Decoding the genetic basis of Cnaphalocrocis medinalis (Guenee) resistance in rice landraces using SSR markers and...

The rice leaffolder, Cnaphalocrocis medinalis, is a major pest threatening rice production, causing significant yield losses. Developing resistant cultivars offers a sustainable and eco-friendly approach to its management. This study aimed to identify leaffolder-resistant rice genotypes and explore associated genomic regions using SSR markers for future marker-assisted breeding. A total of 96 rice landraces were evaluated under both net house and field conditions across two cropping seasons. Based on consistent phenotypic performance, 20 genotypes were classified as resistant, 28 as moderately resistant, and 28 as susceptible. Genetic screening using reported SSR markers for leaffolder resistance revealed high polymorphism, with an average PIC of 0.75 and gene diversity ranging from 0.612 to 0.834. Cluster and structure analysis grouped the genotypes into three major clusters, with most resistant genotypes forming a distinct group. PCA further validated this genetic grouping, effectively separating resistant, moderately resistant, and susceptible genotypes. Additionally, heat map of kinship matrix supported the population differentiation. AMOVA indicated that 86% of total genetic variation was attributed to differences within populations, while 14% was observed among populations. Association analysis using simple linear regression identified three markers viz: RM72, RM48, and RM162, on chromosomes 8, 2 and 6, respectively, linked to leaffolder resistance. Notably, these markers are located near genes, that are involved in rice defense responses against leaffolder as well as other biotic stresses. Overall, the integration of phenotypic and molecular data in this study provides a foundation for marker-assisted selection and provides valuable genomic resources for developing durable leaffolder-resistant rice cultivars.