Genomic confirmation of brown planthopper resistance in indica rice using genic markers

Abstract Brown planthopper, Nilaparvata lugens , is the most devastating rice pest, and its infestations have been recorded more frequently in India in recent decades. Among the control measures, deploying resistant varieties is economical and eco‐friendly. Hence, we have taken 90 rice germplasms and evaluated them for continuous 2 years along with resistant (Salkathi, PTB‐33, Dhobanumberi), susceptible checks (TN‐1, Swarna, Naveen) to identify newer source of resistance. A phenotypic study revealed that only one (TN TRH 99) genotype was found to have a high resistance reaction (Score 1) and four as resistant reaction (Score 3) upon 2 years of screening. Additionally, resistance genotypes had less plant damage (3.63–16.18%), honeydew excretion (4.3–11.3%), nymphal survival (25.4–37.1%) and more time to get wilt (17–23 days) upon exposure to N. lugens in comparison to susceptible genotypes. Genetic analysis reveals an average genetic diversity of 0.262 with a polymorphic information content of 0.218 for the 87 markers linked with 28 genes and 9 QTLs. Cluster and population structure analyses grouped the genotypes into three main genetic categories, a finding further validated by principal coordinate analysis, which distinguished susceptible, moderately resistant and resistant genotypes into separate components. Furthermore, genetic variation analysis indicated that 75% of the total variation was attributed to differences among individuals, with 16% occurring within individuals and 9% among populations. Marker‐trait association analysis using generalized linear models (GLM), mixed‐linear models (MLM), FarmCPU and BLINK identified seven markers, namely RM8101 ( BPH3 ), RM5742 ( BPH6 ), RM250 ( BPH13 (t)), RM20M14 ( BPH15 ), RM309 ( BPH26 ), RM11522 ( BPH33(t) ) and RM335 ( Qbph4 .4), that were significantly associated with various phenotypic parameters related to N. lugens resistance. Among them, RM20M14 ( BPH15 ) showed significance in four all models, that is, GLM, MLM, FarmCPU and BLINK. These identified resistant sources and genes against this bug would be useful for the development of durable resistant varieties against N. lugens .