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

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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.

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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.

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  1. Jens Allmer

    Present address: Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands

Authors and Affiliations

  1. Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey

    Süleyman Can Öztürk, Mehmet Göktay, Jens Allmer, Sami Doğanlar & Anne Frary

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  1. Süleyman Can Öztürk
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Correspondence to Anne Frary.

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

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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)

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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)

High Resolution Image (TIF 559 kb)

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Öztürk, S.C., Göktay, M., Allmer, J. et al. Development of Simple Sequence Repeat Markers in Hazelnut (Corylus avellana L.) by Next-Generation Sequencing and Discrimination of Turkish Hazelnut Cultivars. Plant Mol Biol Rep 36, 800–811 (2018). https://doi.org/10.1007/s11105-018-1120-0

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