Rapid Assessment of Novel Alleles and QTL through Background Genome Selection: From Sequence Variation to Functional Characterization in Tomato

The selection of novel alleles with superior phenotypes based on sequence comparison remains problematic without more complete information about the structural or regulatory consequences of variation. With over 400 sequenced genomes available for tomato (Solanum lycopersicum, L.) and several wild relatives, identification of new alleles for structural genes or regulatory regions is straight-forward. Assessing the function of this variation remains problematic. Classical breeding approaches augmented by marker-assisted selection strategies offer a means to rapidly assess the function of new alleles in uniform genetic backgrounds. We use the competitive allele specific primer extension (KASP™ ) genotyping technology to implement a marker-assisted (MAS) backcross breeding scheme leveraging genome-wide SNPs to rapidly develop genetic resources containing different QTL for disease resistance or alleles of the high β-carotene (B) promoter in a uniform genetic background. 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. The flexibility of the KASP™ platform then allows for marker sets to be modified from one generation to the next in order to optimize informative data points. In our experience, marker-assisted backcrossing leds 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 bacterial spot resistance.