Comparison of a set of allelic QTL-NILs for chromosome 4 of tomato: Deductions about natural variation and implications for germplasm utilization

Quantitative Trait Locus (QTL) allelic variation was studied by analyzing near-isogenic lines (NILs) carrying homologous introgressions on chromosome 4 from three green-fruited wild tomato species. The NILs affect agronomic (yield, brix, fruit weight) and fruit (fruit shape, color, epidermal reticulation) traits in a similar manner. However, significant differences were detected in the magnitudes of the effects, the dominance deviations and epistatic interactions, indicating that those species carry different alleles for the QTL. As the QTL did not show any interaction across environments, genetic backgrounds or other QTLs, it can be used to introduce novel genetic variation into a broad range of cultivars. Analysis of new recombinant NILs showed that fruit traits are controlled by several linked genetic loci, whereas multiple genetic loci control the agronomic traits within the original introgression. The hypothesis that QTLs may be composed of multiple linked genes can not be rejected prior to implement projects for QTL isolation and cloning. Loci involved in color enhancement could not be related to any known gene involved in the carotenoid biosynthesis pathway, therefore it is hypothesized that the function of those loci must be related to the genetic regulation of the carotenoid biosynthetic pathway.