Forest biotechnology is rapidly advancing from conventional breeding toward molecular design, enabling the development of genetically modified trees (GMTs) with traits such as accelerated growth, stress resilience, and improved wood properties. This review systematically examines recent breakthroughs in tree genetic engineering, beginning with traditional methods and progressing to CRISPR-based precision editing and multi-omics-guided trait design. We highlight applications in wood quality (e.g., lignin reduction in Populus spp.), drought tolerance (e.g., PagHyPRP1 and PtoMYB142 editing), phytoremediation (e.g., heavy metal accumulation in poplar), and carbon sequestration. We also evaluate ecological and socio-regulatory challenges, including gene flow risks and public acceptance. Based on this integrated analysis, we outline future directions for responsible deployment of GMTs in sustainable forestry and global carbon neutrality efforts.

Low temperature is a major stress that severely affects tree growth and development. Despite the fact that the molecular mechanisms behind cold tolerance and associated regulatory networks in these trees remain largely unexplored, we conducted a study to examine the overall changes in metabolites and regulatory pathways of Populus ussuriensis kom. when exposed to cold stress, utilizing a comprehensive multi-omics approach. Transcriptomes exposed to cold stress reveal that most of the candidate genes related to the Calvin–Benson–Bassham cycle and flavonoid synthesis were upregulated. Joint analysis revealed that within 6–48 h of low-temperature treatment, differential genes (such as PAL and CHS) in the flavonoid biosynthesis pathway and metabolites (such as quercetin) were significantly upregulated, indicating a positive correlation under short-term stress. However, prolonged treatment (72 h) may trigger metabolic feedback, leading to a decrease in flavonoid content. In addition, the measurements of gas exchange and metabolite assays of P. ussuriensis showed that photosynthetic acclimation led to a change in the sugar accumulation and starch degradation in response to low temperature, indicating that extensive changes occurred due to the cold and improved tolerance in P. ussuriensis. This study provides a new basis for future studies on the molecular mechanism of cold tolerance at the transcriptional and metabolic levels.