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

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dc.contributor.authorCelik, Ibrahim
dc.contributor.authorGurbuz, Nergiz
dc.contributor.authorUncu, Ali Tevfik
dc.contributor.authorFrary, Anne
dc.contributor.authorDoganlar, Sami
dc.date.accessioned2024-02-23T14:27:16Z
dc.date.available2024-02-23T14:27:16Z
dc.date.issued2017
dc.departmentNEÜen_US
dc.description.abstractBackground: 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.en_US
dc.description.sponsorshipScientific and Technological Research Council of Turkey (TUBITAK) [114Z116]en_US
dc.description.sponsorshipThis study was supported by grant 114Z116 from the Scientific and Technological Research Council of Turkey (TUBITAK).en_US
dc.identifier.doi10.1186/s12864-016-3406-7
dc.identifier.issn1471-2164
dc.identifier.pmid28049423en_US
dc.identifier.scopus2-s2.0-85008190868en_US
dc.identifier.scopusqualityQ1en_US
dc.identifier.urihttps://doi.org/10.1186/s12864-016-3406-7
dc.identifier.urihttps://hdl.handle.net/20.500.12452/14529
dc.identifier.volume18en_US
dc.identifier.wosWOS:000391332000001en_US
dc.identifier.wosqualityQ1en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.language.isoenen_US
dc.publisherBmcen_US
dc.relation.ispartofBmc Genomicsen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectFruit Weighten_US
dc.subjectPhen_US
dc.subjectSoluble Solids Contenten_US
dc.subjectTomato Genomeen_US
dc.titleGenome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencingen_US
dc.typeArticleen_US

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