Table 1 Seven of the whole genome sequenced threatened species successfully implemented genome editing (GE) by Agrobacterium or biolistic-mediated delivery, main purpose or motivation, GE tools, and conservation challenges and/or implications

Dendrobium officinale

CR

Orchidaceae

To reduce the lignocellulose content by knocking out genes in the lignocellulose biosynthesis pathway (C3H, C4H, 4CL, CCR, and IRX) [78]

CRISPR/Cas9

10–100^b

D. officinale has been one of the best herbal medicines and food in China and Korea, so wild individuals are rare due to overharvesting. Research is underway on the well-established transformation systems in D. officinale and the application of GE to create new varieties. Perhaps, in the face of future abiotic stress, established and secured GE techniques (e.g., knocking out deleterious genes, replacement of high temperature or drought resistance genes) may be needed for the conservation of remaining populations

Fraxinus nigra

CR

Oleaceae

To achieve transgene containment, reproductive sterility can be produced by disrupting the FnAG gene, which is involved in the development of floral organs [79]

CRISPR/Cas9

2^b

There has been a great demand for ash trees genetically engineered to be resistant to emerald ash borer. However, widespread acceptance and regulatory approval of transgenic trees has been limited due to concerns about transgene flow and potential impacts on the environment. Reproductive sterility achieved by disrupting flower development is one of several efficient strategies for gene containment in transgenic crops and trees. The conservation implications of this approach would include mitigating local ecosystem disturbances

Eucalyptus urophylla

EN

Myrtaceae

To prevent sexual dispersal by pollen and induce male sterility for hybrid breeding by knocking out one involved in meiosis (EREC8) and two regulating early stages of pollen development (ETDF1 and EHEC3‐like). Note that the GE species is the hybrid Eucalyptus grandis x E. urophylla [80]

CRISPR/Cas9

73–100^b

Eucalyptus commonly spreads beyond exotic forest plantations into wild ecosystems, where it could outcompete native trees, reduce water availability, damage local biodiversity, and disturb local ecosystems. Tools to mitigate spread, such as male and/or complete sterility, may be crucial for ecosystem conservation and sustainability and could protect endangered eucalyptus

Taxus chinensis

EN

Taxaceae

To control paclitaxel biosynthesis by knockdown of PAL gene [81]

CRISPR-guided DNA methylation

Note that there was a 61% increase of DNA methylation in the 5′-UTR region of PAL gene which resulted in approximately a 25-fold increase in paclitaxel accumulation^c

Manipulating phenylpropanoid biosynthesis in Taxus species using GE techniques is highly effective in increasing taxane production. If problems with biometabolism may arise in the future probably caused by abiotic factors, newer approaches based on these techniques could be used for in situ and ex situ conservation of this endangered species

Vanilla planifolia

EN

Orchidaceae

To enable targeted domestication of vanilla and to demonstrate it by knocking out the PDS gene that is vital to plastid development and chlorophyll biosynthesis [82]

CRISPR/Cas9

92^b

Successful GE of the V. planifolia PDS gene may pave the way for genetic improvements of domestication traits (e.g., dehiscence of fruits, aroma, disease resistance, and stress tolerance). Interested researchers could manipulate from dry and dehiscent nonaromatic fruits to aromatic indehiscent ones using GE technology. Recent studies have shown that wild indehiscent Neotropical Vanilla fruits are dispersed by mammals [83]. From a conservation perspective, researchers may use GE techniques if populations of these species have dehiscent fruits due to environmental factors. [This approach may require caution because, in indehiscent Neotropical Vanilla, individuals with dehiscent fruits may have lower fitness than indehiscent individuals]

Dionaea muscipula

VU

Droseraceae

To test whether mechanosensitive ion channel genes control the Venus flytrap’s hunting behavior by knocking out hair-expressed MscS-like genes (FLYC1 and FLYC2) [84]

CRISPR/Cas9

Not available

How does the Venus flytrap detect animal prey for nutrients? How will the mechanosensory ion channels respond due to probable environmental change? As for conservation implications, if some carnivorous plants have problems with their mechanosensory ion channels due to probable environmental factors and their leaves do not function properly, the CRISPR-Cas9 system can be used to enable normal responses

Gossypium hirsutum

VU

Malvaceae

To facilitate cotton molecular breeding by precisely targeted insertion of additional trait (herbicide tolerance) genes (hppd, epsps) using re-engineered meganuclease; to improve the abiotic stress tolerance in cotton by knocking out eleven genes (GhPDS, GhCLA1, GhEF1, GhVP, GhARG, GhMYB25-like A, GhMYB25-like D, and GoPGF); to promote cotton hybrid breeding by knocking out potential male sterility-related genes to establish gene editing systems using CRISPR/Cas9; and to demonstrate them by knocking out above eleven genes [85,86,87]

Homologous recombination-mediated targeted insertion (gene stacking) using COT-5/6 meganuclease; CRISPR/Cas9; CRISPR/LbCpf1; CRISPR/Cas12b

48–100^b

Wild species of Gossypium serve as a reservoir of genetic variation for resistance to pests and diseases, as well as tolerance to abiotic stresses [88]. Using genome information in the useful agronomic traits of these species, to develop agronomic and quality traits for cultivated cotton, multi-trait genes are developed for introgressions such as herbicide tolerance, pest (e.g., nematodes, aphids, and spider mites) and disease (e.g., leaf curl virus, Fusarium and Verticillium wilts) resistance, abiotic stress (e.g., mild frost, drought, and salinity) tolerance, and yield enhancement. These GE techniques could be applied to conserve and preserve (e.g., buffering population decline due to climate change) wild populations of G. hirsutum, growing wild in its native Central America, the most widely cultivated species among 53 Gossypium species