The I gene defines a dynamic NLR cluster conferring broad potyvirus resistance in common bean

Authors: ALVAREZ-DIAZ, JEAN - University Of Paris; SOLER-GARZON, ALVARO - Washington State University; TEANO, GIANLUCA - University Of Paris; VERDENAUD, MARION - University Of Paris; KLOPP, CHRISTOPHE - Inrae; PREJEAN, MARIA - University Of Paris; PFLIEGER, STEPHANIE - University Of Paris; Porch, Timothy; DESBIEZ, CECILE - Inrae; LATRASSE, DAVID - University Of Paris; BENHAMED, MOUSSA - University Of Paris; DELANNOY, ETIENNE - University Of Paris; PEDROSA-HARAND, ANDREA - Federal University Of Pernambuco; GRATIAS, ARIANE - University Of Paris; Miklas, Phillip; GEFFROY, VALERIE - University Of Paris

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/13/2026
Publication Date: 5/30/2026
Citation: Alvarez-Diaz, J.C., Soler-Garzon, A., Teano, G., Verdenaud, M., Klopp, C., Prejean, M.V., Pflieger, S., Porch, T.G., Desbiez, C., Latrasse, D., Benhamed, M., Delannoy, E., Pedrosa-Harand, A., Gratias, A., Miklas, P.N., Geffroy, V. 2026. The I gene defines a dynamic NLR cluster conferring broad potyvirus resistance in common bean. Nature Communications. https://doi.org/10.1038/s41467-026-73550-x.
DOI: https://doi.org/10.1038/s41467-026-73550-x

Interpretive Summary: Common bean is the most important grain legume for human consumption. Viral diseases, particularly those caused by potyviruses 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 bean genomes and loss-of-function mutants to clone the I gene. The I gene has a typical resistance ‘R’ gene motif and is located within a dynamic cluster of similar R genes. In one natural mutant, I gene resistance was lost due to the recent insertion of a transposable element, marking a rare example of transposon-mediated R gene inactivation in common bean. These findings provide new avenues for bean improvement including strengthening the molecular tools available for potyvirus resistance breeding.

Technical Abstract: 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 Retand LTR retrotransposon, marking a rare example of transposon-mediated R gene inactivation during seed propagation. While Ogre elements dominate genome expansion in many legumes such as pea and faba bean, we show that Retand elements are the most abundant transposable element family in Phaseolus genomes, 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.