Fig. 1 Representative CRISPR-Cas nucleases for plant applications A：Class Ⅱ type Ⅱ Cas9 nuclease guided by an engineered single gRNA（sgRNA）. SpCas9（Streptococcus pyogenes Cas9） recognizes a 5′-NGG PAM and its conserved histidine-asparagine-histidine（HNH）domain together with the recombination UV C（RuvC）nuclease domain mediates DSBs，generating blunt ends or 1-nucleotide 5′ overhangs. Such breaks are typically repaired by NHEJ，usually resulting in small InDels. B：Class Ⅱ type V Cas12a（Cpf1）nuclease guided by a single crRNA，which recognizes T-rich PAM sequences and，through its single RuvC domain，produces cohesive-end DSBs that predominantly give rise to intermediate-length deletions. C：Class Ⅱ type V Cas12b（C2c1）nuclease guided by an sgRNA，which targets T-rich PAM sequences and generates cohesive-end DSBs via a single RuvC domain，mainly inducing intermediate-length deletions. D：Class II type VI Cas13 nuclease，a crRNA-guided RNase that targets and degrades single-stranded RNA through its Helical-1 domain and higher eukaryotes and prokaryotes nucleotide binding（HEPN）domains

Fig. 2 Genome editing technologies derived from Cas nucleases in plants A：Cytosine base editors（CBEs）catalyse the conversion of cytosine（C）to uracil（U）. This U is recognised as T during DNA replication. Uracil glycosylase inhibitor（UGI）promotes C/G to T/A mutations. Should uracil-N-glycosylase（UNG）excise U，a deamination site is formed，potentially inducing C/G to G/C mutations. B：Adenine base editors（ABEs），which deaminate adenosine to inosine（I）. This I is recognised as G during replication，thereby achieving A/T to G/C mutations. If I is excised by N-methylpurine DNA glycosylase（MPG），this may result in A/T to C/G or A/T to T/A mutations. C：Epigenome engineering tools. By fusing dCas9 with epigenetic effectors[such as RNA-directed DNA methylase（RdDM）or JmjC-family histone demethylase（JMJ）]，it enables site-specific DNA and histone methylation modifications respectively；Whereas dCas13，fused with the METTL3（M3）-M14 complex，enables programmable N6-methyladenosine（m6A）modification of RNA. D：PE functions under（pegRNA）. Following nCas9 cleavage of the target DNA strand，the primer-binding sequence（PBS）within pegRNA hybridises with the 3' end of the cleavage site. This enables reverse transcriptase（RT）to transcribe the target editing sequence onto the 3' terminus of the target strand，using the reverse transcriptase template as a reference. The newly synthesised DNA strand forms a 3'-overhang，which is ultimately randomly integrated into the target site via cellular DNA repair mechanisms. E：PE technique combined with site-specific recombinases to achieve large-fragment DNA insertion：paired pegRNAs install recombination sites（RS）on the genome，and the recombinase mediates the site-specific insertion of target DNA at the RS

Fig. 3 Anthocyanin biosynthetic pathway and its key genes in editing of floral colour traits in ornamental plants（Mekapogu et al.，2023） Yellow and green backgrounds denote enzymes involved in the early and late stages of anthocyanin biosynthesis respectively. CHS：chalcone synthase；CHI：chalcone isomerase；F3H：flavone 3-hydroxylase；F3′H：flavonoid-3′-hydroxylase；F3′5′H：flavonoid-3′5′-hydroxylase；DFR：dihydroflavonol 4-reductase；ANS：anthocyanidin synthase；UFGT：UDP-glucose：flavonoid 3-O-glucosyltransferase. The dotted-line boxes indicating CHS，DFR and F3H denote flower colour-related genes that have been edited in ornamental plants. The colored backgrounds of cyanidin 3-glucoside，pelargonidin 3-glucoside，and delphinidin 3-glucoside represent their respective natural pigmentation

Fig. 4 Genetic regulatory mechanisms of flowering pathways in higher plants and its key genes in editing of flowering traits in ornamental plants（Blümel et al.，2015；Huang et al.，2025） The dotted-line boxes denote FD，TFL1 and FT，which are flowering integration genes already edited in ornamental plants

Fig. 5 Bottlenecks，strategies，and outcomes for enhancing CRISPR-Cas editing efficiency in floral trait improvement of ornamental plants