Highly efficient genomics-assisted development of a library of introgression lines of Solanum pimpinellifolium

Abstract

The Solanum pimpinellifolium L. accession TO-937 is resistant to pests due to the presence of type IV glandular trichomes and also has the potential to increase fruit quality traits in tomato cultivars. This accession was selected to develop a genomic library of introgression lines (IL) in the genetic background of tomato cultivar "Moneymaker." In order to increase the accuracy and speed of the IL development process, high-throughput single-nucleotide polymorphism (SNP) genotyping steps were performed in early backcross generations. Five to seven generations were needed to complete the final set of 53 ILs that were characterized with the 8K SNP SOLCAP Infinium array, which demonstrated that the introgressions present in the IL set covered 94 % of the donor genome and that each IL contained an average of 4.25 % (25 Mb) of the donor genome, defining 71 bins of about 10 Mb on average. Additionally, 37 previously undetected, unwanted introgressions were also detected, and most of them very small (< 2 Mb), probably due to double recombination events among the markers used during IL development. Compared to other IL collections recently characterized with high-throughput SNP technologies, the current IL collection contains a significantly lower number of smaller-sized, non-selected introgressions. The combination of several steps of high-throughput genotyping at early generations and the relatively large population size allowed us to construct a collection of ILs with an extraordinary genetic background isogenicity in a relatively short period of time.