Gene editing in tree and clonal crops: progress and challenges

Abstract

Because of the limitations inherent in conventional breeding of trees and clonally propagated crops, gene editing is of great interest. Dozens of published papers attest to the high efficiency of CRISPR-based systems in clonal crops and trees. The opportunity for “clean” edits is expected to avoid or reduce regulatory burdens in many countries and may improve market acceptance. To date, however, nearly all studies in trees and clonal crops retained all of the gene editing machinery in the genome. Despite high gene editing efficiency, technical and regulatory obstacles are likely to greatly limit progress toward commercial use. Technical obstacles include difficult and slow transformation and regeneration, delayed onset of flowering or clonal systems that make sexual segregation of CRISPR-associated genes difficult, inefficient excision systems to enable removal of functional (protein- or RNA-encoding) transgenic DNA, and narrow host range or limited gene-payload viral systems for efficient transient editing. Regulatory obstacles include those such as in the EU where gene-edited plants are regulated like GMO crops, and the many forms of method-based systems that regulate stringently based on the method vs. product novelty and thus are largely applied to each insertion event. Other major obstacles include the provisions of the Cartagena Protocol with respect to international trade and the need for compliance with the National Environmental Policy Act in the USA. The USDA SECURE act has taken a major step toward a more science- and risk-based—vs. method and insertion event based—system, but much further regulatory and legal innovation is needed in the USA and beyond.

Haplotype-resolvedde novogenome assemblies of four coniferous tree species

“…Genome prediction might be another powerful tool for the selection of elite tree lines from breeding programs (Lebedev et al 2020; Grattapaglia 2022), which usually require a long time. In addition, gene editing technology could also be used as an effective breeding strategy for shortening the duration of tree breeding programs (Bewg et al 2018; Goralogia et al 2021).…”

Lignin engineering in forest trees: From gene discovery to field trials

“…Once elite genotypes have been generated by classical breeding, use of these modern breeding techniques enables them to be further improved without breaking up their genetic constitution. Moreover, these techniques enable the introduction of traits that are not present in the species and the generation of allelic variants that are absent or rare in the population ( Goralogia et al., 2021 ). Use of transgenes enables alteration of target gene expression levels and introduction of genes from pathways that are not found in natural populations.…”

From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees

“…Especially, it would be worth testing whether other CRISPR/Cas12a variants that have recently been discovered and newly developed in rice [154,155] could be harnessed to efficiently generate genome-modified trees. In general, the Cas12a-induced mutations were mainly large deletions in the biallelic, non-mosaic state, suggesting a highly suitable tool for genome editing in forest trees for which the self-pollination practice for screening of the desired homozygous progeny is often very difficult (i.e., due to the time delay to onset of flowering, or intolerance of inbreeding [156]).…”

“…Given that the host range of SYNV and PVX is limited, an extensive search for viruses with similar cargo capacity but that are broadly compatible is needed. The optimization of CRISPR-based genome editing protocols to achieve transgenefree trees will facilitate the rapid deployment where DNA-free editing is not regulated as a GMO (for current regulations of CRISPR-edited plants, read reviews [156,211,212]). Furthermore, in the case where gene flow and seed/pollen dispersal from CRISPR-edited plantation plants to natural populations need to be prevented, full sterile trees (e.g., by knock-out the floral homeotic gene AGAMOUS (AG) and its close homologues [213][214][215]) with desired traits can be vegetatively propagated by the forest or horticulture industries.…”