Breeding for Nutritional Traits in Tomato Using Naturally Occurring Variation in the Fruit Specific Beta-Cyclase Promoter

High-throughput sequencing has expanded opportunities for allele discovery. The B gene of tomato (Solanum lycopersicum, L.) encodes lycopene-B-cyclase, the enzyme responsible for converting trans-lycopene to beta-carotene in the carotenoid biosynthesis pathway. Prior research suggested that variation in the promoter of the B gene may modulate beta-carotene levels in tomato fruit. We compared the promoter region of the B gene in 84 accessions and discovered more than 11 unique haplotypes, 9 of which occurred in high beta-carotene varieties. Association analysis suggested two Single nucleotide polymorphisms (SNPs) as likely candidates for the functional mutations conferring high beta-carotene. To test the effects of different alleles, insertion/deletion variation diagnostic for high beta-carotene was used to develop primers for marker-assisted backcrossing. Variation from the SolCAP 7,720 SNP array was assessed for polymorphism and genome coverage. A set of 96 SNPs spaced along all 12 chromosomes was developed for background genome selection to introgress distinct B alleles into elite processing tomato variety in order to assess functional differences. Different alleles allow the modulation of carotenoid production and provide plant genetic resources to assess bioavailability, bioaccessibility, and nutritional properties of carotenoids within a food matrix.