Rice high in resistant starch is a valuable food for human health, especially for individuals with type 2 diabetes, as it supports effective blood sugar control and provides cardiovascular and intestinal benefits. However, developing rice varieties with a high resistant starch content remains a major challenge. In this study, we identified a mutant with increased chalkiness, chalk2, from the mutant library of indica rice Zhongjian 100. The chalk2 mutants exhibited significantly higher amylose and protein contents, while the total starch and lipid contents were reduced. An analysis of resistant starch in chalk2 revealed substantial increases in two resistant starch (RS) types, RS2 and RS3. Electron microscopy revealed abnormal starch granule development in the endosperm. The chalk2 mutant also showed reduced grain length, width, and thickness, as well as a lower seed-setting rate, which ultimately led to a significant reduction in grain yield. Through physical localization, Mut-Map analysis, and transgene complementation, we found that SBEIIb was responsible for the chalk2 phenotypes, and it is a member of the starch branching enzyme (SBE) family specifically expressed in the endosperm. Furthermore, the expression levels, enzymatic activity, and protein abundance of SBEIIb were significantly reduced in chalk2 mutants. These findings suggest that SBEIIb plays a crucial role in regulating the composition of starch and resistant starch formation in indica rice.

The mesocotyl, a structure located between the basal part of the seminal root and the coleoptile node of seedlings, contributes to pushing the shoot tip through the soil surface, a function that is essential for the uniform emergence of direct-seeded rice. Its elongation is inhibited by light and induced in darkness. This investigation of an indica rice (P25) with vigorous mesocotyl elongation was aimed at identifying the “omics” basis of its light-induced growth inhibition. A transcriptomic comparison between mesocotyl tissues that had developed in the dark and then been exposed to light identified many differentially expressed genes (DEGs) and differentially abundant microRNAs (miRNAs). Degradome sequencing analysis revealed 27 negative miRNA-target pairs. A co-expression regulatory network was constructed based on the miRNAs, their corresponding targets, and DEGs with a common Gene Ontology term. It suggested that auxin and light, probably antagonistically, affect mesocotyl elongation by regulating polyamine oxidase activity.