Genetic Resources and Crop Evolution

, Volume 64, Issue 3, pp 451–466 | Cite as

Discriminating power of microsatellites in cranberry organelles for taxonomic studies in Vaccinium and Ericaceae

  • Brandon Schlautman
  • Giovanny Covarrubias-Pazaran
  • Diego Fajardo
  • Shawn Steffan
  • Juan Zalapa
Research Article


Simple sequence repeats (SSRs) in chloroplast and mitochondrial DNA, which have not been previously developed in the Ericaceae or, more specifically, in the genus Vaccinium, can be powerful tools for determining evolutionary relationships among taxa. In this study, 30 chloroplast, 23 mitochondrial, and 1 mitochondrion-like SSRs were identified in cranberry (V. macrocarpon), and primer-pairs were developed and tested for each locus. Although no polymorphisms were detected for any of the 54 SSR loci in nine diverse cranberry genotypes, all primers were cross-transferable to some extent to a panel of 12 additional Vaccinium taxa and four non-Vaccinium Ericaceae species. A Neighbor-Joining tree of the estimated average squared distances resolved the species by genus and by section within Vaccinium. Similar topologies with increased branch support were observed in Bayesian inference trees constructed from the DNA sequences of six plastid and two mitochondrial SSR loci. Two multiplexing/poolplexing panels of M13 fluorescently labeled primers, which amplify 24 of the 54 markers, were developed and can serve as an efficient, cost-effective means for characterizing the basic molecular phylogeny of Vaccinium. Increased understanding of evolutionary relationships among Vaccinium species should facilitate interspecific hybridization and introgression efforts to improve economically important traits of commercial berry crops.


Cross-species amplification Ericaceae Mitochondria Organelle markers Plastid Phylogenetic analysis SSR markers Vaccinium 



1 Corinthians 10:31. The authors thank James Polashock, Jennifer Johnson-Cicalese, and Nicholi Vorsa for their contribution of plant materials and comments on this manuscript. This project was supported by USDA-ARS (Project No. 3655-21220-001-00 provided to J.Z. and S.S.); WI-DATCP (SCBG Project #14-002); National Science Foundation (DBI-1228280); Ocean Spray Cranberries, Inc.; Wisconsin Cranberry Growers Association; Cranberry Institute; B.S. was supported by the Frank B. Koller Cranberry Fellowship Fund for Graduate Students; G.C.-P. was supported by the Consejo Nacional de Ciencia y Tecnología (CONACYT, Mexico).

Author contribution

B.S., D.F., S.S., and J.Z. conceived the research and designed experiments. B.S. and D.F. performed SSR mining and primer design. B.S. and G.C-P. performed fragment analyses and Sanger sequencing. B.S. and D.F. performed phylogenetic analyses. B.S. developed multiplexing/poolplexing panels. D.F. and S.S. assisted in analyzing results and developing discussion points. B.S. and J.Z. wrote the paper and oversaw the study.

Compliance with ethical standards

Conflicts of interest

The authors declare that there are no conflicts of interest.

Supplementary material

10722_2016_371_MOESM1_ESM.pdf (129 kb)
Bayesian inference tree of nine cranberry (V. macrocarpon); three V. oxycoccos; 11 other Vaccinium spp. from sections Cyanococcus, Vitis-idaea, and Batodendron; and 4 other Ericaceae species based on aligned nucelotide sequences with indels and microsatellite differences coded as binary characters and concatenated as a separate partition to the end of the aligned sequence matrix for six chloroplast SSR loci (CP3, CP8, CP12, CP14, CP16, CP17). Branch labels are posterior probabilities (PP) from Bayesian inference followed by bootstrap support (BS) by maximum likelihood (PDF 129 kb)
10722_2016_371_MOESM2_ESM.pdf (129 kb)
Bayesian inference tree of nine cranberry (V. macrocarpon); three V. oxycoccos; 11 other Vaccinium spp. from sections Cyanococcus, Vitis-idaea, and Batodendron; and four other Ericaceae species based on aligned nucelotide sequences with indels and microsatellite differences coded as binary characters and concatenated as a separate partition to the end of the aligned sequence matrix for two mitochondria SSR loci (MT6 and MT24). Branch labels are posterior probabilities (PP) from Bayesian inference followed by bootstrap support (BS) by maximum likelihood (PDF 128 kb)
10722_2016_371_MOESM3_ESM.pdf (117 kb)
Visualization of alleles of 24 chloroplast and mitochondrial SSR loci in the cranberry cultivar ‘Stevens’ amplified in multiplexing/poolplexing panel one (A) and panel two (B) with M13 FAM (Blue), HEX (Green), NED (Black), or PET (Red) labeled primers (PDF 117 kb)
10722_2016_371_MOESM4_ESM.docx (16 kb)
Supplementary material 4 (DOCX 16 kb)
10722_2016_371_MOESM5_ESM.docx (13 kb)
Supplementary material 5 (DOCX 12 kb)


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Copyright information

© Springer Science+Business Media Dordrecht (outside the USA) 2016

Authors and Affiliations

  • Brandon Schlautman
    • 1
    • 2
  • Giovanny Covarrubias-Pazaran
    • 1
  • Diego Fajardo
    • 3
  • Shawn Steffan
    • 2
  • Juan Zalapa
    • 1
    • 2
  1. 1.Department of HorticultureUniversity of WisconsinMadisonUSA
  2. 2.USDA-ARS, Vegetable Crops Research UnitUniversity of WisconsinMadisonUSA
  3. 3.National Center for Genome ResourcesSanta FeUSA

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