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Development and mapping of microsatellite markers from transcriptome sequences of European hazelnut (Corylus avellana L.) and use for germplasm characterization

Molecular Breeding volume 37, Article number: 16 (2017) Cite this article

Abstract

Microsatellite markers, also known as simple sequence repeat (SSR) markers, are useful in genetics and plant breeding for marker-assisted selection, cultivar fingerprinting, and kinship studies. They were previously developed for European hazelnut (Corylus avellana L.) from enriched libraries, inter-simple sequence repeat (ISSR) fragments, and bacterial artificial chromosome (BAC) sequences. This study utilized the ‘Jefferson’ transcriptome sequence to develop microsatellite markers for hazelnut. Microsatellites were mined from the transcriptome sequence and aligned with the corresponding genomic sequence using a BLASTN search, and primers were designed from the genomic sequence. From a total of 1432 identified microsatellites, 382 primer pairs were designed for repeats with motifs of three base pairs or longer and at least five repeats, and a few di-repeat sequences. The primers were initially screened for polymorphism with a set of 24 C. avellana accessions, and those that were polymorphic were characterized using a set of 63 accessions. One hundred nine polymorphic microsatellite markers that generated one or two fragments per accession were characterized, with AAG, AGC, and ACT being the most common motifs. Two additional SSR primer pairs generated three PCR products in a few accessions. Of the 109 loci, 53 were placed on the linkage map of the mapping population OSU 252.146 × OSU 414.062, and 22 were assigned to linkage groups using alternate segregating populations. A dendrogram constructed from the SSR fingerprints at the 109 new marker loci mostly showed clustering of accessions from similar geographic origins and confirmed the tremendous amount of genetic diversity present within C. avellana. These markers will be useful for fingerprinting, marker-assisted selection, and genetic studies in hazelnut.

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Data archiving statement

DNA sequences containing microsatellites were deposited in GenBank (www.ncbi.nlm.nih.gov/genbank/), and accession numbers (KJ193862-KJ193973) are shown in Supplementary Material 1.

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Author notes

  1. Brooke C. Colburn & Vidyasagar R. Sathuvalli

    Present address: , 25221 Deer Lane, Bend, OR, 97701, USA

  2. Shawn A. Mehlenbacher

    Present address: Hermiston Agricultural Research and Extension Center, 2121 S. First Street, Hermiston, OR, 97838, USA

Authors and Affiliations

  1. Dept. of Horticulture, Oregon State University, 4017 ALS Building, Corvallis, OR, 97331, USA

    Brooke C. Colburn, Shawn A. Mehlenbacher & Vidyasagar R. Sathuvalli

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  1. Brooke C. Colburn
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  2. Shawn A. Mehlenbacher
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  3. Vidyasagar R. Sathuvalli
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Correspondence to Shawn A. Mehlenbacher.

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Funding

This research was supported by the Oregon Hazelnut Commission and state and Hatch Act funds.

Electronic supplementary material

ESM 1

Characteristics and primer sequences of 111 new microsatellite loci from transcriptome sequences of European hazelnut (Corylus avellana L.). Linkage groups were assigend based on segregation in the population OSU 252.146 x OSU 414.062 or an alternative population as indicated. (DOCX 57.6 kb)

ESM 2

Allele sizes of 63 hazelnut accessions at 111 polymorphic microsatellite marker loci (DOCX 176 kb)

ESM 3

Histograms of allele sizes at 111 polymorphic microsatellite loci in hazelnut (PDF 313 kb)

ESM 4

Linkage map for the Corylus avellana population OSU 252.146 x OSU 414.062. * indicates markers developed in this study (DOCX 125 kb)

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Colburn, B.C., Mehlenbacher, S.A. & Sathuvalli, V.R. Development and mapping of microsatellite markers from transcriptome sequences of European hazelnut (Corylus avellana L.) and use for germplasm characterization. Mol Breeding 37, 16 (2017). https://doi.org/10.1007/s11032-016-0616-2

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  • DOI: https://doi.org/10.1007/s11032-016-0616-2

Keywords

  • Microsatellite marker
  • Simple sequence repeat
  • Hazelnut
  • Corylus avellana
  • Characterization
  • Mapping