title: Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey.
authors.forename: Ibrahim
authors.initials: I
authors.lastname: Celik
authors.affiliation: Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey.
authors.forename: Nergiz
authors.initials: N
authors.lastname: Gurbuz
authors.affiliation: Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey.|Pressent Address: Department of Molecular Biology and Genetics, Necmettin Erbakan University, Konya, Turkey.
authors.forename: Ali Tevfik
authors.initials: AT
authors.lastname: Uncu
authors.affiliation: Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey.
authors.forename: Anne
authors.initials: A
authors.lastname: Frary
authors.affiliation: Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey. samidoganlar@iyte.edu.tr.
authors.forename: Sami
authors.initials: S
authors.lastname: Doganlar
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D003433:Crosses, Genetic; D063427:Food Quality; D005638:Fruit / Q000235:genetics*; D017343:Genes, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D018551:Solanum lycopersicum / Q000235:genetics; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D032322:Solanum / Q000235:genetics*
keywords: Fruit weight; Soluble solids content; Tomato genome; pH