Natural variation in IBF1 disrupts its interaction with CHS1 and affects metabolism of hulls in rice

Secondary metabolites in plants have various physiological functions, including antioxidant and antibacterial activities. Previous studies have suggested genes and associated molecular mechanisms involved in the production of diverse secondary metabolites. However, much less is known about the genetic bases underlying within-species diversity in metabolite accumulation patterns, particularly in less focused tissues such as rice hulls. In this study, we aimed to identify the causal variant that affects flavonoid accumulation in rice hulls. We identified an F-box containing protein IBF1 is causal for genotypic differences in hull color through positional cloning. The variety IR64, with straw-white hulls, harbors functional IBF1 proteins that interact with a chalcone synthase, CHS1. Conversely, frame-shift mutations of IBF1 in the variety DJ123, which has pigmented hull color, resulted in a lack of a Kelch domain essential for the IBF1-CHS1 interaction. As a result, the DJ123 variant of IBF1 (IBF1DJ123) no longer interacted with CHS1, which was further supported by deep learning-based protein structural modeling. Further metabolome and transcriptome analyses using IR64 and an IR64-based chromosomal segment substitution line (CSSL) carrying IBF1DJ123 revealed an increase in the content of multiple flavonoids (such as naringenin and luteolin), while suppressing the expression of CAD involved in lignin synthesis. Metabolites in the CSSL carrying IBF1DJ123 suppressed the growth and siderophore generation activity of Pantoea species, which can act as beneficial or pathogenic endophytes. This study highlights the impact of a single gene on diverse metabolite accumulation patterns and suggests that this change may provide defense against pathogens.