Plant Gene and Traits 2024, Vol.15, No.3, 129-140 http://genbreedpublisher.com/index.php/pgt 134 methylation and gene expression contribute to local adaptation, potentially enhancing the fitness of trees under changing climatic conditions (Alakärppä et al., 2018). Moreover, the identification of core 'housekeeping genes' in maritime pine provides a foundation for further research into the genetic basis of seed vigor and viability (Cañas et al., 2017). These insights are crucial for developing strategies to improve seed quality and ensure the sustainability of pine forests. 5 Technological Advances in Genetic Analysis 5.1 Innovations in transcriptomic and genomic technologies Recent advancements in transcriptomic and genomic technologies have significantly enhanced our understanding of gene expression and regulatory mechanisms in pine seed germination (Cullum et al., 2011; Tarazona et al., 2011). One notable innovation is the use of laser capture microdissection followed by transcriptomic analysis, which allows for the precise isolation and examination of specific tissues and cells. This technique has been successfully applied to maritime pine (Pinus pinaster) seedlings, resulting in the identification of 39 841 new transcripts and the characterization of 2 376 ubiquitously expressed genes, which are considered core 'housekeeping genes' in pine (Cañas et al., 2017). Additionally, suppression subtractive hybridization (SSH) has been employed to identify differentially expressed genes in response to environmental stimuli, such as stem inclination in young pine seedlings. This method has facilitated the discovery of genes involved in hormone regulation, the phenylpropanoid pathway, and signal transduction (Ramos et al., 2012). 5.2 Application of next-generation sequencing (NGS) in seed biology Next-generation sequencing (NGS) technologies have revolutionized seed biology by enabling comprehensive analyses of gene expression during critical developmental stages (Jain, 2012). For instance, global microarray analysis using NGS has revealed differential gene expression between quiescent and germinated maize embryo stages, highlighting the translational regulation of ribosomal protein mRNAs during germination (Jiménez-López et al., 2011). In Arabidopsis, pathway-based analysis of transcriptomic datasets has identified key regulatory actors and alternative metabolic routes involved in seed germination, demonstrating the genetic plasticity of this process (Ponnaiah et al., 2019). These studies underscore the power of NGS in uncovering the complex regulatory networks that govern seed germination and development. 5.3 Advances in bioinformatics for gene expression data analysis The integration of bioinformatics tools has been pivotal in analyzing and interpreting the vast amounts of gene expression data generated by modern genomic technologies (Jia et al., 2017; Hwang et al., 2018). Bioinformatic analysis has been instrumental in identifying and categorizing differentially expressed genes, as seen in the study of stem inclination responses in pine seedlings, where 942 unigene elements were identified and classified into functional categories (Ramos et al., 2012). Furthermore, bioinformatics has facilitated the development of pathway-based analysis methods, which allow for the quantification of pathway deregulation and the identification of regulatory mechanisms in seed germination (Ponnaiah et al., 2019). These advances in bioinformatics are essential for translating raw sequencing data into meaningful biological insights, thereby advancing our understanding of gene expression and regulatory mechanisms in pine seed germination. 6 Impact of Research on Forestry Practices 6.1 Enhancing germination rates through genetic insights Recent research has significantly advanced our understanding of the genetic mechanisms underlying seed germination, which has direct implications for improving germination rates in forestry practices. For instance, the study on scots pine (Pinus sylvestris L.) demonstrated that combining stratification/scarification with growth regulator treatments, such as gibberellic acid (GA3), indole-3-acetic acid (IAA), and 1-naphthaleneacetic acid (NAA), can significantly enhance germination rates and seedling development (Nawrot‐Chorabik et al., 2021). Additionally, the gene expression landscape of pine seedling tissues has been mapped, revealing core 'housekeeping genes' and tissue-specific expression profiles that are crucial for understanding the physiological processes during germination (Cañas et al., 2017). These insights can be leveraged to develop targeted treatments and breeding programs aimed at enhancing seed germination rates in forestry.
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