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Cited by 326Genetic Mapping and Diversity in Plants and AnimalsGenetic and phenotypic traits in livestockGenomics and Phylogenetic Studies

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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Celik, Ibrahim, Gurbuz, Nergiz, Uncu, Ali Tevfik, Frary, Anne, Doganlar, Sami·2017·BMC Genomics
DOI 10.1186/s12864-016-3406-7PMC PMC5209891
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Abstract

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.

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  • Combining short- and long-read sequencing technologies in hybrid assemblies recently produced high-quality genomes in fish.

    “Combining short- and long-read sequencing technologies in hybrid assemblies recently produced high-quality genomes in fish8,9.”

    From Hybrid genome assembly and annotation of Danionella translucida (2019) · cites this paper as [9]

    The Methods (Genotyping by sequencing) describe Illumina sequencing of tomato samples, and the Results (GBS) describe aligning sequence tags to a tomato genome assembly. Searches for hybrid short- and long-read assemblies and fish genomes found no passage addressing the cited claim. Page numbers were not provided in our copy. (LLM, conf=0.77)

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Cited by

Sorted by citations

Authors
Celik, I., Gurbuz, N., Uncu, A. T., Frary, A., & Doganlar, S.
Affiliations
Izmir Institute of Technology (TR)
ORCID
Venue
BMC Genomics
Publisher
Springer Science and Business Media LLC
Published
2017-01-03
Volume
18
Issue
1
Pages
1-1
ISSN
1471-2164 (ISSN-L)
DOI
10.1186/s12864-016-3406-7
PMC
PMC5209891
OpenAlex
W2567353202
Cited by
326
References
1
Citations by year
2026: 4 · 2025: 57 · 2024: 30 · 2023: 32 · 2022: 38 · 2021: 91 · 2020: 36 · 2019: 17 · 2018: 19 · 2017: 2
FWCI
13.12
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • BMC Genomics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • İYTE (İZMİR YÜKSEK TEKNOLOJİ ENSTİTÜSÜ) (submittedVersion, other-oa)
  • IYTE GCRIS Database (Izmir Institute of Technology) (submittedVersion, other-oa)
Funders
Türkiye Bilimsel ve Teknolojik Araştirma Kurumu (114Z116)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
Solanum pimpinellifolium, wild tomato, SNP discovery, QTL mapping, fruit quality traits, interspecific hybridization, introgression, tomato breeding, genotyping-by-sequencing, marker-assisted selection
MeSH terms
Breeding, Chromosome Mapping, Crosses, Genetic, Fruit, Genotype, Phenotype, Genes, Plant, Solanum lycopersicum, Quantitative Trait, Heritable, Polymorphism, Single Nucleotide, Solanum, Genome-Wide Association Study, High-Throughput Nucleotide Sequencing, Food Quality

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