Revolutionizing the tomato cultivation: advances and frontiers in virus-resistant tomato breeding

Plant viruses are major pathogens that significantly reduce the quality and yield of tomato crops. The most influential viruses belong to the genera Crinivirus, Begomovirus, Tobamovirus, and Potyvirus. Tomato breeders have successfully incorporated virus-resistance genes, such as Ty, Sw, Tm, and Pot 1, from wild germplasms into cultivated varieties. However, the challenge remains that most resistance genes confer only qualitative resistance, making them vulnerable to new viruses, recombination, and mixed infections. To our knowledge, this review is the first to systematically compare the synergy and complementarity among three antiviral breeding strategies—conventional R-gene pyramiding (e.g. Ty, Sw, Tm), RNA interference (RNAi)-based transgenics, and CRISPR/Cas genome editing—in tomato. We also innovatively incorporate the emerging genus Amalgavirus into the antiviral framework and propose targeted countermeasures against its escape mechanisms, including synthetic NLR decoys and Cas13-mediated transcriptional degradation. Using the three breeding methodologies, we concluded by outlining the difficulties and offering recommendations for future improvements in tomato antiviral breeding.