Mapping and candidate gene screening of Cladosporium fulvum resistance gene Cf-12 in tomato (Solanum lycopersicum) by high-throughput sequencing

Tomato leaf mould disease is a serious foliar disease caused by Cladosporium fulvum, resulting in a significant reduction in yield and quality, especially under protected cultivation. Finding new resistant genes against leaf mould has become one of the important goals of tomato breeding. Cf-12-tomato showed good resistance to several C. fulvum races. The Cf-12 was mapped using re-sequencing and BSA methods. Allelism test for Cf-12, Cf-5 and Cf-9 was performed. The results showed that Cf-12 is an independently assigned C. fulvum resistance gene. About 67,853 high-quality polymorphic SNPs were found and 233 genes were annotated in three associated regions of 5.85 Mb on Chr. 6s. Three genes with typical Cf-type characters encoding the leucine-rich repeat receptor-like protein were screened out. Using qRT-PCR, structural and phylogenetic analysis, only the Solyc06g008265.1.1-CGN7495 was finally identified. An effective InDel marker, InD-3F/1R, was designed for MAS breeding. Our research provides new insights into the mapping of the Cf-12, and provides a basis for Cf-12 cloning and the Cf genetic evolution analysis.