Cloning of the I gene reveals a dynamic NLR cluster conferring durable and broad-spectrum potyvirus resistance in common bean

Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption. Viral diseases, particularly those caused by bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV), severely constrain bean production worldwide. The dominant I gene has provided durable and broad-spectrum resistance to potyviruses for nearly a century, yet its molecular identity remained unknown. Here, we combine high-quality chromosome-scale genome assemblies and two loss-of-function mutants to clone I and functionally validate it as a Toll/interleukin-1 receptor-like NLR (TNL). The I gene is located within a highly dynamic TNL-rich resistance cluster characterized by extensive structural variation with dramatic differences in TNL copy number between genotypes (ranging from 1 to 34). In one natural mutant, I gene resistance was lost due to the recent insertion of a non-autonomous LTR/Ty3/Gypsy Retand retrotransposon, marking a rare example of transposon-mediated R gene inactivation during seed propagation. While Ogre transposable elements dominate genome expansion in many legumes such as pea and faba bean, we show that Phaseolus genomes are enriched in Retand elements, highlighting a distinct trajectory of genome evolution in this clade. Retand transcription is activated by biotic stress, suggesting stress-responsive mobility. Our findings resolve a long-standing question in common bean genetics that will open up new avenues for plant improvement.