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.

弱势籽粒与强势籽粒在发育进程与代谢活动上存在显著差异，进而导致籽粒产量与品质不稳定。尽管目前对弱势籽粒生理机制的研究已取得长足进展，但多数研究主要聚焦于胚乳（endosperm），而胚胎（embryo）的作用在很大程度上被忽视。本研究选用两个武育粳3号（Wuyujing-3）突变体：DW024（灌浆相对同步，syn-DW024）与DW179（灌浆显著异步，asyn-DW179），二者籽粒灌浆模式存在差异。分别于受精后5至60天（days after fertilization, DAF）间隔取样强势籽粒与弱势籽粒，随后将其解剖分离为胚与胚乳亚样本。本研究结合组织化学染色、生化分析与RNA测序（RNA-seq）技术，系统对比了强势与弱势籽粒的发育及生理特征。通过对mRNA数据集进行层级聚类分析，明确了胚乳与胚胎的三个发育阶段：形态建成期、胚乳灌浆期/胚胎膨大期以及成熟期。在syn-DW024与asyn-DW179两个突变体中，强势与弱势籽粒的胚乳/胚胎形态建成期时长一致。与对应强势籽粒相比，asyn-DW179的弱势籽粒胚乳灌浆期延长10天，胚胎膨大期延长20天。弱势籽粒的胚乳中糖与游离氨基酸含量更高，但贮藏物质积累速率更慢，这与淀粉合成及脱落酸（ABA）信号通路相关基因的下调表达密切相关。此外，介导胚乳与胚胎间养分交换的转运蛋白编码基因表达下调，提示胚胎可能在调控胚乳灌浆进程中发挥潜在作用。综上，本研究结果显示，胚乳灌浆期与胚胎膨大期的延长可能是弱势籽粒发育缺陷的核心机制，为培育籽粒品质均一的水稻品种提供了全新的研究思路。