PPDKB Deficiency Impairs Starch Biosynthesis and Redirects Carbon Flux to Lipid and Amino Acid Synthesis in Rice

The central endosperm of a chalky rice mutant JM03 , which was isolated from a 60 Co-irradiated mutant population of the indica rice variety 93-11, contains numerous small, irregularly shaped starch granules with looser packing than wild-type (WT). JM03 starch showed lower gelatinization onset and peak temperatures, reduced pasting viscosities, and consistently decreased dynamic rheological parameters compared to WT. Through BSA-seq, complementation tests and immunoblot analysis, we identified the pyruvate orthophosphate dikinase ( PPDKB , Os05g0405000 ) as the causal gene for JM03 . Multi-omics analysis of developing endosperm at 15 days after flowering revealed that PPDKB deficiency profoundly redirected central carbon and amino acid metabolism. On the one hand, impaired phosphoenolpyruvate regeneration disrupted the gluconeogenic conversion of hexoses into starch biosynthesis precursors, consequently suppressing starch accumulation through downregulation of all starch synthesis related genes and enzymes. The impaired starch synthesis diminished sucrose unloading capacity due to reduced expression of sucrose synthase, triggering accumulations of sucrose and other soluble sugars. On the other hand, excess pyruvate diverted metabolic flux towards acetyl-CoA production, stimulating TCA cycle activity and enhancing lipid biosynthesis. Meanwhile, amino acid synthesis was enhanced due to increased levels of multiple precursors and genes/enzymes involved in amino acid synthesis. The reduction in starch accumulation, combined with the downregulation of key grain weight regulators such as mitogen-activated protein kinase 6 and BAHD acyltransferase-like protein collectively led to a significant reduction in grain weight in JM03 . Taken together, our study unraveled a functional cross talk between starch, soluble sugars, protein and lipids in rice endosperm during seed development in JM03 , which provided important germplasm resources and theoretical basis for genetic improvement of rice yield and quality.