Mapping of flumioxazin tolerance in a snap bean diversity panel leads to the discovery of a master genomic region controlling multiple stress resistance genes

Effective weed management tools are crucial for maintaining the profitable production of snap bean (Phaseolus vulgaris [L.]). Preemergence herbicides help the crop to gain a size advantage over the weeds, but the few preemergence herbicides registered in snap bean have poor waterhemp (Amaranthus tuberculatus) control, a major pest in snap bean production. Waterhemp and other difficult-to-control weeds can be managed by flumioxazin, an herbicide that inhibits protoporphyrinogen oxidase (PPO). However, there is limited knowledge about crop tolerance to this herbicide. We aimed to quantify the degree of snap bean tolerance to flumioxazin and explore the underlying mechanisms. A genome-wide association mapping approach was employed, utilizing field-collected data from a snap bean diversity panel. The response to a preemergence application of flumioxazin was measured by assessing plant population density and shoot biomass variables. Snap bean tolerance to flumioxazin is associated with a single genomic location in chromosome 02. Tolerance is influenced by several factors, including those that are indirectly affected by seed size/weight and those that directly impact the herbicide's metabolism and protect the cell from reactive oxygen species induced damage. Transcriptional profiling and co-expression network analysis identified biological pathways likely involved in flumioxazin tolerance, including oxidoreductase processes. Upregulation of genes involved in those processes is possibly orchestrated by a transcription regulator located in the region identified in the GWAS analysis. Several entries belonging to the Romano class, including Bush Romano 350, Roma II, and Romano Purpiat presented high levels of tolerance in this study. The alleles identified in the diversity panel that condition snap bean tolerance to flumioxazin shed light on a novel mechanism of herbicide tolerance and can be used in crop improvement. Overall design: We aimed to identify the biological pathways likely involved in flumioxazin tolerance. Snap bean seedlings of 12 cultivars shown to have contrasting phenotypic response to the application (6 sensitive and 6 tolerant) and carrying contrasting versions of a genomic region identified by GWAS, were germinated and harvested at emergence. Herbicide was not applied, with the assumption that differential gene expression contributing to tolerance would be constitutive