Analysis and fine mapping of a gene controlling the folded-leaf phenotype of a mutant tomato line

Tomato (Solanum lycopersicum L.) is one of the most popular cultivated vegetables worldwide. Tomato leaves are determinate organs with important functions affecting plant growth and development. In addition to the other leaf phenotypes, folded leaves have recently been observed in several tomato varieties. In the present study, an F2 population was generated from a cross between tomato inbred lines 14g-677 (i.e., folded leaves) and 14g-683 (i.e., wild-type leaves). A genetic analysis of the folded-leaf trait in 199 F2 individuals revealed this leaf phenotype is controlled by a single recessive gene, which was designated as fl. This gene was initially localized to chromosome 11 based on insertion/deletion (InDel) markers and a bulked segregant analysis (BSA). According to a genetic map consisting of new markers and recombinants, the fl gene was mapped between the SNP-1 and dcaps-10 markers at the distal end of the long arm of tomato chromosome 11. The physical distance between the two markers was approximately 62.2 kb. The annotation and functional characterization of the genes in this region indicated fl may be ARF4, which encodes an auxin response factor. A sequence analysis revealed that the ARF4 of line 14g-677 is missing a single C in the third exon region. Furthermore, a quantitative real-time polymerase chain reaction detected an approximate fourfold difference in ARF4 transcript abundance between lines 14g-677 and 14g-683. Thus, a mutation to ARF4 is likely responsible for the folded-leaf phenotype of tomato mutants.