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 highthroughput SNP technologies, the current IL collection contains a significantly lower number of smallersized, 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 Electronic supplementary material The online version of this article (

Genomic Tools for the Enhancement of Vegetable Crops: A Case in Eggplant

“…A reliable reference genome would indeed speed up the development and precision of these populations in eggplant. Barrantes et al (2014) developed most of the lines of an ILs between tomato and S. pimpinellifolium L. from a BC3S1 generation, four generations versus eight required to develop the set of ILs with S. incanum (Gramazio et al, 2016b). Both tomato and S. pimpinellifolium parents had advanced assemblies that allowed designing arrays to perform high-throughput genotyping since the early generations of ILs population development.…”

Genetics and Genomics of Cultivated Eggplants and Wild Relatives

“…Selection based just on genetic maps could under-represent telomeric regions and drag large centromeric regions (Wang et al, 2000), as happened in our case, while a selection based exclusively on physical maps tends to reduce the adequate marker density of high-recombination regions, running the risk of not detecting double recombinants and of overrepresenting centromeric regions (Barrantes et al, 2014), which is not cost-effective due to the low-recombination ratio. The most efficient approach for reducing the time for the IL population development, avoiding most of the non-target introgressions and double recombinants, and detecting regions undetected by low-medium genotyping, could be to perform high-throughput genotyping in the first cycles of backcrossing.…”

“…For other crops, where two or even three growing cycles per year are possible, the entire set of ILs could be obtained in three or four years (Eduardo et al, 2005;Barrantes et al, 2014). The strategy to bypassing the screening of the non-targeted chormosomes of the selected plants, even if it has the advantage of reducing the time and the cost for genotyping, increases the number of rounds of backcrosses required to recover the almost totality of the recipient parent background (Frisch et al, 1999).…”

“…The most efficient approach for reducing the time for the IL population development, avoiding most of the non-target introgressions and double recombinants, and detecting regions undetected by low-medium genotyping, could be to perform high-throughput genotyping in the first cycles of backcrossing. In this way, most of the ILs can be developed just in four generations, as was the case for Barrantes et al, (2014), who developed a set of tomato ILs with Solanum pimpinellifolium introgressions, where most of the lines derived from a BC3S1 generation. Even though a few years ago the cost of massive genotyping techniques was high and prohibitive for many labs, currently, the decreasing cost of sequencing and the emergence of new genotyping technologies, like GBS and similar (Campbell et al, 2015), have made the task of genotyping more affordable and precise.…”

“…Barrantes et al (2014) developed most of the lines of an ILs between tomato and S. pimpinellifolium L. from a BC3S1 generation, four generations versus eight required to develop the set of ILs with S. incanum (Gramazio et al, 2016b). Both tomato and S. pimpinellifolium parents had advanced assemblies that allowed designing arrays to perform high-throughput genotyping since the early generations of ILs population development.…”