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Plant Molecular Biology Reporter

, Volume 36, Issue 5–6, pp 800–811 | Cite as

Development of Simple Sequence Repeat Markers in Hazelnut (Corylus avellana L.) by Next-Generation Sequencing and Discrimination of Turkish Hazelnut Cultivars

  • Süleyman Can Öztürk
  • Mehmet Göktay
  • Jens Allmer
  • Sami Doğanlar
  • Anne FraryEmail author
Original Paper
  • 243 Downloads

Abstract

European hazelnut (Corylus avellana) is a diploid tree species and is widely used in confections. Hazelnuts are, to a large part, produced in Turkey with the cultivar “Tombul” widely grown in the Black Sea region. In this work, the “Tombul” genome was partially sequenced by next-generation sequencing technology yielding 29.2% (111.85 Mb) of the ~ 385 Mb (1C). This sequence information was used to develop genetic markers in order to enable differentiation of material before the long maturation process and to facilitate future breeding strategies. A total of 90,142 simple sequence repeats (SSRs) were identified in the contigs giving a frequency of 1 SSR per 1240 nt in the assembly. Mononucleotides were the most abundant SSR marker type (60.9%) followed by di- and trinucleotides. Primer pairs were designed for 75,139 (83.3%) of the SSRs. Fifty SSR primers were applied to 47 hazelnut accessions from nine countries to test their effectiveness and polymorphism. The markers amplified an average of 3.2 fragments. The highest polymorphism information content value was for cavSSR11062 (0.97) and the lowest (0.04) was for cavSSR13386. Two markers were monomorphic: cavSSR12855 and cavSSR13267. Single-copy SSR primers were also assessed for their ability to discriminate 19 Turkish cultivars, and it was found that seven primer pairs (Cav4217, Cav14875, Cav14418, Cav2704, Cav12862, Cav3909, Cav1361) were sufficient for this task. Thus, this study developed new SSR markers for use in hazelnut breeding and genetic studies and also provide a method to distinguish and identify true-type Turkish cultivars.

Keywords

Illumina sequencing Filbert genomic SSRs Fingerprinting Genetic diversity Microsatellites Population structure Barcode 

Notes

Acknowledgements

This research was supported by funding from an Izmir Institute of Technology Scientific Research Project (BAP-2016IYTE71) and The Scientific and Technological Research Council of Turkey (212T201). We are grateful to the Hazelnut Research Institute, Giresun, Turkey, for plant samples.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Data Archiving Statement

Data will be available at http://plantmolgen.iyte.edu.tr/data/ upon publication.

Supplementary material

11105_2018_1120_Fig5_ESM.png (8 kb)
Suppl. Figure 1

Delta K values of the Structure program outcome for each subpopulation assumption. The value of K with the highest Delta K value was chosen as the best number of subpopulations for the hazelnut accessions (K = 4). (PNG 7 kb)

11105_2018_1120_MOESM1_ESM.tif (56 kb)
High Resolution Image (TIF 56 kb)
11105_2018_1120_Fig6_ESM.png (23 kb)
Suppl. Figure 2

Population structure plots of the 47 hazelnut accessions. Cultivars are shown on the x-axis and are numbered according to Table 1. The y-axis shows the proportion of identity to each subpopulation (represented by different colored bars). (PNG 23 kb)

11105_2018_1120_MOESM2_ESM.tif (560 kb)
High Resolution Image (TIF 559 kb)
11105_2018_1120_MOESM3_ESM.docx (12 kb)
ESM 1 (DOCX 12 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Molecular Biology and GeneticsIzmir Institute of TechnologyIzmirTurkey
  2. 2.Applied Bioinformatics, Wageningen University and ResearchWageningenThe Netherlands

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