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The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci

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Abstract

The first genetic map of cranberry (Vaccinium macrocarpon) has been constructed, comprising 14 linkage groups totaling 879.9 cM with an estimated coverage of 82.2 %. This map, based on four mapping populations segregating for field fruit-rot resistance, contains 136 distinct loci. Mapped markers include blueberry-derived simple sequence repeat (SSR) and cranberry-derived sequence-characterized amplified region markers previously used for fingerprinting cranberry cultivars. In addition, SSR markers were developed near cranberry sequences resembling genes involved in flavonoid biosynthesis or defense against necrotrophic pathogens, or conserved orthologous set (COS) sequences. The cranberry SSRs were developed from next-generation cranberry genomic sequence assemblies; thus, the positions of these SSRs on the genomic map provide information about the genomic location of the sequence scaffold from which they were derived. The use of SSR markers near COS and other functional sequences, plus 33 SSR markers from blueberry, facilitates comparisons of this map with maps of other plant species. Regions of the cranberry map were identified that showed conservation of synteny with Vitis vinifera and Arabidopsis thaliana. Positioned on this map are quantitative trait loci (QTL) for field fruit-rot resistance (FFRR), fruit weight, titratable acidity, and sound fruit yield (SFY). The SFY QTL is adjacent to one of the fruit weight QTL and may reflect pleiotropy. Two of the FFRR QTL are in regions of conserved synteny with grape and span defense gene markers, and the third FFRR QTL spans a flavonoid biosynthetic gene.

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Abbreviations

FFRR:

Field fruit-rot resistance

QTL:

Quantitative trait locus/loci

SSR:

Simple sequence repeat

SCAR:

Sequence-characterized amplified region

COS:

Conserved orthologous set

TAcy:

Total anthocyanin

PAC:

Proanthocyanidin

KW:

Kruskal–Wallis

IM:

Interval mapping

MQM:

Multiple QTL mapping

MRR:

Mean rot rating

RR:

Rot rating

MFW:

Mean fruit weight

SFY:

Sound fruit yield

GAIIx:

Genome Analyzer IIx

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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 Kristia Adams, Dayani Stinson, and Theodore Bunch, for technical assistance, and Dylan Baker for genotyping on the AdvanCE platform.

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Author notes

  1. Laura Georgi

    Present address: The American Chestnut Foundation Meadowview Research Farms, Meadowview, VA, 24361, USA

  2. Sushma Parankush Das

    Present address: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA

Authors and Affiliations

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

    Laura Georgi, Jennifer Johnson-Cicalese & Nicholi Vorsa

  2. Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, 08901, USA

    Josh Honig & Nicholi Vorsa

  3. Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA

    Sushma Parankush Das, Veeran D. Rajah & Debashish Bhattacharya

  4. USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR, 97333, USA

    Nahla Bassil

  5. USDA-ARS, Genetic Improvement of Fruits and Vegetables Lab, Beltsville, MD, 20705, USA

    Lisa J. Rowland

  6. USDA-ARS, Genetic Improvement of Fruits and Vegetables Lab, Chatsworth, NJ, 08019, USA

    James Polashock

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Correspondence to Laura Georgi or Nicholi Vorsa.

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Communicated by H. Nybom.

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Georgi, L., Johnson-Cicalese, J., Honig, J. et al. The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci. Theor Appl Genet 126, 673–692 (2013). https://doi.org/10.1007/s00122-012-2010-8

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