It is evident that seed dormancy and germination play a key role in plant initial survival against submergence. Growth regulators like ABA and GA and their ratio compete with each other, favoring either dormancy or germination depending on the physiological needs
[10]. ABA suppresses the physiologically assisted genes for germination whereas GAs can erase the effects. Embryo activity at the cellular level overcoming mechanical distances via tests is important. All of the activity of developing embryos is regulated by GA-assisted genes. The latter, with their increasing rates of transcription and translation, may support ABA-suppressed activities of quiescence strategies
[11]. In seeds, a precise concentration of GA is maintained by a balance between biosynthesis and its turnover via oxidative degradation. Regulation for de novo biosynthesis is also important in the context of GA activity on seedling development. This becomes more complicated given that under water a significant level of reactive oxygen species (ROS) and Ca
2+-dependent signaling are prerequisites. This may integrate downstream pathways for anoxia tolerance and the germination of seeds
[12]. This is explained more by the fact that ROS can upregulate a number of ABA-metabolizing gene (particularly
ABAI3 and
AP2) transcription factors (TFs). Auxins (Au) are also involved to allow the binding of a few TFs, and thereby they induce downstream genes related to ABA metabolism. Au, like GA involvement, in this aspect may concern other TFs like
AP2 and DELLA and other proteins. These often cause GA oxidation pathways involving genes like
GA20ox, GA3ox, and
PIL5 TF
[13]. After the ripening of embryos in seeds, a number of genes are involved, like
RGA,
RGL2, and
GAI, from different insensitive mutants to GA. For the up- or downregulation of ABA-inducing genes, growth substances are involved including jasmonic acid (JA), brassinosteroid (BR), ethylene (ET), salicylic acid (SA), etc.
[14]. ABA, through its auxin inductive cascade, can induce a number of genes via some auxin response factors (ARF10/16). These factors are involved to allow the binding of other TFs. Likewise, ABA can induce MYB96 factor, which otherwise induces TF ABI4. The latter is responsible for the suppression of CYP707A1/2 factor activity, which is likely to bind the α-amylase promoter and promotes seed germination
[15]. ABA can induce other TFs (ABI5, BIN2, PKS5, etc.) which also inhibit seed germination. All of these are related to the precise concentration of ROS, which collectively are key balancing factors for gene regulation. ABA, under anaerobic conditions, is more active with regard to its regulation of catabolism as well. On the seeds and vegetative parts of plants, a number of ABA receptor components are grouped and these regulate protein phosphatase 2C (PP2C) when ABA is present. PP2C is inactive under aerobic conditions but is activated with sucrose non-fermenting 1 (SNF1)-related kinase 2. The latter allows for specific response element binding TFs
[16]. Increased dormancy is also related to ABA, where a particular factor, DELAY OF GERMINATION 1 (DOG1), becomes the master regulator of the primary dormancy activator. This is in turn regulated by a specific PP2C, activated by ABA
[17]. DOG1 modifies ABA signaling where PP2C acts on seeds, particularly regarding those depending on ABA hypersensitive germination. Even after grain development,
OsDOG1-like gene expression is also involved for immature seed development. This is co-dominantly expressed with an over expression of
OsNCED2 and
OsABA8’OH3. Seed germination under water is independent of primary dormancy, where susceptible varieties can germinate but fail through downstream development. Not only embryos under submergence stress but also heat-stressed embryos are dependent on DNA methylation. The DNA methylation of ABA-catabolizing genes and the α-amylase promoter are also subjected to anaerobic stress
[18]. Another two genes,
ABA deficient 4 (ABA4) and
Neoxanthin deficient 1 (NXD1), are required for ABA biosynthesis and its regulation
[19]. Therefore, more studies on ABA-GA cross talk in the germination phenomenon with molecular insights into submergence or anoxic germination are required (
Figure 1).