Carbon reserves in rice stems (culm and sheath) before flowering contribute to a significant portion of grain filling. In this study, super rice LYP9 and conventional rice 9311 showed different carbon reserve remobilization behaviors. The transcriptomic profiles of stems of LYP9 and 9311 were analyzed at three stages of grain filling. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene Ontology (GO) classification of DGs both shown that carbohydrate catabolic pathway, plant hormone signal transduction and photosynthesis pathway were DGs-enriched, suggesting their roles in carbon reserve remobilization, which somewhat explain the difference of NSC content, photosynthesis and ABA content between the two cultivars during grain filling. Further analysis suggest that genes involved in trehalose synthesis (TPP, TPS), starch degradation (beta-amylase) and sucrose synthesis (SPS, SS) were important for carbon reserves remobilization whereas ABA content was determined by counteraction of NCED1 and ABA8ox1 gene. The higher expression level of all these genes and ABA content in 9311 resulted in better efficiency of carbon reserves remobilization in 9311 than cultivar of LYP9.

Moderate soil drying (MD) imposed at post-anthesis stages can increase starch accumulation in inferior grains. Based on the accumulation dynamics of soluble sugars and starch in inferior grains under well-watered (CK) and MD treatments at postanthesis in the YD cultivar, RNA-seq analysis of the inferior grains was carried out. We found that the elevated ABA level induced by MD was consistent with the downregulation of the ABA8ox2 gene, which belongs to the ABA catabolism family, suggesting that the lower expression level of ABA8ox2 might be responsible for a higher ABA content, potentially resulting in better grain filling in inferior grains. Furthermore, the MD treatment altered the expression pattern of genes related to ABA signal transduction, which might participate in the process of starch accumulation in the inferior grains. Besides, genes encoding five key enzymes involved in the conversion of sucrose to starch were up-regulated, which are responsible for soluble sugar reduction and starch accumulation in inferior grains under MD. Furthermore, the ABA8ox2 -mediated increase in ABA levels might be involved in the process of inferior grain filling under MD.

The trehalose-6-phosphate phosphatase 1 (TPP1) gene, which is reported to play roles in improving yield in maize and stress tolerance in rice, also promoted seed germination. tpp1 mutant seeds germinated significantly more slowly than ZH11 seeds. The ABA content of dry tpp1 seeds was higher than that of ZH11 seeds. In addition, tpp1 seeds were hypersensitive to ABA and an ABA catabolism inhibitor (diniconazole). Both exogenous ABA and diniconazole also inhibited the expression of the OsTPP1 gene in seeds. Further analysis showed that the tpp1 mutant was sensitive to the gibberellin (GA) biosynthesis inhibitor paclobutrazol (PAC). The expression levels of the hormone genes ABA 8'-hydroxylase 3 (OsABA8ox3) and GA 2-oxidase 1 (OsGA2ox1) were increased, while the GA 20-oxidase 1 (OsGA20ox1) was reduced in the tpp1 mutant during seed germination. Overall, TPP1-regulated seed germination was found to be mediated by ABA catabolism, GA synthesis and GA catabolism in imbibed seeds.