Plant Gene and Traits 2024, Vol.15, No.3, 129-140 http://genbreedpublisher.com/index.php/pgt 130 environmental factors and genetic variations on these processes. Understanding these mechanisms will provide valuable insights for improving seed germination and seedling establishment, ultimately contributing to the sustainable management and conservation of pine forests. 2 Gene Expression Dynamics in Pine Seed Germination 2.1 Overview of key stages in pine seed germination Pine seed germination is a complex process that involves multiple stages, each characterized by distinct physiological and molecular changes. The initial stage involves imbibition, where the seed absorbs water, leading to the reactivation of metabolic processes. This is followed by the activation of various signaling pathways and the mobilization of stored reserves to support the growth of the embryo (Stasolla et al., 2004; Ratnaparkhe et al., 2009). The final stage is marked by the emergence of the radicle, signifying the completion of germination and the beginning of seedling growth (Han et al., 2019; Xu et al., 2020). 2.2 Major genes involved in germination and their functions Several key genes play crucial roles in the regulation of pine seed germination. For instance, MADS-box transcription factors such as MADS11 and DAL1 have been identified as important regulators of the vegetative-to-reproductive transition in pine, which is closely linked to the germination process. These genes are involved in the aging pathway and have distinct roles in flowering regulatory networks (Ma et al., 2021). Additionally, genes associated with cell wall degradation, biosynthesis, and remodeling are highly expressed during pollen germination, indicating their importance in the germination process (Salazar and Fernando, 2019). DNA methylation and gene expression variations in genes such as DNMTs and circadian clock genes also contribute to local adaptation and germination in Scots pine populations (Alakärppä et al., 2018). 2.3 Techniques used for gene expression analysis in pine seeds Various techniques have been employed to analyze gene expression in pine seeds. Temporal dynamic transcriptome analysis is one such method, which involves sampling at different developmental stages to identify differentially expressed genes and regulatory modules (Ma et al., 2021). Yeast secretion trap (YST) coupled with computational prediction has been used to isolate cDNAs encoding secretory proteins associated with pollen germination, providing insights into the diversity and functions of these proteins (Salazar and Fernando, 2019). Comparative transcriptomic analysis has also been utilized to study transcriptional changes at different stages of seed development and germination, helping to identify key regulatory genes and pathways (Han et al., 2019; Xu et al., 2020). These techniques collectively enhance our understanding of the molecular mechanisms underlying pine seed germination. 3 Regulatory Mechanisms Influencing Gene Expression 3.1 Hormonal regulation during seed germination Hormonal regulation plays a pivotal role in seed germination, with abscisic acid (ABA) and gibberellins (GA) being the primary hormones involved. ABA generally acts as an inhibitor of germination, maintaining seed dormancy, while GA promotes germination by breaking dormancy and stimulating growth processes(Bogamuwa and Jang, 2013). The balance between these hormones is crucial for the regulation of seed germination. For instance, the PIF1-miR408-PLANTACYANIN repression cascade in Arabidopsis thaliana demonstrates how light signals are translated into hormonal profiles that control germination by modulating ABA and GA levels (Jiang et al., 2021). Additionally, the expression of ABA receptors such as PYR1/PYL/RCAR is regulated by transcription factors like ABI5, which modulates ABA sensitivity during germination (Figure 1) (Zhao et al., 2020). In rice, similar hormonal pathways involving ABA and GA have been identified, highlighting the conserved nature of these regulatory mechanisms across different plant species (Gong et al., 2022). The research of Zhao et al. (2020) illustrates the role of PYLs (abscisic acid receptors) and ABI5 in seed germination and their interaction under the influence of abscisic acid (ABA). During germination without ABA, SnRK2, a kinase, is inhibited by PP2C, preventing the phosphorylation of ABI5. As a result, ABI5 is degraded, and ABA-responsive genes are not activated, allowing germination to proceed. In the presence of ABA, ABA binds to PYLs, which inhibit PP2C, releasing SnRK2 from inhibition. Activated SnRK2 phosphorylates ABI5,
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