced honeydew excretion (4.8%–6.5%), lower nymphal survival (29%–47%) and delayed wilting (18–23 days) compared to susceptible genotypes. Genetic analysis revealed an average genetic diversity of 0.269 and a polymorphism information content of 0.228 across 89 markers linked to 31 resistance QTLs/genes. Cluster and population structure analyses grouped the genotypes into three primary genetic clusters, which were further validated by principal coordinate analysis, distinguishing susceptible, moderately resistant, and resistant genotypes. Genetic variation analysis indicated that 92% of the variation was within the population, while 8% was among the populations. Marker-trait association analysis using generalised linear models (GLM) and mixed-linear models (MLM) identified five significant markers associated with N. lugens resistance, viz. RM261 (Bph15), RM1305 (Bph12), RM6843 (Qbph2), RM6869 (Bph2) and RM16853 (Bph27). Among them, RM261 (Bph15) was found significantly associated (p < .05) with N. lugens resistance in both GLM and MLM approaches. These identified resistant sources and genes against BPH biotype-4 would be useful for the development of durable resistant varieties against N. lugens.