Unveiling distinct storage composition and starch properties in developing indica rice grains via transcriptional profiling and enzymatic activity analysis

The starch and protein in rice grains determine their nutritional value, eating and cooking quality (ECQ), and potential applications as a biopolymer. Building on previously identified functional differences between two Thai indica cultivars, waxy RD6 and high-amylose RD57, we examined the transcriptional regulation of their storage polymers by profiling key starch-biosynthetic and storage-protein genes in developing endosperms at 7-, 14-, 21-, and 28-days post-anthesis (DPA). Major differentially expressed genes were cross-validated with enzymatic activities and grain starch and storage-protein composition. Transcriptome dynamics varied significantly between cultivars, and were predominant at 14 DPA, which coincided with the period of active expression of the starch biosynthetic genes, while for storage protein gene expression, it was strongest at 7 DPA. At 21 and 28 DPA, most starch and glutelin biosynthesis genes in RD6 showed stronger expression than those in RD57. However, the GBSSI-to-SS expression ratio was higher in RD57, which correlated with its higher amylose content and associated differences in starch properties compared to RD6. Gene co-expression network analysis identified potential regulators of these pathways, including transcription factors bZIP10-like and bZIP44-like, and the energy signaling SnRK2.10-like kinase. Binding motif predictions indicated a bZIP10-like and bZIP44-like association with several starch genes, warranting further investigation as potential targets for improving rice starch. Collectively, this study provides a comprehensive understanding of the regulation of storage biomolecule biosynthesis in the previously understudied indica rice, laying the groundwork for breeders to develop new varieties with improved ECQ and health-beneficial traits for users in the food and biomaterial industries.