Variation in Lycopene Epsilon-Cyclase Gene in Selected Tomato Genotypes Revealed by EcoTILLING and Sequencing

Selected tomato genotypes with contrasting fruit colors of orange and red were investigated for sequence-level variations of candidate genes involved in lycopene cyclization. Sequence-specific markers for tomato lycopene beta-cyclase (3) and lycopene epsilon-cyclase (1) genes were designed and used to screen for putative single nucleotide polymorphisms (SNPs) through Ecotype Targeted Induced Local Lesions IN Genome (EcoTILLING) and Sanger sequencing. Despite being regarded as among the evolutionarily conserved genes in the carotenoid biosynthetic pathway of tomato, four homozygous and heterozygous SNPs were identified in lycopene epsilon-cyclase gene at the upstream of Exon 1 (1 SNP) and the intronic region between Exons 1 and 2 (3 SNPs) based on multiple sequence alignment of the processing tomato hybrid ‘Ilocos Red’ and table type inbred ‘Hawaii7996’. These SNPs may have a regulatory association with variations in tomato carotenoid metabolism. Interestingly, no sequence difference was found between FLA456 and ‘Super Apollo’ despite being characterized by orange and red fruit colors, respectively. The results support prior studies suggesting that lycopene cyclase genes are transcriptionally controlled as evidenced by their highly conserved sequences. The SNPs characterized in this study at the promoter and intronic regions of lycopene epsilon-cyclase are starting loci to investigate further the genetic control of this gene in regulating carotenoid metabolism and products that result in varying tomato fruit phenotypes.