A dominant mutation in tomato DNA POLYMERASE DELTA 1 causes geminivirus DNA replication catastrophe

Geminiviruses pose a severe threat to grain and vegetable crops worldwide, often resulting in significant economic losses. In cultivated tomato (Solanum lycopersicum), Ty resistance alleles have been introduced from wild tomato relatives, providing partial to strong resistance to geminivirus infections. The Ty-6 resistance locus from Solanum chilense was previously mapped to chromosome 10. It was recently shown to contain a mutant allele of the DNA POLYMERASE DELTA 1 (POLD1) gene that provides resistance to Tomato yellow leaf curl virus (TYLCV) infections. However, the resistance mechanism remained unknown. Here, we report another POLD1 allele at the Ty-6 locus of S. chilense with an E622D mutation in the catalytic site of the POLD1 protein. POLD1^E622D is maintained as a heterozygous dominant allele in S. chilense and the AVTO2225 breeding line. It provides full resistance to the severe TYLCV Thailand (TYLCTHV) strain. The E622D amino acid change does not alter the predicted structure of POLD1. Replication of the TYLCTHV genome in plants carrying the POLD1^E622D allele is severely compromised by a high frequency of mutations that accumulate in viral DNA, which results in nonfunctional proteins that are essential for continuous viral replication. Ectopically expressing the POLD1^E622D allele cDNA alone causes mutations in TYLCTHV genes in inoculated leaves. S. chilense and AVTO2225 plants carrying the POLD1^E622D allele mount a hypersensitive response after TYLCTHV infection, indicating that the defective virus genome cannot suppress the plant defense. The dominant POLD1^E622D allele is therefore an effective resistance gene that geminiviruses cannot overcome.