Evidence That Sri Lanka is the Origin of a Rare Nematode Resistance Gene in Rice

Meloidogyne graminicola is a destructive and widespread pest in tropical rice-growing systems, whereas resistance in Oryza sativa remains exceptionally rare. A major quantitative trait locus (QTL) associated with resistance has previously been identified at the distal end of chromosome 11 in the resistant varieties, LD 24 (Sri Lanka) and KPM (Thailand). In this study, we combined bioinformatic and molecular approaches to characterize this locus and phenotypically screened a collection of Sri Lankan landraces to investigate the distribution and potential origin of resistance. We identified a rare 7-bp deletion in LOC_Os11g44580 completely associated with the resistance phenotype, along with a notable occurrence of heterozygosity at this locus in some accessions. The deletion is located within a genomic region recently reported to harbor the resistance gene MG1 in the Chinese cultivar Zhonghua 11. Among 121 Sri Lankan landraces screened using the 7-bp deletion marker, eight accessions carried the deletion, whereas 12 were heterozygous; all exhibited resistance to Mg. Notably, the majority of resistant landraces belonged to the distinct Sri Lankan subgroup indica 2 and were predominantly collected from the Northern Province of Sri Lanka, suggesting a potential geographic origin of this resistance-associated allele. This study identifies 20 novel resistant varieties and highlights a regional concentration of resistance, providing valuable resources for breeding and insights into the evolutionary basis of nematode resistance in rice.