The Prolonged Endosperm Filling and Embryo Enlargement Phases Contribute to the Impaired Development of Inferior Grains in Japonica Rice

Inferior grains exhibit significant differences compared to superior grains in terms of developmental processes and metabolic activities, leading to unstable grain yield and quality. While substantial progress has been made in understanding the physiology of inferior grains, most studies have primarily focused on the endosperm, with the role of the embryo largely overlooked. Two Wuyujing-3 mutants, DW024 (relatively synchronous; syn-DW024) and DW179 (significantly asynchronous; asyn-DW179), with different grain-filling patterns were used in this study. Samples of superior and inferior grains were collected at intervals from 5 to 60 days after fertilization (DAF) and subsequently dissected into subsamples of the embryo and endosperm. Histochemical staining, biochemical analysis, and RNA sequencing (RNA-seq) were combined to systematically compare developmental and physiological traits between superior and inferior grains. Combining hierarchical clustering of mRNA datasets revealed three developmental phases of the endosperm and embryo: morphogenesis, endosperm filling/embryo enlargement, and maturation. In both syn-DW024 and asyn-DW179, the duration of the endosperm/embryo morphogenesis phase was identical in superior and inferior grains. The inferior grains of asyn-DW179 exhibited a 10-day prolongation in the endosperm filling phase and a 20-day extension in the embryo enlargement phase as compared with the superior grains. The endosperm of inferior grains exhibited higher contents of sugars and free amino acids, along with slower accumulation of storage compounds, which is associated with the down-regulation of genes for starch synthesis and ABA signaling. In addition, transporters for nutrient exchanges between endosperm and embryo were down-regulated, suggesting a potential role of the embryo in adjusting the endosperm filling process. Collectively, our results reveal that the prolonged phases of endosperm filling and embryo enlargement may underlie the impaired development of inferior grains, offering a new perspective for breeding or cultivating rice with uniform grain quality.