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 L.) is one of the most important staple foods that feed more than 50% of the world’s population. With the improving of people’s living standard, eating quality of rice become the most important aims in current breeding programs. Amylose content (AC) and gelatinization temperature (GT) are the two main measures to estimate the rice grain quality. In rice, a total of 27 genes directly involved the rice starch biosynthesis effecting on the rice eating quality. It clearly identified chromosome 6 to be rich in the genes related to AC and GT properties (GBSS I, SSIIa and SBE I) along with other genomic regions scattered in rice genome. Rice blast, caused by the fungal pathogen M. oryzae, is the most devastating disease of rice and severely affects crop stability and sustainability worldwide. Many fungal genes involved in pathogenicity and rice genes involved in effector recognition and defense responses have been identified over the past decade. A total of 99 and 22 blast resistance genes have been identified and cloned; in which 45% were found in japonica cultivars, 51% in indica cultivars, and the rest 4% in wild rice species. Among them, three major resistance gene clusters have been characeterized: the Pik locus on Chromosome 11, and the Pita locus on Chromosome 12, the Piz locus on Chromosome 6 closely to the starch synthesis-related genes. These results could be important clues for studying the relationship between resistance / susceptible materials and eating quality.

One of the biotic stresses in rice production is rice blast disease caused by Magnaporthe oryzae, which is one of the most destructive fungal diseases in rice. We outlined an approach towards genome wide association study for the blast disease resistance in rice. In total, 295 rice accessions including 137 Heuristic Set accessions (HS) and 158 Korean Bred varieties (KB) were screened for the rice blast disease resistance. Firstly, Magnaporthe oryzae were inoculated to the rice seedlings of two weeks after germinations. Then, evaluation of the disease symptoms and checking the crossing point (CP) value were conducted one week after inoculation. To quantify the CP value, real-time polymerase chain reaction (PCR) was employed in combination with the primer pair and Taqman probe specific to Magnaporthe oryzae HYDROPHOBIN class 1 (MHP1) which is an indispensable unigene encoding HYDROPHOBIN for normal virulence expression. Based on these CP values from the PCR reactions containing a series of increasing concentration of cloned amplicon or fungal genomic DNA, correlation among the template’s copy number or its amount and amplification pattern was calculated. Reliability of this equation was further confirmed using the DNA samples from the rice leaves infected with compatible or incompatible strains of M. oryzae. These steps are still being undertaken, and after the complete process of disease resistance phenotyping for the whole population containing 295 accessions, GWAS will be performed to examine the associated genes involving in blast resistance mechanism using the whole genome resequencing data of 295 accessions. This approach would be a useful technique for identifying genetic loci responsible for natural variation in rice blast disease resistance and ultimately, new R genes which can improve the blast resistance in rice.

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.