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

Di Wu, Jennifer Koch, Mark Coggeshall, John Edward Carlson

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

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. Abstract: 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.

Original languageEnglish (US)
Pages (from-to)251-264
Number of pages14
JournalPlant molecular biology
Volume99
Issue number3
DOIs
StatePublished - Feb 1 2019

Fingerprint

Fraxinus
Fraxinus pennsylvanica
Genetic Linkage
Coffee
chromosome mapping
Single Nucleotide Polymorphism
Synteny
Genome
Lycopersicon esculentum
North America
Gene Order
Expressed Sequence Tags
Diploidy
Genetic Markers
Gene Frequency
Microsatellite Repeats
Genetic Recombination
single nucleotide polymorphism
Agrilus planipennis
linkage groups

All Science Journal Classification (ASJC) codes

  • Agronomy and Crop Science
  • Genetics
  • Plant Science

Cite this

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title = "The first genetic linkage map for Fraxinus pennsylvanica and syntenic relationships with four related species",
abstract = "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. Abstract: 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.",
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The first genetic linkage map for Fraxinus pennsylvanica and syntenic relationships with four related species. / Wu, Di; Koch, Jennifer; Coggeshall, Mark; Carlson, John Edward.

In: Plant molecular biology, Vol. 99, No. 3, 01.02.2019, p. 251-264.

Research output: Contribution to journalArticle

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