Tree Genetics and Molecular Breeding 2024, Vol.14, No.3, 119-131 http://genbreedpublisher.com/index.php/tgmb 120 2 Advances in Gene Identification Technologies 2.1 Evolution of gene identification methods from traditional to modern techniques Historically, gene identification in trees relied heavily on traditional methods such as phenotypic selection and classical breeding techniques. These approaches, while effective to some extent, were time-consuming and limited by the complex genetic architecture of trees. The advent of molecular markers, such as RFLP (Restriction Fragment Length Polymorphism) and SSR (Simple Sequence Repeats), marked a significant leap forward, allowing for the identification of specific regions of the genome associated with stress resistance traits. As technology progressed, marker-assisted selection (MAS) became a critical tool in forestry, enabling more precise and faster breeding decisions. However, the true revolution in gene identification came with the development of high-throughput genomic technologies, which have dramatically accelerated the discovery of stress resistance genes. Genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping have become standard methods for linking genetic variation with stress resistance traits in trees, providing a more comprehensive understanding of the underlying genetics (Younessi-Hamzekhanlu and Gailing, 2022). 2.2 Current state-of-the-art technologies: genomic sequencing, CRISPR, and beyond Today, the field of gene identification in trees is dominated by state-of-the-art technologies that offer unprecedented precision and efficiency. Next-generation sequencing (NGS) has revolutionized genomics by allowing for the rapid and cost-effective sequencing of entire tree genomes. This has enabled researchers to identify stress resistance genes at a much finer scale, facilitating the development of more resilient tree species. CRISPR-Cas9 gene editing technology represents another transformative advancement. This technology allows for the precise modification of specific genes, enabling the direct manipulation of genetic pathways involved in stress resistance. CRISPR has been used to enhance traits such as drought tolerance and disease resistance in various tree species, offering a powerful tool for improving forest sustainability (Cao et al., 2022). In addition to NGS and CRISPR, emerging technologies such as transcriptomics and epigenomics are expanding our understanding of gene expression and regulation in response to environmental stressors. These technologies allow for the exploration of how genes are turned on or off in response to stress, providing insights that are critical for developing trees that can better withstand the challenges posed by climate change (Naidoo et al., 2019). 2.3 Challenges and limitations in current gene identification methods Despite the significant advances in gene identification technologies, several challenges and limitations remain. One of the primary challenges is the complex and often polygenic nature of stress resistance traits in trees. Unlike annual crops, trees have long lifecycles and large genomes, which complicate the identification of specific genes responsible for stress tolerance. Moreover, environmental factors can greatly influence gene expression, making it difficult to isolate genetic effects from environmental ones (Guevara-Escudero et al., 2021). Another limitation is the current reliance on model species and limited genetic diversity in gene editing studies. Many CRISPR-based studies focus on a few model tree species, which may not fully capture the genetic diversity found in natural forest populations. This can limit the applicability of findings to other species or environments. Additionally, while CRISPR technology holds great promise, its application in forestry is still in its infancy, and large-scale field studies are needed to validate the effectiveness of edited genes under natural conditions (Polle et al., 2019). 3 Genetic Basis of Stress Resistance in Trees 3.1 Key genes involved in drought, cold, and salt resistance Several key genes have been identified as playing crucial roles in enabling trees to tolerate drought, cold, and salt stresses. For instance, the ICE (Inducer of CBF Expression) gene family is known for its involvement in cold and drought tolerance. In Malus baccata, the gene MbICE1 has been shown to enhance drought and cold resistance by regulating antioxidant capacity and stress-responsive genes (Duan et al., 2022). Similarly, the SnRK1 (Sucrose
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