Virus-mediated, heritable gene editing in groundcherry (Physalis grisea)

Virus-induced gene editing (VIGE) provides a powerful alternative to conventional plant genome engineering by enabling in planta delivery of genome-editing reagents without repeated use of tissue culture. Here, we establish Tobacco rattle virus (TRV)-mediated VIGE as an efficient system for somatic and heritable genome editing in groundcherry (Physalis grisea).

Using Cas9-expressing plants, we targeted the visual marker gene PHYTOENE DESATURASE (PDS) and the domestication gene CLAVATA1 (CLV1) via TRV-mediated delivery of guide RNAs. Editing efficiencies were evaluated in somatic tissues and across progeny to assess heritability.

Targeting of PDS resulted in somatic editing frequencies of 80-95% and consistent recovery of heritable edits, with all infected plants (n = 5) producing edited progeny, including fully albino seedlings carrying frameshift mutations in all alleles. The primary Cas9-expressing line was unexpectedly tetraploid, likely due to genome duplication during tissue culture. Despite this, VIGE efficiently generated mono-, bi-, tri-, and tetra-allelic mutations, demonstrating robust editing across four alleles simultaneously. Targeting of CLV1 achieved somatic editing frequencies of up to 73%, with 60% of T0 plants producing heritable edits. Edited plants exhibited increased floral organ number and multilocular fruits, consistent with CLV1 loss-of-function phenotypes.

These results demonstrate that VIGE enables rapid, efficient, and heritable genome editing in groundcherry, even in a tetraploid context, highlighting its potential to accelerate genetic improvement and de novo domestication of underutilized crops.