Tomato fruit as a model for tissue-specific gene silencing in crop plants

Authors: FEDER, ARI - Boyce Thompson Institute; JENSEN, SARAH - Cornell University; WANG, ANQUAN - Boyce Thompson Institute; COURTNEY, LANCE - Cornell University; MIDDLETON, LESLEY - Boyce Thompson Institute; VAN ECK, JOYCE - Boyce Thompson Institute; LIU, YONGSHENG - Hefei University Of Technology; Giovannoni, James

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/11/2020
Publication Date: 12/19/2020
Citation: Feder, A., Jensen, S., Wang, A., Courtney, L., Middleton, L., Van Eck, J., Liu, Y., Giovannoni, J.J. 2020. Tomato fruit as a model for tissue-specific gene silencing in crop plants. Horticulture Research. 7:142. https://doi.org/10.1038/s41438-020-00363-4.
DOI: https://doi.org/10.1038/s41438-020-00363-4

Interpretive Summary: Given the importance of fruit biology to human food and nutritional security, we have driven gene editing via a fruit-specific promoter, enabling generation of plants with fruit-specific gene editing inherited through the next generation. Assessment of this technology was performed through fruit-specific gene editing of a constitutively expressed GFP (green fluorescent protein) transgene in addition to the SlEZ2 gene sequence. Comparison of SlEZ2 silencing to previous whole plant RNAi-mediated silencing both clarified the interpretation of prior results and suggests an additional role in fruit maturation. The fruit genome editing platform presented here should prove an effective tool facilitating the bypass of detrimentaleffects of genes involved in fruit biology when edited in all tissues.

Technical Abstract: Use of genome editing has proliferated for use in numerous plant species to modify gene function and expression, usually in the context of either transient or stably inherited genetic alternations. While extremely useful in many applications, modification of some loci yields outcomes detrimental to further experimental evaluation or viability of the target organism. Expression of Cas9 under a promoter conferring gene knockouts in a tissue-specific subset of genomes has been demonstrated in insect and animal models, and recently in Arabidopsis. We developed an in planta GFP (green fluorescent protein) assay system to demonstrate fruit-specific gene editing in tomato using a phosphoenolpyruvate carboxylase 2 gene promoter. We then targeted a SET-domain containing polycomb protein, SlEZ2, previously shown to yield pleiotropic phenotypes when targeted via 35S-driven RNA interference and we were able to characterize fruit phenotypes absent additional developmental perturbations. Tissue-specific gene editing will have applications in assessing function of essential genes otherwise difficult to study via germline modifications and will provide routes to edited genomes in tissues that could not otherwise be recovered when their germline modification perturbs their normal development.