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RESEARCH PRODUCT

Simple Sequence Repeat Marker Development and Mapping Targeted to Previously Unmapped Regions of the Strawberry Genome Sequence

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description

The genome sequence of the woodland strawberry (Fragaria vesca L.) is an important resource providing a reference for comparative genomics studies and future sequenced rosaceous species and has great utility as a model for the development of markers for mapping in the cultivated strawberry Fragaria ×ananassa Duchesne ex Rozier. A set of 152 microsatellite simple sequence repeat (SSR) primer pairs was developed and mapped, along with 42 previously published but unmapped SSRs, permitting the precise assignment of 28.2 Mbp of previously unanchored genome sequence scaffolds (13% of the F. vesca genome sequence). The original ordering of F. vesca sequence scaffolds was performed without a physical map, using predominantly SSR markers to order scaffolds via anchoring to a comprehensive linkage map. This report complements and expands resolution of the Fragaria spp. reference map and refi nes the scaffold ordering of the F. vesca genome sequence using newly devised tools. The results of this study provide two signifi cant resources: (i) the concurrent validation of a substantial set of SSRs associated with these previously unmapped regions of the Fragaria spp. genome and (ii) the precise placement of previously orphaned genomic sequence. Together, these resources improve the resolution and completeness of the strawberry genome sequence, making it a better resource for downstream studies in Fragaria spp. and the family Rosaceae. F is the most commercially important soft fruit genus, primarily due to the cultivation of the genetically complex octoploid species F. ×ananassa (2n = 8x = 56). In 2009, the world production of strawberries exceeded 4.1 million t and the crop was valued in excess of US$4 billion (FAO, 2011). Due to its economic importance, F. ×ananassa has been the subject of much genetic research aimed at developing superior cultivars with enhanced disease resistance, fruit quality, and other characters, prompting the development of a number of molecular marker maps for this species (Rousseau-Gueutin et al., 2008; Sargent et al., 2009; van Dijk et al., 2010). Simple sequence repeats (SSRs) have been the marker of choice in the genus Fragaria for linkage map development to date (Rousseau-Gueutin et al., 2008; Sargent et al., 2006; Sargent et al., 2009; Spigler et al., 2010; van Dijk et al., 2010) due to their abundance in the genome, their codominant and highly polymorphic nature, and their relative ease of development from enriched genomic libraries and expressed sequence tag (EST) collections (Celton et al., 2009; Sargent et al., 2003). Th e diploid Fragaria spp. reference map has been constructed using Published in The Plant Genome 4:165–177. Published 19 Aug. 2011. doi: 10.3835/plantgenome2011.05.0014 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. D.J. Sargent, E. Lopez Girona, A. Marchese, and D. W. Simpson, East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK; P Kuchta and M Korbin, Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland; H. Zhang, The Glycomics Center, Univ. of New Hampshire, Durham, NH; T.M. Davis, Dep. of Biological Sciences, University of New Hampshire, Durham, NH; J.M. Celton, Biotechnology Dep., Univ. of the Western Cape, Private Bag X17, Bellville 7535, South Africa; K. M. Folta, Horticultural Sciences Dep., Univ. of Florida, Gainesville, FL; V. Shulaev, Dep. of Biological Sciences, Univ. of North Texas, 1155 Union Cir., Denton, TX. Received 12 May 2011. *Corresponding author (dan.sargent@emr.ac.uk). Abbreviations: EMBL, European Molecular Biology Laboratory; EST, expressed sequence tag; FC, Fragaria pseudochromosome; FG, Fragaria linkage group; FV×FB, Fragaria vesca ‘815’ × Fragaria bucharica ‘601’; FvH4, Fragaria vesca L. ‘Hawaii 4’; PCR, polymerase chain reaction; SSR, simple sequence repeat; STS, sequence tagged site.