Genome engineering of woody plants: past, present and future

Abstract

Engineered endonucleases that digest the specific sequences can be used to modify target genomes precisely. This is called ''genome editing'' and is used widely to modify the genome of various organisms. 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. These are powerful tools with which targeted gene modifications can be introduced in various organisms, including various plant species. A key step in genome editing is the generation of a double-stranded DNA break that is specific to the target gene. 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. 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. We also discuss how these strategies can provide insights into molecular breeding technology for woody plants.

Induced Genetic Variations in Fruit Trees Using New Breeding Tools: Food Security and Climate Resilience

“…The genetic improvement of the tree plant genome can be accelerated through two distinct approaches: MAB through quantitative trait loci (QTL) mapping, and direct gene transfer through genetic engineering. The whole genomes of many tree plants have been completely sequenced; consequently, comprehensive genetic architecture of useful genetic traits are now available, which can be helpful for marker-assisted breeding, MAB [ 68 , 69 ]. The availability of such datasets can widely assist in genetic expression, and functional and comparative genomics.…”

Metabolic engineering in woody plants: challenges, advances, and opportunities

“…Utility of model systems and omics approaches in metabolic engineering of woody plants With the availability of various genetic, genomic, and biochemical tools, poplar have emerged as suitable model systems for woody plant biology, particularly for important tree-specific traits such as crown size, trunk diameter, and wood density. Multiple annotated, high coverage genome sequences exist for Populus species, such as P. trichocarpa, P. deltoides, P. tremula 9 alba hybrid, P. euphratica, and P. tremula (Osakabe et al 2016;Tuskan et al 2018). A subset of these genomes and a standardized gene expression atlas of P. trichocarpa are also integrated into the Phytozome platform for easier exploration (Goodstein et al 2012).…”

“…As a widely used gene editing technology, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR-Cas9) endonuclease systems have been used in woody plants such as poplar (Populus tomentosa Carr. ), mandarin orange (Citrus reticulata), apple, pear (Pyrus communis), and grape (Charrier et al 2019;Fan et al 2015;Osakabe et al 2016;Sandhya et al 2020;Wang et al 2018b). A great advantage of (modified) CRISPR-Cas9 is that multiple genes and gene homoeologs (in polyploid species) can be edited simultaneously in woody plants where pyramiding multiple gene mutations/overexpression by crossing is often not feasible (Armario Najera et al 2019).…”

The theory and applications of CRISPR in plant and tree improvement.

“…The genome sequence of the target plant is used to identify GE target(s) from which computational tools can design sgRNAs to maximise efficiency and minimise offtarget effects (1). The sgRNA and Cas cassettes are cloned into expression vectors or expressed in vitro and isolated as RNPs (2). Transformation of plant cells using agrobacterium, protoplasts or biolistics delivers the CRISPR/Cas toolkit (3).…”

“…By the year 2050, the global population is expected to increase from the current ~7.6 billion, to over 9 billion [1], placing additional strain on the earth's natural systems [2]. Woody plants play a crucial role in maintaining the stability of earth systems by limiting greenhouse gas emissions, retaining water (and so preventing flooding) and preserving diverse ecosystems, among others [2]. Trees such as eucalypt, poplar, and pines are widely planted and may provide both economic and ecological value.…”