Allele Mining: From Sequence Variation to Functional Evaluation in Tomato

The selection of new alleles imparting superior phenotypes is the goal of plant improvement. In tomato (Solanum lycopersicum, L.) there are potentially over 400 publically available re-sequenced genomes, including several wild relatives. These resources open the possibility of identifying novel alleles through sequence comparison. We have evaluated sequence variation for the Tm2^a resistance gene, disease resistance QTL, and structural genes and their cis-regulatory regions for the carotenoid biosynthesis pathway. The lack of structure-function information has made assessing the function of this variation problematic. In contrast, classical breeding approaches augmented by marker-assisted selection strategies have allowed us to rapidly assess the function of new alleles in uniform genetic backgrounds. This approach is facilitated by high density SNP data for over 1,000 tomato accessions, permitting market-class and pedigree based strategies to optimize polymorphic marker sets. Marker-assisted backcrossing leads to the selection of plants that share 93-98% of the recurrent parent in only two generations, permitting rapid phenotypic evaluation. Using this approach we have identified functional allelic variation for β-carotene (pro-vitamin A) content and identified superior QTL for resistance.