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Background    Solanum pimpinellifolium  has high breeding potential for fruit quality traits and has been used as a donor in tomato breeding programs. Unlocking the genetic potential of  S. pimpinellifolium  requires high-throughput polymorphism identification protocols for QTL mapping and introgression of favourable alleles into cultivated tomato by both positive and background selection.    Results  In this study we identified SNP loci using a genotyping by sequencing (GBS) approach in an IBL mapping population derived from the cross between a high yielding fresh market tomato and  S. pimpinellifolium  (LA1589) as the recurrent and donor parents, respectively. A total of 120,983,088 reads were generated by the Illumina HiSeq next-generation sequencing platform. From these reads 448,539 sequence tags were generated. A majority of the sequence tags (84.4%) were uniquely aligned to the tomato genome. A total of 3.125 unique SNP loci were identified as a result of tag alignment to the genome assembly and were used in QTL analysis of 11 fruit quality traits. As a result, 37 QTLs were identified.  S. pimpinellifolium  contributed favourable alleles for 16 QTLs (43.2%), thus confirming the high breeding potential of this wild species .Conclusions  The present work introduced a set of SNPs at sufficiently high density for QTL mapping in populations derived from  S. pimpinellifolium  (LA1589). Moreover, this study demonstrated the high efficiency of the GBS approach for SNP identification, genotyping and QTL mapping in an interspecific tomato population.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3406-7) contains supplementary material, which is available to authorized users.

bmc genomics

Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing