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.

Interaction between the embryo and endosperm affects seed development, an essential process in yield formation in crops such as rice. Signals that mediate communication between embryo and endosperm are largely unknown. We used the notched-belly (NB) mutant with impaired communication between embryo and endosperm to investigate the effect of the embryo on developmental staging of the endosperm and signaling pathways in the embryo that regulate endosperm development. Hierachical clustering of mRNA datasets from embryo and endosperm samples collected during development in NB and a wild type showed a delaying effect of the embryo on the developmental transition of the endosperm by extension of the middle stage. K-means clustering further identified coexpression modules of gene sets specific to embryo and endosperm development. Combined gene expression and biochemical analysis showed that T6P–SnRK1, gibberellin and auxin signaling by the embryo regulate endosperm developmental transition. We propose a new seed developmental staging system for rice and identify the most detailed signature of rice grain formation to date. These will direct genetic strategies for rice yield improvement.

Carbon isotope composition (δ¹³C) of a plant organ is an inherent signature reflecting its physiological property, and thus is used as an integrative index in crop breeding. It is also a non-intrusive method for quantifying the relative contribution of different source organs to grain filling in cereals. Using the samples collected from two-year field and pot experiments with two nitrogen (N) fertilization treatments, we investigated the temporal and spatial variations of δ¹³C in source organs of leaf, sheath, internode, and bracts, and in sink organ grain. Constitutive nature of δ¹³C was uncovered, with an order of leaf (−27.84‰) < grain (−27.82‰) < sheath (−27.24‰) < bracts (−26.81‰) < internode (−25.67‰). For different positions of individual organs within the plant, δ¹³C of the leaf and sheath presented a diminishing trend from the top (flag leaf and its sheath) to the bottom (the last leaf in reverse order and its sheath). No obvious pattern was found for the internode. For temporal variations, δ¹³C of the leaf and sheath had a peak (the most negative) at 10 days after anthesis (DAA), whereas that of the bracts showed a marked increase at the time point of anthesis, implying a transformation from sink to source organ. By comparing the δ¹³C in its natural abundance in the water-soluble fractions of the sheath, internode, and bracts with the δ¹³C in mature grains, the relative contribution of these organs to grain filling was assessed. With reference to the leaf, the internode accounted for as high as 32.64% and 42.56% at 10 DAA and 20 DAA, respectively. Meanwhile, bracts presented a larger contribution than the internode, with superior bracts being higher than inferior bracts. In addition, N topdressing reduced the contribution of the internode and bracts. Our findings clearly proved the actual significance of non-foliar organs of the internode and bracts for rice yield formation, thus extending our basic knowledge of source and sink relations.