MOLECULAR CHARACTERIZATION AND CLUSTERING OF BIOTIC STRESS-RESISTANCE ALLELES IN NEPALESE RICE LANDRACES FOR BROAD-SPECTRUM RESISTANCE

Abstract

Nepal's diverse agro-ecological environments contain a rich reservoir of rice landraces with considerable potential for developing cultivars resistant to biotic stresses. However, the distribution and combination of alleles conferring resistance to multiple diseases and insect pests have not been sufficiently characterized. In this study, 188 Nepalese rice landraces were evaluated using 40 trait-associated molecular markers representing seven major biotic stress categories: brown planthopper, gall midge, rice tungro virus, bacterial leaf blight, blast, rice stripe virus, and rice yellow mottle virus. A multi-stress breadth score (ranging from 0 to 7) was calculated based on the presence of discriminating traits. Hierarchical clustering using Jaccard distance and average linkage identified five molecular clusters (C1–C5) based on 32 biotic stress-associated markers. Cluster C1, comprising 126 landraces (67.0%), represented the predominant group with moderate allele accumulation across categories and notable enrichment for blast (mean 58.9%) and rice stripe virus (mean 68.3%) resistance. Cluster C2 (23 landraces; 12.2%) contained the highest accumulation of favorable alleles (mean 10.2 ± 1.5) and was strongly enriched for bacterial leaf blight (64.3%), blast (72.5%), gall midge (34.8%), and brown planthopper (28.3%) resistance loci. Cluster C3 (29 landraces; 15.4%) was specifically enriched for brown planthopper (56.9%) and rice tungro virus (62.1%) resistance alleles. Cluster C4 (2 landraces; 1.1%) exhibited an admixed multi-stress profile with balanced allele frequencies across stresses, while Cluster C5 (1 landrace; 0.5%, Tharu Anadhi) demonstrated a highly specialized blast-enriched profile (92.3%) while lacking resistance alleles for brown planthopper, gall midge, rice tungro virus, and bacterial leaf blight. The distribution of resistance alleles was highly uneven: the blast-resistance allele Pid2-Digu was present in 99.5% of genotypes, whereas resistance to rice yellow mottle virus and the bacterial leaf blight genes Xa21 and Xa23 were absent. Multilocus profiling identified promising landraces, such as Balamsari, NGRC08267, Yobo, NGRC07899, Rajbhog, Tauli, Kalo Jhinuwa, and Jhinuwa Basmati, which carry favorable allele combinations across multiple stress categories. These molecular profiles provide a foundation for targeted donor selection and climate-resilient rice improvement. Nevertheless, phenotypic validation under relevant disease and pest pressures remains necessary.