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

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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.

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Acknowledgments

This work was funded by the Johnson's Family Forest Biotechnology Endowment, the Natural Sciences and Engineering Research Council of Canada—Discovery, and the IRC grants to YAK.

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Authors and Affiliations

  1. Centro Internacional de Mejoramiento de Maiz y Trigo, CIMMYT, El Batan, 56130, Texcoco, Mexico

    Charles Chen

  2. Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA

    Sharon E. Mitchell, Robert J. Elshire & Edward S. Buckler

  3. Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA

    Edward S. Buckler

  4. U.S. Department of Agriculture-Agriculture Research Service (USDA-ARS), Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA

    Edward S. Buckler

  5. Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, V6T 1Z4, Canada

    Yousry A. El-Kassaby

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  1. Charles Chen
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  2. Sharon E. Mitchell
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  3. Robert J. Elshire
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  5. Yousry A. El-Kassaby
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Corresponding author

Correspondence to Yousry A. El-Kassaby.

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Communicated by J. Wegrzyn

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Chen, C., Mitchell, S.E., Elshire, R.J. et al. Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform. Tree Genetics & Genomes 9, 1537–1544 (2013). https://doi.org/10.1007/s11295-013-0657-1

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  • DOI: https://doi.org/10.1007/s11295-013-0657-1

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