Forest trees still exist in an undomesticated stage and they carry a variety of wild and productive alleles. These genetic variations determine many traits of economic and ecological significance. The development of efficient DNA marker systems for genetic improvement of tree species would benefit from knowledge of genetic variability. Tree breeding projects aim to maximize the genetic gain for a variety of beneficial qualities. Genetic variability is the fundamental resource for the development of disease and pest resistant varieties and to create climate-ready tree types. Sequencing initiatives in woody perennials have increased dramatically as a result of remarkable developments in high-throughput sequencing technology and decreasing sequencing costs. Numerous genes that are activated as a result of stress responses, as well as their related signaling and regulatory networks, are identified and characterized using genomic technologies to comprehend the functional genetic architecture in trees. The development of superior planting stock with multiple traits would be accelerated by the convergence of conventional quantitative genetics and genomics-based selection. Further, integration of precision genome engineering approaches in conjunction with traditional genetic transformation methods are expected to hasten generation and delivery of improved planting stock in a short span of time.