Tree Genetics & Genomes

, Volume 9, Issue 6, pp 1537–1544

Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform

  • Charles Chen
  • Sharon E. Mitchell
  • Robert J. Elshire
  • Edward S. Buckler
  • Yousry A. El-Kassaby
Short Communication

DOI: 10.1007/s11295-013-0657-1

Cite this article as:
Chen, C., Mitchell, S.E., Elshire, R.J. et al. Tree Genetics & Genomes (2013) 9: 1537. doi:10.1007/s11295-013-0657-1

Abstract

Next-generation sequencing (NGS) technologies are revolutionizing both medical and biological research through generation of massive SNP data sets for identifying heritable genome variation underlying key traits, from rare human diseases to important agronomic phenotypes in crop species. We evaluated the performance of genotyping-by-sequencing (GBS), one of the emerging NGS-based platforms, for genotyping two economically important conifer species, lodgepole pine (Pinus contorta) and white spruce (Picea glauca). Both species have very large genomes (>20,000 Mbp), are highly heterozygous, and lack reference sequences. From a small set (six accessions each) of independent replicated DNA samples and a 48-plex read depth, we obtained ~60,000 SNPs per species. After stringent filtering, we obtained 17,765 and 17,845 high-coverage SNPs without missing data for lodgepole pine and white spruce, respectively. Our results demonstrated that GBS is a robust and suitable method for genotyping conifers. The application of GBS to forest tree breeding and genomic selection is discussed.

Keywords

Next-generation sequencingGenotyping-by-sequencing (GBS)SNP diversityConifers

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Charles Chen
    • 1
  • Sharon E. Mitchell
    • 2
  • Robert J. Elshire
    • 2
  • Edward S. Buckler
    • 2
    • 3
    • 4
  • Yousry A. El-Kassaby
    • 5
  1. 1.Centro Internacional de Mejoramiento de Maiz y Trigo, CIMMYTTexcocoMexico
  2. 2.Institute for Genomic DiversityCornell UniversityIthacaUSA
  3. 3.Department of Plant Breeding and GeneticsCornell UniversityIthacaUSA
  4. 4.U.S. Department of Agriculture-Agriculture Research Service (USDA-ARS)Robert W. Holley Center for Agriculture and HealthIthacaUSA
  5. 5.Department of Forest and Conservation Sciences, Faculty of ForestryThe University of British ColumbiaVancouverCanada