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Induction of nine-cis-epoxycarotenoid dioxygenase 6 (NCED6), an abscisic acid (ABA) biosynthesis gene, alone is sufficient to suspend germination in testaruptured seeds, which are at the final step of germination. Molecular consequences of NCED6 induction in imbibed seeds were investigated by RNA sequencing. The analysis identified many unknown and uncharacterized genes that were up-regulated by NCED6 induction, in addition to the major regulators of ABA signalling. Interestingly, other NCEDs were upregulated by NCED6 induction, suggesting that the major rate-limiting enzymes in the ABA biosynthesis pathway are subject to positive-feedback regulation. ZEAXANTHIN EPOXIDASE and ABSCISIC ALDEHYDE OXIDASE3, which function upstream and downstream of NCED, were also up-regulated in seeds by NCED6 induction, which suggests that the distinct layers of positive feedback loops are coordinately operating in the NCED6-induced seeds. SOMNUS (SOM), which was also up-regulated by NCED6 induction, was the major mediator of enhanced ABA signalling in NCED6-induced seeds. SOM exerted negative effects on GA biosynthesis, which also contributes to a high ABA-GA ratio and reinforces the suppressive state of germination. Besides these coding genes, long intergenic non-coding RNAs (lincRNAs) were also upregulated upon NCED6 induction (termed N6LINCRs). Conditional expression of N6LINCR1 altered gene expression profiles in seeds. Twenty-six genes were up-regulated and 66 genes were down-regulated by the induction of N6LINCR1. These results suggest that some of N6LINCRs have a regulatory role in gene expression in seeds, which potentially contributes to the regulation of germination by ABA. [ABSTRACT FROM AUTHOR]

Germination and early seedling development are critical for successful stand establishment of plants. Following germination, the cotyledons, which are derived from embryonic tissue, emerge from the seed. Arabidopsis seedlings at post-germinative stages are supported mainly by the supply of nutrition from the cotyledons until vegetative leaves emerge and initiate photosynthesis. The switch to autotrophic growth is a significant transition at the post-germinative stage. Here, we provide evidence that down-regulation of SQUAMOSA PROMOTER-BINDING PROTEIN LIKE13 (SPL13) by microRNA156 (miR156) plays an important role in the regulation of the post-germinative switch from the cotyledon stage to the vegetative-leaf stage. Silent mutations created in the SPL13 sequence in the region that is complementary to the miR156 sequence caused the deregulation of the mutant form of SPL13 (mSPL13) mRNA from miR156. Mutant seedlings over-accumulated miRNA-resistant messages and exhibited a delay in the emergence of vegetative leaves compared to wild-type seedlings. The delay was not observed in control transgenic plants expressing nonmutated SPL13, indicating that the phenotype was caused specifically by the silent mutations and deregulation of SPL13 from miR156. Characterization of the SPL13 promoter indicated that this gene is expressed mainly in the hypocotyl and affects leaf primordium development. These results suggest that the repression of SPL13 by miR156 is essential for normal post-germinative growth in Arabidopsis. [ABSTRACT FROM AUTHOR]