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Construction of a Framework Genetic Linkage Map in Gleditsia triacanthos L.

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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.

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Acknowledgments

The study was supported by grant # TRPGR IOS-1025974 from the National Science Foundation Plant Genome Research Program. Additional support was provided by the Ecosystem Science Center and the Biotech Research Center at Michigan Technological University.

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Authors and Affiliations

  1. School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA

    Oliver Gailing & Sandra A. Owusu

  2. Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996-4563, USA

    Margaret E. Staton & Thomas Lane

  3. Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, 37996-4563, USA

    Scott E. Schlarbaum

  4. Floragenex, Inc, 44 West Broadway, Eugene, OR, 97401, USA

    Rick Nipper

  5. Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA

    John E. Carlson

  6. Department of Plant Science, Pennsylvania State University, University Park, PA, 16802, USA

    John E. Carlson

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  1. Oliver Gailing
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  2. Margaret E. Staton
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Correspondence to Oliver Gailing.

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ESM 1

Supplementary Fig. 1. Alignment of honey locust maps calculated from the marker set that was derived from the stringent (left-hand side) and relaxed (right-hand side) RAD-Seq clustering protocol. (PPTX 82 kb)

ESM 2

Supplementary Fig. 2. Individual sample sequence performance including number of reads and sequence coverage. (DOCX 536 kb)

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Gailing, O., Staton, M.E., Lane, T. et al. Construction of a Framework Genetic Linkage Map in Gleditsia triacanthos L.. Plant Mol Biol Rep 35, 177–187 (2017). https://doi.org/10.1007/s11105-016-1012-0

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