A sugary mutant with low total starch and high sugar content was compared with its wild type Sindongjin for grain-filling caryopses. In the present study, developing seeds of Sindongjin and sugary mutant from the 11th day after flowering (DAF) were subjected to RNA sequencing (RNA-Seq). A total of 30,385 and 32,243 genes were identified in Sindongjin and sugary mutant. Transcriptomic changes analysis showed that 7,713 differentially expressed genes (DEGs) (log2 Fold change ≥1, false discovery rate (FDR) ≤ 0.001) were identified based on our RNA-Seq data, with 7,239 genes up-regulated and 474 down-regulated in the sugary mutant. A large number of DEGs were found related to metabolic, biosynthesis of secondary metabolites, plant-pathogen interaction, plant hormone signal transduction and starch/sugar metabolism. Detailed pathway dissection and quantitative real time PCR (qRT-PCR) demonstrated that most genes involved in sucrose to starch synthesis are up-regulated, whereas the expression of the ADP-glucose pyrophosphorylase small subunit (OsAGPS2b) catalyzing the first committed step of starch biosynthesis was specifically inhibited during the grain-filling stage in sugary mutant. Further analysis suggested that the OsAGPS2b is a considerable candidate gene responsible for phenotype of sugary mutant.

Rice (Oryza sativa) is an excellent model monocot with a known genome sequence for studying developmental seeds. In the study, the seeds of 10th day after flowering (DAF) were conducted RNA-Seq of the variety Shindongjin and Sugary mutant using RNA-seq technique. Approximately 202 and 214 million high-quality paired-end reads (101-bp in size) were generated in Shindongjin and Sugary mutant, respectively. Comprehensive analysis on the transcript levels of genes which encode starch-synthesis enzymes is fundamental for the assessment of the function of each enzyme and the regulatory mechanism of starch biosynthesis in seeds. Quantitative real-time PCR was also used to validate the expression profiles of 28 rice genes encoding six classes of enzymes, viz., ADPglucose pyrophosphorylase (AGPase), starch synthase, starch branching enzyme, starch debranching enzyme, starch phosphorylase, and disproportionating enzyme at different developmental grain- filling stages (DAF 1-14) between Shindongjin and Sugary mutant. The results showed that the expression of most of starch synthesis genes were up-regulated except the cytosolic AGPase small subunit2b (AGPS2b), which sharply decreased at grain-filling stages in Sugary mutant. These results will expand our understanding of the complex molecular and cellular events in rice grain-filling stages and provide a fundamental understanding of future studies on developmental endosperm in rice and other cereal crops.

Grain size is one of the most important trait determining yield in cereal crops, apart from number of grains per panicle, number of panicles per plant and 1000 seed weight. Other than grain characteristics, plant architecture is another very important factor influencing yield by affecting the amount plant surface area directly exposed to the sun light. Erect panicle is important morphological characteristic which helps in enhancing the yield by allowing sun light to fall directly on leaves unlike curved panicle which blocks sunlight and consequently reduce photosynthesis. A small round grain and erect panicle mutant was obtained by treating Hwacheong rice (japonica) with MNU (N-methyl-N-nitrosourea) chemical mutagen. Through bulked segregant analysis (BSA) using STS (Sequence-Tagged Sites) and SS-STS (Sub-species Specific Sequence-Tagged Site) markers we located the mutated gene on the long arm of chromosome 7 and narrowed down candidate region to 168.75kbp through fine mapping. Mutant manifested characteristics like reduced grain size and plant height, dense and erect panicle and relatively erect plant compared to the wild type. When we crossed the mutant with its parent (Hwacheong), F1 panicle and grain characteristics showed intermediate phenotype, therefore, we concluded that wild type allele of this gene shows incomplete dominance. Scanning electron microscopy(SEM) result shows that increase in width of mutant grain, which changes its shape, is due to increase in width of glume cells. Phenotypic examination shows that dense and erect panicle phenotype is result of reduction in length of rachis, primary and secondary branch.