Transcriptomics of Mature Rice (Oryza Sativa L. Koshihikari) Seed under Hot Conditions by DNA Microarray Analyses

Abstract

Higher temperature conditions during the final stages of rice seed development (seed filling and maturation) are known to cause damage to both rice yield and rice kernel quality. The western and central parts of Japan especially have seen record high temperatures during the past decade, resulting in the decrease of rice kernel quality. In this study, we looked at the rice harvested from a town in the central Kanto-plains (Japan) in 2010. The daytime temperatures were above the critical limits ranging from 34 to 38 °C at the final stages of seed development and maturity allowing us to investigate high-temperature effects in the actual field condition. Three sets of dry mature rice seeds (commercial), each with specific quality standards, were obtained from Japan Agriculture (JA Zen-Noh) branch in Ami-town of Ibaraki Prefecture in September 2010: grade 1 (top quality, labeled as Y1), grade 2 (medium quality, labeled as Y2), and grade 3 (out-of-grade or low quality, labeled as Y3). The research objective was to examine particular alterations in genome-wide gene expression in grade 2 (Y2) and grade 3 (Y3) seeds compared to grade 1 (Y1). We followed the high-temperature spike using a high-throughput omics-approach DNA microarray (Agilent 4 × 44 K rice oligo DNA chip) in conjunction with MapMan bioinformatics analysis. As expected, rice seed quality analysis revealed low quality in Y3 > Y2 over Y1 in taste, amylose, protein, and fatty acid degree, but not in water content. Differentially expressed gene (DEG) analysis from the transcriptomic profiling data revealed that there are more than one hundred upregulated (124 and 373) and downregulated (106 and 129) genes in Y2 (grade 2 rice seed) and Y3 (grade 3 rice seed), respectively. Bioinformatic analysis of DEGs selected as highly regulated differentially expressed (HRDE) genes revealed changes in function of genes related to metabolism, defense/stress response, fatty acid biosynthesis, and hormones. This research provides, for the first time, the seed transcriptome profile for the classified low grades (grade 2, and out-of-grade; i.e., grade 3) of rice under high-temperature stress condition.