Differential ABA sensitivity of superior and inferior rice grains is linked to cell cycle entry into endoreduplication

Suboptimal grain filling in rice (<i>Oryza sativa</i>) inferior spikelets poses a constraint to maximizing the yield potential. The differential grain filling between superior and inferior spikelets has been primarily attributed to differences in endogenous phytohormone levels that determine grain sink capacity. In this study, we aimed to gain molecular insights into the role of two phytohormones, abscisic acid (S-ABA or ABA) and cytokinin (6-benzyladenine or BA) through exogenous applications on superior and inferior grains in rice. We found that ABA and a combination of ABA and BA (ABA+BA) applications increased the grain yield in field studies, primarily by improving the grain weight of both superior and inferior grains. Transcriptomic analysis of developing grains shows differences in the expression of core cell cycle genes between the superior and inferior grains at four days after fertilization between the control and phytohormone applications. ABA and ABA+BA applications induce DNA replication genes and cell cycle inhibitory genes in superior grains only, likely promoting endoreduplication for increased cell storage capacity. ABA and BA applications suppressed the expression of cytokinin signaling genes in superior grains but induced them in inferior grains emphasizing the key roles for cytokinins and ABA in superior and inferior grains, respectively. An early induction of several grain storage-related genes in inferior grains is associated with accelerated entry into the grain storage stage, thus limiting sink capacity and poor grain fill. Our results indicate that ABA alone promotes photosynthate remobilization into both superior and inferior grains while ABA + BA regulates grain filling via cell cycle-related transcriptomic changes. Overall, our study reveals an intrinsic difference in ABA+BA sensitivity between inferior and superior grains that is linked to regulation of cell cycle checkpoints and entry into endoreduplication in the endosperm.