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Abstract: microRNAs (miRNAs) are small (21-24 nucleotides), single-stranded RNAs that regulate target gene expression at transcriptional and posttranscriptional levels. miRNAs play crucial roles in plant development, maintenance of homeostasis, and [...]

Summary: The DELAY OF GERMINATION1 (DOG1) family genes (DFGs) in Arabidopsis thaliana are involved in seed dormancy, reserve accumulation, and desiccation tolerance. Decoding the molecular evolution of DFGs is key to understanding how these seed programs evolved. This article demonstrates that DFGs have diverged in the four lineages DOG1, DOG1‐LIKE4 (DOGL4), DOGL5 and DOGL6, whereas DOGL1, DOGL2 and DOGL3 arose separately within the DOG1 lineage. The systematic DFG nomenclature proposed in this article addresses the current issues of inconsistent DFG annotation and highlights DFG genomic synteny in angiosperms. DFG pseudogenes, or collapsed coding sequences, hidden in the genomes of early‐diverging angiosperms are documented here. They suggest ancient birth and loss of DFGs over the course of angiosperm evolution. The proposed models suggest that the origin of DFG diversification dates back to the most recent common ancestor of living angiosperms. The presence of a single form of DFG in nonflowering plants is discussed. Phylogenetic analysis of gymnosperm, lycophyte, and liverwort DFGs and similar genes found in mosses and algae suggests that DFGs diverged from the TGACG motif‐binding transcription factor genes before the divergence of the bryophyte lineage. [ABSTRACT FROM AUTHOR]

ABA regulates various biological programs in seeds. This article initially introduces the basic information about the regulation of seed reserve accumulation and desiccation tolerance by ABA, and then delves into the emerging mechanisms of ABA signaling during embryo de-greening, seed dormancy and germination. Pioneering research on seed reserve accumulation and desiccation tolerance many years ago identified the major ABA signaling components, such as the purine (R) and pyrimidine (Y) motif (RY motif) and ABA response/responsive element (ABRE), which established the foundation of our current understanding of ABA signaling. Recent research is further advancing our knowledge on the involvement of ABA in other seed programs. ABA INSENSITIVE3 (ABI3) regulates embryo de-greening through STAY-GREEN (SGR), a rate-limiting enzyme for chlorophyll degradation. ABI1 and ABI2, protein phosphatases 2C (PP2C), are involved in ABA signaling associated with seed dormancy and germination. Unlike ABI1 and ABI2, ABA HYPERSENSITIVE GERMINATION1 (AHG1), another PP2C involved in germination, is resistant to the inhibition by the ABA receptor, which highlights a unique ABA signaling pathway in seeds. This pathway seems to create a byway that allows the germination program to operate even in the presence of ABA. On the other hand, the long-awaited biochemical function of DELAY OF GERMINATION1 (DOG1), a master regulator of seed dormancy, is now understood to sequestrate AHG1 to shut down this pathway, enhance ABA sensitivity in seeds and impose dormancy. Interesting regulatory mechanisms of DOG1 and antisense DOG1 expression, which are also relevant to ABA signaling in plant responses to drought, are also discussed in this article. [ABSTRACT FROM AUTHOR]

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]