Managing Trait Trade-Offs in Tomato Breeding Through Genome Editing.
- 1Department of Molecular Genetic Engineering, Dong-A University, Busan 49315, Republic of Korea.
- 2Department of Microbiology, Thiagarajar College, Madurai 625009, Tamil Nadu, India.
- 3National Center of Excellence in Statistical and Mathematical Modelling on Bio-Resources Management, Thiagarajar College, Madurai 625009, Tamil Nadu, India.
Abstract
Tomato improvement often involves trade-offs between fruit yield and quality, sweetness and fruit size, disease resistance and growth, reproductive performance and stress adaptation, and shelf life and flavour. Although CRISPR-Cas-mediated genome editing enables targeted modification of tomato genes, DNA-level precision does not guarantee an agronomically favourable phenotype because pleiotropy, functional redundancy, allele dosage, linkage, epistasis, genetic background, and environmental conditions can alter editing outcomes. This review evaluates genome editing as a strategy to manage, rather than merely document, these trade-offs. We examine how knockout, multiplex, cis-regulatory, base, prime, and direct allele-repair approaches can match the causal architecture of a breeding constraint. We critically assess representative studies involving plant architecture, reproductive development, fruit size, sugar accumulation, ripening, nutritional composition, disease resistance, and heat resilience, with an emphasis on heritability, molecular identity, multi-trait effects, and agronomic penalties. We further consider domestication-associated variation, structural variation, transformation and regeneration limitations, genotype-by-environment interactions, breeding deployment, and regulatory translation. We propose a trade-off-aware framework that links causal-allele identification, mechanism-matched editing, quantitative allele design, multidimensional phenotyping, and validation across generations, genetic backgrounds, and production-relevant environments. This framework can guide the development of balanced, breeding-ready tomato cultivars rather than lines optimized for a single trait.
Related
- Whole genome resequencing in tomato reveals variation associated with introgression and breeding events
- Phenotype rescue through the restoration of full-length dystrophin using CRISPR/Cas9 genome editing in Duchenne muscular dystrophy patient-derived iPSCs carrying the deletion of two exons
- LiP-MS reveals a feedback loop of tomato UDP-glucosyltransferases managing bioactive jasmonate homeostasis
- A highly contiguous genome assembly of Cyclamen persicum to accelerate functional genomics and breeding
- Short TALE-binding domains enable mitochondrial genome editing in Arabidopsis thaliana
BibTeX
@article{chae2026managing,
title = {{Managing Trait Trade-Offs in Tomato Breeding Through Genome Editing.}},
author = {Jia Chae and Seong Ju Han and Hye Jeong Kim and Jee Hye Kim and Hyeon Ju Nam and Young-Soo Chung and Sivabalan Karthik and Jae Bok Heo},
journal = {Plants (Basel, Switzerland)},
year = {2026},
month = sep,
doi = {10.3390/plants15192994},
url = {https://europepmc.org/article/MED/42884858},
note = {CC BY},
}
RIS
TY - JOUR
TI - Managing Trait Trade-Offs in Tomato Breeding Through Genome Editing.
AU - Jia Chae
AU - Seong Ju Han
AU - Hye Jeong Kim
AU - Jee Hye Kim
AU - Hyeon Ju Nam
AU - Young-Soo Chung
AU - Sivabalan Karthik
AU - Jae Bok Heo
PY - 2026
DA - 2026/09/30
JO - Plants (Basel, Switzerland)
DO - 10.3390/plants15192994
UR - https://europepmc.org/article/MED/42884858
AB - Tomato improvement often involves trade-offs between fruit yield and quality, sweetness and fruit size, disease resistance and growth, reproductive performance and stress adaptation, and shelf life and flavour. Although CRISPR-Cas-mediated genome editing enables targeted modification of tomato genes, DNA-level precision does not guarantee an agronomically favourable phenotype because pleiotropy, functional redundancy, allele dosage, linkage, epistasis, genetic background, and environmental conditions can alter editing outcomes. This review evaluates genome editing as a strategy to manage, rather than merely document, these trade-offs. We examine how knockout, multiplex, cis-regulatory, base, prime, and direct allele-repair approaches can match the causal architecture of a breeding constraint. We critically assess representative studies involving plant architecture, reproductive development, fruit size, sugar accumulation, ripening, nutritional composition, disease resistance, and heat resilience, with an emphasis on heritability, molecular identity, multi-trait effects, and agronomic penalties. We further consider domestication-associated variation, structural variation, transformation and regeneration limitations, genotype-by-environment interactions, breeding deployment, and regulatory translation. We propose a trade-off-aware framework that links causal-allele identification, mechanism-matched editing, quantitative allele design, multidimensional phenotyping, and validation across generations, genetic backgrounds, and production-relevant environments. This framework can guide the development of balanced, breeding-ready tomato cultivars rather than lines optimized for a single trait.
SN - 2223-7747
ER -