Recent advances in sequencing technologies have resulted in the availability of whole genome sequences of a number of industrially important woody plants. As a result, many genetically engineered trees with superior traits have been produced. Various genetic engineering tools have been used to analyze such factors, and important target genes have been manipulated. A good understanding of the key genetics factors regulating the phenotypes involved in those processes is crucial. Various useful traits of woody plants have been investigated for sustainable production of biomass, bioremediation using trees, and improvements in the efficiency of energy production from woody plant materials. In addition, woody plants are a major biomass resource and are gaining attention as a source of biofuel. Woody plants are important components of the global ecosystem they play an important role in limiting emissions of carbon dioxide and other greenhouse gases, and the water-retaining capacity of forests is critical for flood control. We also discuss how these strategies can provide insights into molecular breeding technology for woody plants. This review provides an overview of the current status of genomics and genetic engineering of woody plants, and recent advances in genome editing technologies in plants as well as fungi. This is achieved using custom-designed endonucleases, which enable site-directed mutagenesis via a non-homologous end joining repair pathway and/or gene targeting via homologous recombination to occur efficiently at specific sites in the genome. A key step in genome editing is the generation of a double-stranded DNA break that is specific to the target gene. These are powerful tools with which targeted gene modifications can be introduced in various organisms, including various plant species. The DNA-binding domains of zinc finger (ZF) proteins were the first to be used as a genome editing tool, in the form of designed ZF nucleases and, more recently, transcription activator-like effector as well as the clustered, regularly interspaced, short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9) system that targets RNA–DNA rather than protein–DNA interactions have been used successfully. This is called “genome editing” and is used widely to modify the genome of various organisms. Engineered endonucleases that digest the specific sequences can be used to modify target genomes precisely.
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