Advances in genomics-driven genetic decoding and genomic design breeding in tomato

Abstract Tomatoes are highly nutritious and represent one of the important vegetable fruits worldwide. Both historically and moving forward, genetic decoding and precision breeding remain fundamental to tomato improvement. Here, we summarize pivotal advances in decoding tomato genomes across domestication, improvement and evolution processes and provide a perspective on future breeding through precision design. In-depth population genetic studies have revealed how artificial selection systematically prioritized yield-related alleles at the cost of narrowing genetic diversity, especially at flavor-related loci–highlighting the urgent need to reconcile these trade-offs. Comparative genomics across species, viewed through an evolutionary lens, has uncovered critical insights into functional genes, deepening our understanding of the genetic architecture and regulatory mechanisms underlying key traits. Collectively, these advances have enabled precise identification and functional characterization of key genetic elements, paving the way for systematic re-domestication of tomato through precision genomic design. Looking ahead, more efficient and precise breeding strategies will be required to accelerate genetic gains in tomato in the coming decades. The integration of recent genomic advances, coupled with genomic selection and artificial intelligence, into genomic design breeding offers a transformative framework, unlocking unprecedented opportunities for developing highly flavorful and consumer-customized tomato varieties.