Genome-wide association studies (GWAS) for resistance to Meloidogyne graminicola in an association panel of Oryza rufipogon

The rice root-knot nematode (RRKN), Meloidogyne graminicola, is an obligate pathogen responsible for considerable yield losses in both upland and rainfed lowland rice cultivation in India. Identifying and mapping quantitative trait loci (QTLs) associated with resistance to M. graminicola could provide a sustainable and cost-effective management strategy for farmers. Genetic resources for resistance to M. graminicola are limited in Asian rice (Oryza sativa) cultivars. Therefore, a study was conducted to identify potential sources of resistance in wild rice. In this study, 93 accessions of Oryza rufipogon were screened for resistance to RRKN, alongside the susceptible check PR126, under artificial inoculation conditions over 2 years at the Department of Plant Pathology, Punjab Agricultural University, Ludhiana, Punjab, India. The evaluation of RRKN resistance was based on the root galling index (RGI), soil nematode population and reproduction factor (Rf). A genome-wide association study (GWAS) for RRKN traits identified significant associations for RGI on chromosomes 1, 2, 5, 6 and 11. For soil nematode population, significant associations were found on chromosomes 2, 4, 5, 6 and 7. Notably, QTLs on chromosomes 2 and 6 were consistently detected across traits and models, providing robust candidate regions for resistance. Among these, SNP S6_23144943 on chromosome 6 showed consistent association across all models and may represent a stable genetic source of resistance. These loci highlight the polygenic nature of resistance to M. graminicola in wild rice and represent valuable resources for marker-assisted breeding.