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Genome-Wide Comparative Transcriptional Analysis of Developing Seeds among Seven Oryza sativa L. Subsp. Japonica Cultivars Grown near the Northern Limit of Rice Cultivation

Sho Takano, Shuichi Matsuda, Yuji Hirayama, Takashi Sato, Itsuro Takamure and Kiyoaki Kato

Improved grain quality is a major breeding target in rice (Oryza sativa L. subsp. japonica), owing to market demand. Rice cultivars grown in Hokkaido (42-45°N), the northernmost region of rice paddy cultivation in Japan and near the northern limit of rice cultivation, have been bred for over 100 years for adaptation to low temperature together with high yield and grain quality. In this study, for seven closely related rice cultivars released in Hokkaido in the last 70 years, we investigated the transcriptome profiles of developing seeds 8 days after flowering (DAF, middle stage) and 15 DAF (late stage) under natural conditions in Hokkaido (42.52°N) using a whole-genome oligonucleotide microarray. The transcriptome profiles were divided into two groups depending on stage and were more variable at the late than that at the middle stage. The genome-wide transcriptome data revealed the features of differentially expressed genes in two first-generation cultivars compared to that in the parental cultivars. Starch properties were varied and correlated with the expression of starch biosynthesis genes among Hokkaido cultivars. Apparent amylose content was positively correlated with Waxy gene expression at the late stage. The expression of starch biosynthesis genes and starch properties were varied among Hokkaido cultivars. The transcriptomes of the most recent cultivars reveal the expression of ideal genes for the development of cultivars with high grain yield, grain quality, and grain traits essential for rice production near the northern and southern limits of rice cultivation.