Construction of a Framework Genetic Linkage Map in Gleditsia triacanthos L

Oliver Gailing, Margaret E. Staton, Thomas Lane, Scott E. Schlarbaum, Rick Nipper, Sandra A. Owusu, John E. Carlson

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Genomic resources are sparse in most ecologically and economically important North American hardwood species. As part of the Hardwood Genomics project (http://www.hardwoodgenomics.org/), we evaluated the utility of restriction site associated DNA sequencing (RAD-Seq) for framework genetic linkage map construction in honeylocust (Gleditsia triacanthos L.), a leguminous tree common in eastern North America. Starting with a large open-pollinated family of progeny from a single tree, a mapping pedigree of 92 putative full-sibs was identified by kin group assignment and paternity analyses with microsatellite markers. RAD-Seq using Illumina next-generation DNA sequencing (NGS) generated over 117 M reads among the 92 plants. De novo reference genome clustering and alignment of samples to the reference genome revealed 5849 candidate single nucleotide polymorphisms (SNPs), of which 1570 were retained after quality filtering. Of the 1570 SNPs, 236 were in pseudo-testcross mapping configuration in the maternal parent and segregated approximately in the expected 1:1 ratio. The final map generated has a total length of 815.57 cM and consists of 178 markers on 14 linkage groups, corresponding to the haploid chromosome number in honey locust. Synteny and collinearity between honey locust and model legumes Glycine max, Medicago truncatula, and Phaseolus vulgaris were found for six of the honey locust linkage groups. RAD-Seq proved to be useful for framework linkage map construction in honey locust, a species for which no genomic resources had previously been available. However, greater sequence coverage and larger full-sib mapping pedigrees are necessary for the development of high-density linkage maps with future applications in quantitative trait locus (QTL) mapping.

Original languageEnglish (US)
Pages (from-to)177-187
Number of pages11
JournalPlant Molecular Biology Reporter
Volume35
Issue number2
DOIs
StatePublished - Apr 1 2017

Fingerprint

Gleditsia
Gleditsia triacanthos
Genetic Linkage
Grasshoppers
Honey
DNA Sequence Analysis
chromosome mapping
Pedigree
sequence analysis
Single Nucleotide Polymorphism
Medicago truncatula
Genome
Synteny
genomics
linkage groups
hardwood
pedigree
single nucleotide polymorphism
Phaseolus
Quantitative Trait Loci

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Plant Science

Cite this

Gailing, O., Staton, M. E., Lane, T., Schlarbaum, S. E., Nipper, R., Owusu, S. A., & Carlson, J. E. (2017). Construction of a Framework Genetic Linkage Map in Gleditsia triacanthos L. Plant Molecular Biology Reporter, 35(2), 177-187. https://doi.org/10.1007/s11105-016-1012-0
Gailing, Oliver ; Staton, Margaret E. ; Lane, Thomas ; Schlarbaum, Scott E. ; Nipper, Rick ; Owusu, Sandra A. ; Carlson, John E. / Construction of a Framework Genetic Linkage Map in Gleditsia triacanthos L. In: Plant Molecular Biology Reporter. 2017 ; Vol. 35, No. 2. pp. 177-187.
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Gailing, O, Staton, ME, Lane, T, Schlarbaum, SE, Nipper, R, Owusu, SA & Carlson, JE 2017, 'Construction of a Framework Genetic Linkage Map in Gleditsia triacanthos L', Plant Molecular Biology Reporter, vol. 35, no. 2, pp. 177-187. https://doi.org/10.1007/s11105-016-1012-0

Construction of a Framework Genetic Linkage Map in Gleditsia triacanthos L. / Gailing, Oliver; Staton, Margaret E.; Lane, Thomas; Schlarbaum, Scott E.; Nipper, Rick; Owusu, Sandra A.; Carlson, John E.

In: Plant Molecular Biology Reporter, Vol. 35, No. 2, 01.04.2017, p. 177-187.

Research output: Contribution to journalArticle

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Gailing O, Staton ME, Lane T, Schlarbaum SE, Nipper R, Owusu SA et al. Construction of a Framework Genetic Linkage Map in Gleditsia triacanthos L. Plant Molecular Biology Reporter. 2017 Apr 1;35(2):177-187. https://doi.org/10.1007/s11105-016-1012-0