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

Common bean (Phaseolus vulgaris) is a major grain legume for human consumption, but its production is severely constrained by viral diseases, especially those caused by bean common mosaic virus and bean common mosaic necrosis virus. The function of the dominant I gene conferring broad-spectrum resistance to potyviruses has been known for nearly a century, yet its molecular identity remains unresolved. Here, we combine chromosome-scale genome assemblies and two loss-of-function mutants to clone the I gene and show that it encodes a Toll/interleukin-1 receptor-like nucleotide-binding leucine-rich-repeat (NLR) (TNL) protein. I resides in a dynamic TNL-rich resistance cluster exhibiting dramatic differences in TNL copy number among genotypes. In one natural mutant, resistance is lost through the recent insertion of a non-autonomous Retand retrotransposon, providing a rare example of transposon-mediated R gene inactivation during seed propagation. More broadly, we show that Phaseolus genomes are enriched in Retand elements, representing a distinct legume genome evolution trajectory comparing to pea and faba bean. These findings resolve a long-standing question in common bean genetics and open avenues for crop improvement.

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Publication Details

Journal
Nature Communications
Published
2026-05-30
DOI
https://doi.org/10.1038/s41467-026-73550-x
Primary Topic
Plant pathogens and resistance mechanisms
Type
article
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article

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

Ariane Gratias, David Latrasse, Timothy G. Porch, Étienne Delannoy et al.
Nature Communications
Plant pathogens and resistance mechanisms
article

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

Ariane Gratias, David Latrasse, Timothy G. Porch, Étienne Delannoy, Gianluca Teano, Valérie Geffroy, Phillip N. Miklas, Maria-Victoria Prejean, Marion Verdenaud, alexandre roudaut, Andrea Pedrosa-Harand, Stéphanie Pflieger, Christophe Klopp, Cécile Desbiez, Alvaro Soler-Garzón, Moussa Benhamed, Juan C. Alvarez-Díaz
article en

Abstract

Common bean (Phaseolus vulgaris) is a major grain legume for human consumption, but its production is severely constrained by viral diseases, especially those caused by bean common mosaic virus and bean common mosaic necrosis virus. The function of the dominant I gene conferring broad-spectrum resistance to potyviruses has been known for nearly a century, yet its molecular identity remains unresolved. Here, we combine chromosome-scale genome assemblies and two loss-of-function mutants to clone the I gene and show that it encodes a Toll/interleukin-1 receptor-like nucleotide-binding leucine-rich-repeat (NLR) (TNL) protein. I resides in a dynamic TNL-rich resistance cluster exhibiting dramatic differences in TNL copy number among genotypes. In one natural mutant, resistance is lost through the recent insertion of a non-autonomous Retand retrotransposon, providing a rare example of transposon-mediated R gene inactivation during seed propagation. More broadly, we show that Phaseolus genomes are enriched in Retand elements, representing a distinct legume genome evolution trajectory comparing to pea and faba bean. These findings resolve a long-standing question in common bean genetics and open avenues for crop improvement.

Nature Communications
Centre National de la Recherche Scientifique (FR), Agricultural Research Service (US), Université Paris Cité (FR), Universidade Federal de Pernambuco (BR), Université Paris-Saclay (FR), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Institut des Sciences des Plantes de Paris Saclay (FR), Génétique Physiologie et Systèmes d'Elevage (FR), University of Puerto Rico-Mayaguez (PR), Washington State University (US)
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Openalex Percentile: Top 7%
Plant pathogens and resistance mechanisms
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