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Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing

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Abstract

The construction of the first genetic map in autotetraploid blueberry has been made possible by the development of new SNP markers developed using genotyping by sequencing in a mapping population created from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum). The novel SNP markers were supplemented with existing SSR markers to enable the alignment of parental maps.  In total, 1794 single nucleotide polymorphic (SNP) markers and 233 simple sequence repeat (SSR) markers exhibited segregation patterns consistent with a random chromosomal segregation model for meiosis in an autotetraploid. Of these, 700 SNPs and 85 SSRs were utilized for construction of the ‘Draper’ genetic map, and 450 SNPs and 86 SSRs for the ‘Jewel’ map.  The ‘Draper’ map comprises 12  linkage groups (LG), associated with the haploid chromosome number for blueberry, and totals 1621 cM while the ‘Jewel’ map comprises 20 linkage groups totalling 1610 cM. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents.

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Acknowledgments

This work was funded through Horticulture Link (HL0190), and all contributing partners are gratefully acknowledged. Project collaboration with the Specialty Crop Research Initiative-funded project (Grant 2008-51180-04861 entitled ‘Generating genomic tools for blueberry improvement’) has provided valuable access to plant material, genetic resources and advice. Support for this work from the Scottish Government’s Rural and Environment Science and Analytical Services Division (RESAS) is gratefully acknowledged. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the James Hutton Institute or any of the other agencies involved in this research. We thank all reviewers for their comments and Sue Gardiner for assisting in preparation of this ms.

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Authors and Affiliations

  1. Cell and Molecular Science Programme, James Hutton Institute, Dundee, Scotland, UK

    Susan McCallum, Julie Graham & Linzi Jorgensen

  2. Genetic Improvement of Fruits and Vegetables Laboratory, USDA-ARS, Beltsville, MD, USA

    Lisa J. Rowland

  3. National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR, USA

    Nahla V. Bassil

  4. Department of Horticulture, Michigan State University, East Lansing, MI, USA

    James F. Hancock

  5. MBG Marketing, Berry Blue, Grand Junction, MI, USA

    Edmund J. Wheeler

  6. Department of Horticulture, Oregon State University, Corvallis, OR, USA

    Kelly Vining

  7. Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA

    Jesse A. Poland

  8. Horticultural Sciences Department, University of Florida, Gainesville, FL, USA

    James W. Olmstead

  9. The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North, 4442, New Zealand

    Emily Buck & Claudia Wiedow

  10. General Mills Crop Biosciences, Wheat Innovation Center, Manhattan, KS, 66502, USA

    Eric Jackson

  11. Plants for Human Health Institute, Department of Horticultural Science, North Carolina State University, Kannapolis, NC, USA

    Allan Brown

  12. Biomathematics and Statistics Scotland, Dundee, Scotland, UK

    Christine A. Hackett

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  1. Susan McCallum
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  2. Julie Graham
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  3. Linzi Jorgensen
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  5. Nahla V. Bassil
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  11. Emily Buck
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  14. Allan Brown
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  15. Christine A. Hackett
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Correspondence to Susan McCallum.

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McCallum, S., Graham, J., Jorgensen, L. et al. Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing. Mol Breeding 36, 41 (2016). https://doi.org/10.1007/s11032-016-0443-5

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