Advanced backcross QTL analysis in a Solanum lycopersicum x Solanum habrochaites (acc. LA1721) cross

Advanced backcross QTL (AB-QTL) analysis is a mapping strategy that integrates the process of QTL discovery with variety development, by simultaneously identifying and transferring useful QTL alleles from unadapted (e.g., land races, wild species) to elite germplasm, thus broadening the genetic diversity available for breeding. In this study the AB-QTL method was used to explore the potentials of Solanum habrochaites acc. LA1721 as a source of valuable QTL alleles for productivity and fruit quality traits. A total of 88 PCR-based markers (45 CAPSs and 43 SSRs) were developed and used to genotype a population of 199 BC2 plants, derived from a S. lycopersicum TA496 x LA1721 cross. Phenotypic data for 13 yield, processing and fruit-appearance traits were collected from 199 BC2F1 families, which were grown in replicated field trials in two different locations in California. Significant QTL were identified for all traits, for a total of 99 putative QTL, ranging from a minimum of 3 QTL detected for firmness to a maximum of 15 QTL found for fruit weight. A total of 55 (56%) of these QTL were conserved across locations. At 47 loci (48%), corresponding to seven traits (54%), the trait-improving allele originated from the wild parent, despite the overall inferior phenotype of S. habrochaites. QTL alleles that could be targeted for marker-assisted breeding for improving traits of economic importance were identified. This work extends tomato AB-QTL analysis to a second S. habrochaites accession, for a total of six different tomato wild species sampled so far.