Abstract
Red rice fully dormant seeds do not germinate even under favorable germination conditions. In several species, including rice, seed dormancy can be removed by dry-afterripening (warm storage); thus, dormant and non-dormant seeds can be compared for the same genotype. A weedy (red) rice genotype with strong dormancy was used for mRNA expression profiling, by RNA-Seq, of dormant and non-dormant dehulled caryopses (here addressed as seeds) at two temperatures (30 °C and 10 °C) and two durations of incubation in water (8 h and 8 days). Aim of the study was to highlight the differences in the transcriptome of dormant and non-dormant imbibed seeds. Transcript data suggested important differences between these seeds (at least, as inferred by expression-based metabolism reconstruction): dry-afterripening seems to impose a respiratory impairment onto non-dormant seeds, thus glycolysis is deduced to be preferentially directed to alcoholic fermentation in non-dormant seeds but to alanine production in dormant ones; phosphoenolpyruvate carboxykinase, pyruvate phosphate dikinase and alanine aminotransferase pathways appear to have an important gluconeogenetic role associated with the restoration of plastid functions in the dormant seed following imbibition; correspondingly, co-expression analysis pointed out a commitment to guarantee plastid functionality in dormant seeds. At 8 h of imbibition, as inferred by gene expression, dormant seeds appear to preferentially use carbon and nitrogen resources for biosynthetic processes in the plastid, including starch and proanthocyanidins accumulation. Chromatin modification appears to be a possible mechanism involved in the transition from dormancy to germination. Non-dormant seeds show higher expression of genes related to cell wall modification, suggesting they prepare for acrospire/radicle elongation.
Highlights
“Red rice” is the common name used for the heterogeneous group of the weedy rices, congeneric to crop rice and usually characterized by a red caryopsis [1]
Transcript data suggested important differences between these seeds: dry-afterripening seems to impose a respiratory impairment onto non-dormant seeds, glycolysis is deduced to be preferentially directed to alcoholic fermentation in non-dormant seeds but to alanine production in dormant ones; phosphoenolpyruvate carboxykinase, pyruvate phosphate dikinase and alanine aminotransferase pathways appear to have an important gluconeogenetic role associated with the restoration of plastid functions in the dormant seed following imbibition; correspondingly, co-expression analysis pointed out a commitment to guarantee plastid functionality in dormant seeds
Beside to basic informative data, this section shows an overall view of the findings as depicted by available bio-informatic tools such as PageMan and MapMan, whereas a more detailed picture, based on the biological functions of individual differentially expressed genes (DEGs) and on a careful re-construction of the related pathways as established according to the literature, is offered in the Discussion
Summary
“Red rice” is the common name used for the heterogeneous group of the weedy rices, congeneric to crop rice and usually characterized by a red caryopsis [1]. These rices show various degrees of seed dormancy and can have much stronger dormancy than the cultivated rice [1]. Fully non-dormant rice seeds do not show a well-defined second phase as they germinate rapidly when they are imbibed at 30 ◦C [11] and their embryos quickly show an evident resumption of water uptake (third phase) in concomitance with the rupture of the pericarp [13]. A comparison of dormant and non-dormant seeds must be accomplished before the third phase takes place for non-dormant seeds, to avoid comparing seeds that are at different developmental stages
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