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Conservation Genetics Resources

, Volume 6, Issue 3, pp 647–648 | Cite as

Development of novel polymorphic microsatellite markers by technology of next generation sequencing in western white pine

  • Jun-Jun LiuEmail author
  • Craig Hammett
Microsatellite Letters

Abstract

The invasive fungal pathogen Cronartium ribicola has seriously damaged five-needle pines in North America. Genetic diversity assessment using DNA markers among natural populations will benefit conservation and restoration programs. This report presents characterization of the first set of microsatellite markers developed by analyzing a reference transcriptome de novo assembled from RNA-seq data and expressed sequence tags in western white pine (Pinus monticola). A total of 1,948 microsatellite loci were detected in 1,876 contigs. Forty-six loci were verified to be polymorphic, with allele number per locus ranging from 2 to 12. The mean observed and expected heterozygosity per locus was measured as 0.671 and 0.485, respectively. These microsatellite markers will be useful for characterizing genetic diversity and gene-flow among natural stands and population structure among seed families for conservation of this conifer species across western North America.

Keywords

Expressed sequence tag (EST) Microsatellites Next generation sequencing Pinus monticola 

Notes

Acknowledgments

This research was supported, in part, by the Canadian Forest Service and the CFS–GRDI fund awarded to JJL. We thank L. Baerg at CFS for technical support on genomic DNA extraction.

Supplementary material

12686_2014_168_MOESM1_ESM.xls (40 kb)
Supplementary material 1 (XLS 40 kb)
12686_2014_168_MOESM2_ESM.xls (34 kb)
Supplementary material 2 (XLS 34 kb)

References

  1. da Maia LC, Palmieri DA, de Souza VQ, Kopp MM, de Carvalho FI, Costa de Oliveira A (2008) SSR locator: tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int J Plant Genomics 2008:412696PubMedCentralPubMedGoogle Scholar
  2. Liu J-J, Hammett C, Sniezko RA (2013a) Pinus monticola pathogenesis-related gene PmPR10-2 alleles as defense candidates for stem quantitative disease resistance against white pine blister rust (Cronartium ribicola). Tree Genetics Genomes 9(2):397–408CrossRefGoogle Scholar
  3. Liu J-J, Sturrock RN, Benton R (2013b) Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola. BMC Genom 14(1):884CrossRefGoogle Scholar
  4. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539PubMedCentralPubMedCrossRefGoogle Scholar
  5. Sniezko RA (2006) Resistance breeding against non-native pathogens in forest trees- current successes in North America. Can J Plant Pathol 28:S270–S279CrossRefGoogle Scholar

Copyright information

© Her Majesty the Queen in Right of Canada 2014

Authors and Affiliations

  1. 1.Pacific Forestry Centre, Canadian Forest Service, Natural Resources CanadaVictoriaCanada

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