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Cranberry microsatellite marker development from assembled next-generation genomic sequence

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Abstract

The large-fruited cranberry (Vaccinium macrocarpon Ait.) is a native North American fruit that is a rich source of dietary phytochemicals with demonstrated and potential benefits for human health. Cranberry is a perennial, self-fertile 2n = 2x = 24 diploid, with a haploid genome size of about 570 Mbp. Present commercial cultivars are only a few breeding and selection cycles removed from their wild progenitors. With an irreducible minimum of 2 years per generation, and significant space and time requirements for phenotypic selection of traits of horticultural interest, genetic enhancement of cranberry could be facilitated by marker-assisted selection (MAS); however, the necessary resources, such as transcript or genomic sequences, molecular genetic markers, and genetic linkage maps, are not yet available. We have begun to generate these resources, starting with next-generation [sequencing by oligonucleotide ligation and detection (SOLiD) mate-paired] sequencing of an inbred cranberry clone, assembling the reads, and developing microsatellite markers from the assembled sequence. Evaluation of the resulting cranberry genomic microsatellite primers has provided a test of the accuracy of the sequence assembly and supplied much-needed molecular markers for a genetic linkage map of cranberry. Mapping these markers will permit sequence scaffolds to be anchored on the genetic map.

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Acknowledgments

Funding for this work was provided by USDA SCRI grant number 2008-51180-04878, with additional funding from Ocean Spray Cranberries, Incorporated. We thank Dayani Stinson for technical support and Mark Diamond for assistance in manuscript preparation.

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Authors and Affiliations

  1. Marucci Center for Blueberry and Cranberry Research and Extension, Rutgers University, Chatsworth, NJ, 08019, USA

    Laura Georgi & Nicholi Vorsa

  2. Laboratório de Genômica e Expressão, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, Campinas, SP, 13083-970, Brazil

    Roberto H. Herai, Ramon Vidal, Marcelo Falsarella Carazzolle & Gonçalo Guimarães Pereira

  3. UCSD Stem Cell Program, Department of Pediatrics, School of Medicine, University of California San Diego-UCSD, 9500 Gilman Drive-CMM-E, Room #2021D, La Jolla, CA, 92093-0695, USA

    Roberto H. Herai

  4. Centro Nacional de Processamento de Alto Desempenho em São Paulo, Universidade Estadual de Campinas, CP 6141, Campinas, SP, 13083-970, Brazil

    Marcelo Falsarella Carazzolle

  5. Laboratório Nacional de Biociências-CNPEM/ABTLuS, Campinas, Brazil

    Ramon Vidal

  6. USDA-ARS, Chatsworth, NJ, 08019, USA

    James Polashock

Authors
  1. Laura Georgi
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  2. Roberto H. Herai
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  3. Ramon Vidal
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  4. Marcelo Falsarella Carazzolle
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  5. Gonçalo Guimarães Pereira
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  6. James Polashock
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  7. Nicholi Vorsa
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Corresponding author

Correspondence to Nicholi Vorsa.

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Persons wishing access to the cranberry sequence should contact the authors directly.

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Georgi, L., Herai, R.H., Vidal, R. et al. Cranberry microsatellite marker development from assembled next-generation genomic sequence. Mol Breeding 30, 227–237 (2012). https://doi.org/10.1007/s11032-011-9613-7

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  • DOI: https://doi.org/10.1007/s11032-011-9613-7

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