Prolonged endosperm filling and embryo enlargement phases contribute to the impaired development of inferior grains in japonica rice

Inferior grains exhibit delayed developmental processes and reduced metabolic activities compared to superior grains, leading to unstable rice yield and quality. While significant advancements have been achieved in elucidating the physiology of endosperm filling in inferior grains, the role of the embryo remains underexplored and warrants comprehensive investigation. 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 d after fertilization 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 compared to 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 was 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.