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Functional & Integrative Genomics

, Volume 17, Issue 5, pp 493–501 | Cite as

Transcriptome-based SNP discovery by GBS and the construction of a genetic map for olive

  • Ahmet İpekEmail author
  • Meryem İpek
  • Sezai Ercişli
  • Nesrin Aktepe Tangu
Original Article

Abstract

Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique. An analysis was done for 125 olive DNA samples (123 DNA samples from a cross-pollinated F1 mapping population, and two samples from parents). From 45 to 66% of Illumina reads from GBS analysis were aligned to the olive transcriptome. A total of 22,033 transcriptome-based SNP markers were identified, and 3384 of these were mapped in the olive genome. The genetic linkage map constructed in this study consists of 1 cleaved amplified polymorphic sequence (CAPS), 19 SSR, and 3384 transcriptome-based SNP markers. The map covers 3340.8 cM of the olive genome in 23 linkage groups, with the length of the linkage groups ranging from 55.6 to 248.7 cM. Average map distance between flanking markers was 0.98 cM. This genetic linkage map is a saturated genetic map and will be a useful tool for the localization of quantitative trait loci (QTLs) and gene(s) of interest and for the identification of candidate genes for economically important traits.

Keywords

Olive Transcriptome SNP Genetic mapping CAPS SSR 

Notes

Acknowledgments

This work was supported by the Commission of Scientific Research Projects of Uludag University, project number OUAP(Z)-2013/33.

Supplementary material

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Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Ahmet İpek
    • 1
    Email author
  • Meryem İpek
    • 1
  • Sezai Ercişli
    • 2
  • Nesrin Aktepe Tangu
    • 3
  1. 1.Faculty of Agriculture, Horticulture DepartmentUludag UniversityBursaTurkey
  2. 2.Faculty of Agriculture, Horticulture DepartmentAtatürk UniversityErzurumTurkey
  3. 3.Atatürk Horticultural Central Research InstituteYalovaTurkey

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