Comparative transcriptome profiling of developing caryopses from two rice cultivars with differential dormancy

Abstract

Pre-harvest sprouting (PHS) in rice causes poor grain quality and results in significant reductions in yield, leading to significant economic losses. In contrast, deep dormancy can lead to equally unwanted non-uniform germination. Therefore, a suitable level of dormancy is a critically important agronomic trait. In this study, an analysis of PHS in developing seeds of two Korean rice cultivars (vivipary), Gopum and Samgwang, revealed differences in dormancy in caryopses at 25 d after heading (DAH). To assess the transcriptomic characteristics associated with vivipary, we compared RNA profiles at early (3-6 DAH), middle (25 DAH), and late (40 DAH) developmental stages. Transcriptomic differentiation was most pronounced in caryopses at 25 DAH, the developmental stage at which differential dormancy was also the most prominent. A k-means clustering analysis of the two cultivars revealed groups of genes with similar or dissimilar expression profiles. Many of the genes that showed distinct differential expression profiles were those involved in seed maturation. Intriguingly, differential gene expression levels between the two cultivars were positively correlated with fold-changes in their expression during the early half of caryopsis development. This implies that the establishment of seed dormancy is strongly correlated with the altered transcriptomic patterns related to the progression of maturation. Our global RNA profiling suggests that caryopsis development in Gopum proceeds at a greater speed than in the Samgwang cultivar. Thus, a high degree of maturity and early dormancy release may be present in 25 DAH caryopses of Gopum, although we cannot exclude the possibility of genetic defects modifying dormancy. The comparative transcriptomic analysis of the two cultivars did not reveal noticeable differences in RNA profiles with respect to differences in abscisic acid (ABA) content or ABA sensitivity. Therefore, it is unlikely that ABA is directly involved in the differences in dormancy observed between the two cultivars.