Franz Marielle C. Nogoy | Sophia S. Sandoval | Joni Rey H. Campilan | Francis A. Tablizo | Yong-gu Cho
MR7-3, a stable mutant line from mature Korean cultivar Donganbyeo (WT) subjected to 70 Gy, was known to have a 20 times greater amino acid content but chalky grain quality. To elucidate the transcriptional changes in MR7-3, microarray data generated from RiceXPro using 5, 10, 15, and 20 days after pollination (DAP) grain develop-mental stages of WT and MR7-3 were analyzed. Differentially expressed genes (DEGs) were filtered using the limma package for R using the following conditions: p-value 0.05, fold change (FC) ≥ 2, and false discovery rate 0.05 using a Benjamini-Hochberg correction. There were 43, 245, 338, and 661 DEGs found in 5, 10, 15, and 20 DAP, respectively. Gene ontology of DEGs using Panther classification showed that most of the DEGs belong to catalytic activity (GO:0003824) in terms of molecular function, metabolic (GO:0008152) for the biological process, and most of the DEGs belong to cells (GO:0005623). DEGs were mapped in the KEGG database for pathway analysis to show changes in the starch and sucrose metabolism pathways as well as in the biosynthesis of amino acids. Coexpression analysis was conducted to show possible connections between the high amino acid content and chalkiness in rice grains using a weighted correlation network analysis via the WGCNA package for R. Through coexpression analysis, it was revealed that known gene related to chalkiness, AGPase, found in the starch and sucrose metabolism pathway, was highly correlated to threonine aldolase and chorismate mutase, both found in the biosyn-thesis of amino acids pathway. Connecting and related pathways between the two are glycolysis and gluconeogenesis, suggesting it is worth looking into these pathways for more concrete explanations between the relationship of amino acid content and chalkiness. These insights on the gene expression of chalky rice with high
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