Managing Trait Trade-Offs in Tomato Breeding Through Genome Editing

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.