Plant Molecular Biology

, Volume 99, Issue 3, pp 251–264 | Cite as

The first genetic linkage map for Fraxinus pennsylvanica and syntenic relationships with four related species

  • Di Wu
  • Jennifer Koch
  • Mark Coggeshall
  • John CarlsonEmail author


Key message

The genetic linkage map for green ash (Fraxinus pennsylvanica) contains 1201 DNA markers in 23 linkage groups spanning 2008.87cM. The green ash map shows stronger synteny with coffee than tomato.


Green ash (Fraxinus pennsylvanica) is an outcrossing, diploid (2n = 46) hardwood tree species, native to North America. Native ash species in North America are being threatened by the rapid spread of the emerald ash borer (EAB, Agrilus planipennis), an invasive pest from Asia. Green ash, the most widely distributed ash species, is severely affected by EAB infestation, yet few genomic resources for genetic studies and improvement of green ash are available. In this study, a total of 5712 high quality single nucleotide polymorphisms (SNPs) were discovered using a minimum allele frequency of 1% across the entire genome through genotyping-by-sequencing. We also screened hundreds of genomic- and EST-based microsatellite markers (SSRs) from previous de novo assemblies (Staton et al., PLoS ONE 10:e0145031, 2015; Lane et al., BMC Genom 17:702, 2016). A first genetic linkage map of green ash was constructed from 90 individuals in a full-sib family, combining 2719 SNP and 84 SSR segregating markers among the parental maps. The consensus SNP and SSR map contains a total of 1201 markers in 23 linkage groups spanning 2008.87 cM, at an average inter-marker distance of 1.67 cM with a minimum logarithm of odds of 6 and maximum recombination fraction of 0.40. Comparisons of the organization the green ash map with the genomes of asterid species coffee and tomato, and genomes of the rosid species poplar and peach, showed areas of conserved gene order, with overall synteny strongest with coffee.


Green ash Linkage map Single nucleotide polymorphism (SNP) Simple sequence repeats (SSRs) Genotyping-by-sequencing (GBS) Synteny 



The authors would like to thank Wanyan Wang and Teodora Best for assistance with sample collection. We also thank Lianna Johnson and Byron Bredael for help with DNA extractions and screening SSR primers. Finally, we appreciate assistance from Nicole Zembower and Maureen Mailander on seedling planting and field maintenance. This work was supported by grants from NSF’s Plant Genome Research Program (IOS-1025974) to JEC and the USDA National Institute of Food and Agriculture Federal Appropriations under Project PEN04532 and Accession number 1000326.

Author contributions

DW conducted all of the research for her dissertation and prepared the first draft of the manuscript. JK conducted the controlled pollinations, reared the seedlings, provided the seedlings for mapping, and provided comments and edits on the manuscript. MC provided nursery space and advice for rearing the seedlings, and provided comments and edits on the manuscript. JC obtained funding, supervised the research, and provided comments and edits on the manuscript.

Compliance with ethical standards

Conflict of interest

The authors have declared that no competing interests exit.

Supplementary material

11103_2018_815_MOESM1_ESM.pdf (161 kb)
Supplementary material 1 (PDF 160 KB)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Di Wu
    • 1
  • Jennifer Koch
    • 2
  • Mark Coggeshall
    • 3
    • 4
  • John Carlson
    • 1
    Email author
  1. 1.Department of Ecosystem Science and ManagementPennsylvania State UniversityUniversity ParkUSA
  2. 2.USDA Forest Service, Northern Research Station, Project NRS-16DelawareUSA
  3. 3.Department of Forestry, Center for AgroforestryUniversity of MissouriColumbiaUSA
  4. 4.USDA Forest Service, Northern Research Station, Hardwood Tree Improvement and Regeneration Center, Project NRS-14West LafayetteUSA

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