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Identification, characterisation and mapping of simple sequence repeat (SSR) markers from raspberry root and bud ESTs

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Abstract

Raspberry breeding is a long, slow process in this highly heterozygous out-breeder. Selections for complex traits like fruit quality are broad-based and few simple methodologies and resources are available for glasshouse and field screening for key pest and disease resistances. Additionally, the timescale for selection of favourable agronomic traits requires data from different seasons and environmental locations before any breeder selection can proceed to finished cultivar. Genetic linkage mapping offers the possibility of a more knowledge-based approach to breeding through linking favourable traits to markers and candidate genes on genetic linkage maps. To further increase the usefulness of existing maps, a set of 25 polymorphic SSRs derived from expressed sequences (EST-SSRs) have been developed in red raspberry (Rubus idaeus). Two different types of expressed sequences were targeted. One type was derived from a root cDNA library as a first step in assessing sequences which may be involved in root vigour and root rot disease resistance and the second type were ESTs from a gene discovery project examining bud dormancy release and seasonality. The SSRs detect between 2 and 4 alleles per locus and were assigned to linkage groups on the existing ‘Glen Moy’ × ‘Latham’ map following genotyping of 188 progeny and examined for association with previously mapped QTL. The loci were also tested on a diverse range of Rubus species to determine transferability and usefulness for germplasm diversity studies and the introgression of favourable alleles.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

cDNA:

Complementary DNA library

EST:

Expressed sequence tag

RAPD:

Randomly amplified polymorphic DNA

QTL:

Quantitative trait locus

SSR:

Simple sequence repeat

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Acknowledgements

This work was funded by RERAD, DEFRA and HDC through Horticulture Link. We thank C. Booth and M. Macauley for sequencing and genotyping assistance.

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Authors and Affiliations

  1. Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK

    M. Woodhead, S. McCallum, K. Smith, L. Cardle, L. Mazzitelli & J. Graham

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  1. M. Woodhead
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  2. S. McCallum
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  3. K. Smith
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  4. L. Cardle
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  5. L. Mazzitelli
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  6. J. Graham
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Correspondence to J. Graham.

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Woodhead, M., McCallum, S., Smith, K. et al. Identification, characterisation and mapping of simple sequence repeat (SSR) markers from raspberry root and bud ESTs. Mol Breeding 22, 555–563 (2008). https://doi.org/10.1007/s11032-008-9198-y

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  • DOI: https://doi.org/10.1007/s11032-008-9198-y

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