Genomic analysis and finding of candidate genes for Nilaparvata lugens (stål) resistance in Indian pigmented and other indigenous rice genotypes

Abstract

Rice production is facing serious threats due to frequent outbreak of brown plant hopper, Nilaparvata lugens (Stål.) population. Globally, four biotypes of N. lugens has been recorded, of which biotype-4 is the utmost damaging one prevailing in Asian subcontinents particularly in India. Therefore, effective management of N. lugens requires durable resistant rice variety with multiple resistant traits and genes. Hence, in the present study 268 rice genotypes were screened against N. lugens. From initial screening results, 96 genotypes were selected for further genotyping using 93 molecular markers linked to 26 different N. lugens resistant (R) genes. Genetic analysis revealed the mean genetic diversity of 0.275 and polymorphic information content of 0.240 for all 93 markers. Genetic association through cluster and population structure analysis clearly differentiated the 96 genotypes into three major genetic groups with resistant genotypes grouped in a separate cluster. Likewise, Principal co-ordinate analysis supported the above claim with susceptible, moderately resistant and resistant genotypes accommodated in separate components. Further, genetic variation among population showed a 92% variation among individuals of the population and only 8% between populations. Marker trait association via generalized linear model (GLM) and multi linear model (MLM) picked out five markers for their significant association with different phenotypic parameters such as percent damage, nymphal survival, feeding mark and honeydew excretion. Three markers viz. RM19291 (Bph30), RM28472 (Bph18) and RM28449 (Bph17) were common for both GLM and MLM analysis. These identified resistant genes in rice landrace will serves as the source for development of durable resistant variety against N. lugens.