Mutations in , , and confer embryonic lethality and alter flavonoid accumulation in Rice ( L.) seed.

Morphological and biochemical changes accompanying embryogenesis and seed development are crucial for plant survival and crop productivity. Here, we identified a novel () mutant of the rice cultivar Sindongjin ( L.), namely, -. Seeds of the - mutant showed a yellowish pericarp and black embryo, and were embryonic lethal. Compared with wild-type seeds, the - mutant seeds exhibited significantly reduced grain size, grain weight, and embryo weight, and a remarkably lower rate of embryo retention in kernels subjected to milling. However, the volume of air space between embryo and endosperm, density of embryo, and total phenolic content (TPC) and antioxidant activity of mature grains were significantly higher in the - mutant than in the wild type. Genetic analysis and mapping revealed that the - mutant was non-allelic to the null mutants -, -, and -, and its phenotype was controlled by a single recessive gene, _, an ortholog of (). The - mutant carried a 7 bp deletion in the second exon of . Seeds of the knockout mutant, generated CRISPR/Cas9-based gene editing, displayed the mutant phenotype. Consistent with the fact that OsDET1 interacts with CONSTITUTIVE PHOTOMORPHOGENIC 10 (OsCOP10) and UV-DAMAGED DNA BINDING PROTEIN 1 (OsDDB1) to form the COP10-DET1-DDB1 (CDD), seeds of and knockout mutants also showed the phenotype. These findings will enhance our understanding of the functional roles of and the CDD complex in embryogenesis and flavonoid biosynthesis in rice seeds.