Fine-mapping and evolutionary history of R-BPMV, a dominant resistance gene to Bean pod mottle virus in Phaseolus vulgaris L.

Authors: MEZIADI, CHOUAIB - Université Paris-Saclay; ALVAREZ DIAZ, JUAN - Université Paris-Saclay; THAREAU, VINCENT - Université Paris-Saclay; GRATIAS, ARIANE - Université Paris-Saclay; MARANDE, WILLIAM - Université Paris-Saclay; SOLER GARZON, ALVARO - Washington State University; Miklas, Phillip - Phil; PFLIEGER, STEPANIEPHILLIP - Université Paris-Saclay; GEFFROY, VALERIE - Université Paris-Saclay

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/21/2023
Publication Date: 12/13/2023
Citation: Meziadi, C., Alvarez Diaz, J., Thareau, V., Gratias, A., Marande, W., Soler Garzon, A., Miklas, P.N., Pflieger, S., Geffroy, V. 2023. Fine-mapping and evolutionary history of R-BPMV, a dominant resistance gene to Bean pod mottle virus in Phaseolus vulgaris L. Theoretical and Applied Genetics. 137. Article 8. https://doi.org/10.1007/s00122-023-04513-9.
DOI: https://doi.org/10.1007/s00122-023-04513-9

Interpretive Summary: Bean pod mottle virus (BPMV) is a comovirus that infects common bean and legumes in general. BPMV is distributed throughout the world and is a major threat on soybean, a closely related species of common bean. In common bean, BAT93 was reported to carry the R-BPMV resistance gene conferring an extreme resistance to BPMV and located within the I resistance cluster. To fine map R-BPMV, 182 recombinant inbred lines (RILs) derived from the cross BAT93 x JaloEEP558 were genotyped with polymerase-chain (PCR)-based markers developed using genome assemblies from G19833 and BAT93, as well as BAT93 BAC clone sequences. Analysis of RILs carrying key recombination events positioned R-BPMV to a target region containing at least 16 TIR-NB-LRR (TNL) gene sequences in BAT93. Because the I cluster presents a suppression of recombination and a large number of repeated sequences, none of the 16 TNLs could be excluded as R-BPMV candidate gene. The evolutionary history of the TNLs for the I cluster were reconstructed using microsynteny and phylogenetic analyses within the legume family. A single I TNL was present in Medicago truncatula and lost in soybean, mirroring the absence of complete BPMV resistance in soybean. Amplification of TNLs in the I cluster predates the divergence of the Phaseolus species, in agreement with the emergence of R-BPMV before the separation of the common bean wild centers of diversity. This analysis provides PCR-based markers useful in marker-assisted selection (MAS) and laid the foundation for cloning of R-BPMV resistance gene in order to transfer the resistance into soybean.

Technical Abstract: Bean pod mottle virus (BPMV) is a problematic disease in common bean and for grain legumes in general. BPMV is a serious problem in Soybean, in part, because there is no effective resistance. For common bean, genetic resistance provides the best control against BPMV. This study fine maps the dominant R-BPMV resistance gene to a cluster of R-genes on chromosome 2 in common bean. The evolution of the R gene cluster among legumes, present in Alfalfa, absent in Soybean, and expanding in common bean, explains the absence of BPMV resistance in soybean and the presence of a large cluster of R genes in common bean. In addition to BPMV, this large gene cluster is associated with resistance to 11 other viruses, and fungal and bacterial pathogens. Our research confirms the physical location of R-BPMV gene and developed molecular markers that can be used by breeder to select for and track the resistance gene in common bean breeding lines. The work also lays a foundation for potential cloning of the resistance gene for transfer into soybean.