Abstract

BackgroundDecades of intensive tomato breeding using wild-species germplasm have resulted in the genomes of domesticated germplasm (Solanum lycopersicum) being intertwined with introgressions from their wild relatives. Comparative analysis of genomes among cultivated tomatoes and wild species that have contributed genetic variation can help identify desirable genes, such as those conferring disease resistance. The ability to identify introgression position, borders, and contents can reveal ancestral origins and facilitate harnessing of wild variation in crop breeding.ResultsHere we present the whole-genome sequences of two tomato inbreds, Gh13 and BTI-87, both carrying the begomovirus resistance locus Ty-3 introgressed from wild tomato species. Introgressions of different sizes on chromosome 6 of Gh13 and BTI-87, both corresponding to the Ty-3 region, were identified as from a source close to the wild species S. chilense. Other introgressions were identified throughout the genomes of the inbreds and showed major differences in the breeding pedigrees of the two lines. Interestingly, additional large introgressions from the close tomato relative S. pimpinellifolium were identified in both lines. Some of the polymorphic regions were attributed to introgressions in the reference Heinz 1706 genome, indicating wild genome sequences in the reference tomato genome.ConclusionsThe methods developed in this work can be used to delineate genome introgressions, and subsequently contribute to development of molecular markers to aid phenotypic selection, fine mapping and discovery of candidate genes for important phenotypes, and for identification of novel variation for tomato improvement. These universal methods can easily be applied to other crop plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0287-2) contains supplementary material, which is available to authorized users.

Highlights

  • Decades of intensive tomato breeding using wild-species germplasm have resulted in the genomes of domesticated germplasm (Solanum lycopersicum) being intertwined with introgressions from their wild relatives

  • The findings provide insight into the genome structure of tomato inbreds derived from a breeding program, and demonstrate how breeding can greatly benefit from whole-genome sequencing (WGS), which can diminish time consuming phenotypic screening

  • Detection of putative introgressions To identify potential introgressions, we identified Single nucleotide polymorphism (SNP) between Gh13 and the reference genome, and discovered regions that were significantly different from the reference genome

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Summary

Introduction

Decades of intensive tomato breeding using wild-species germplasm have resulted in the genomes of domesticated germplasm (Solanum lycopersicum) being intertwined with introgressions from their wild relatives. Comparative analysis of genomes among cultivated tomatoes and wild species that have contributed genetic variation can help identify desirable genes, such as those conferring disease resistance. Tomato (Solanum lycopersicum) is an important food crop and a model species for studying processes such as fleshy fruit ripening, fruit development [1], and the molecular basis of disease resistance [2,3]. Tomato originated in the South American Andean mountains, deserts, and coastal plains [4]. During the species such as Solanum chilense [10,11,12], S. peruvianum [13,14,15], S. habrochaites [16], S. pennellii [17], and S. pimpinellifolium [7,18]. At least four loci have been introgressed into tomato from three accessions of S. chilense and S. habrochaites [11,16,21,23]

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