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Article|19 Sep 2022|OPEN
Recoloring tomato fruit by CRISPR/Cas9-mediated multiplex gene editing
Tianxia Yang1,2,6 , Muhammad Ali1,2,6 , Lihao Lin1,2,6 , Ping Li3 , Hongju He4 , Qiang Zhu1,2 , Chuanlong Sun1,2 , Ning Wu1,2 , Xiaofei Zhang1,2 , Tingting Huang3 , Chang-Bao Li5 , Chuanyou Li1,2 , , Lei Deng,1,2 ,
1State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
2CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
3Institute of Vegetable, Qingdao Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
4Institute of Agri-food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
5Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
6Equal contribution
*Corresponding author. E-mail:,

Horticulture Research 10,
Article number: uhac214 (2023)
Views: 329

Received: 15 Jul 2022
Accepted: 14 Sep 2022
Published online: 19 Sep 2022


Fruit color is an important horticultural trait, which greatly affects consumer preferences. In tomato, fruit color is determined by the accumulation of different pigments, such as carotenoids in the pericarp and flavonoids in the peel, along with the degradation of chlorophyll during fruit ripening. Since fruit color is a multigenic trait, it takes years to introgress all color-related genes in a single genetic background via traditional crossbreeding, and the avoidance of linkage drag during this process is difficult. Here, we proposed a rapid breeding strategy to generate tomato lines with different colored fruits from red-fruited materials by CRISPR/Cas9-mediated multiplex gene editing of three fruit color-related genes (PSY1MYB12, and SGR1). Using this strategy, the red-fruited cultivar ‘Ailsa Craig’ has been engineered to a series of tomato genotypes with different fruit colors, including yellow, brown, pink, light-yellow, pink-brown, yellow-green, and light green. Compared with traditional crossbreeding, this strategy requires less time and can obtain transgene-free plants with different colored fruits in less than 1 year. Most importantly, it does not alter other important agronomic traits, like yield and fruit quality. Our strategy has great practical potential for tomato breeding and serves as a reference for improving multigene-controlled traits of horticultural crops.