Shotguns and SNPs: how fast and cheap sequencing is revolutionizing plant biology

Authors

  • Steven D. Rounsley,

    1. School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
    2. BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
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  • Robert L. Last

    Corresponding author
    1. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
    2. Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
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  • Note: The authors were employees of Cereon Genomics LLC, a wholly owned subsidiary of Monsanto Co., when they participated in the generation and analysis of the Landsberg erecta shotgun sequence.

For correspondence (fax 517 353 9334; e-mail lastr@msu.edu).

Summary

In 1998 Cereon Genomics LLC, a subsidiary of Monsanto Co., performed a shotgun sequencing of the Arabidopsis thaliana Landsberg erecta genome to a depth of twofold coverage using ‘classic’ Sanger sequencing. This sequence was assembled and aligned to the Columbia ecotype sequence produced by the Arabidopsis Genome Initiative. The analysis provided tens of thousands of high-confidence predictions of polymorphisms between these two varieties of A. thaliana, and the predicted polymorphisms and Landsberg erecta sequence were subsequently made available to the not-for-profit research community by Monsanto. These data have been used for a wide variety of published studies, including map-based gene identification from forward genetic screens, studies of recombination and organelle genetics, and gene expression studies. The combination of resequencing approaches with next-generation sequencing technology has led to an increasing number of similar studies of genome-wide genetic diversity in A. thaliana, including the 1001 genomes project (http://1001genomes.org). Similar approaches are becoming possible in any number of crop species as DNA sequencing costs plummet and throughput rapidly increases, promising to lay the groundwork for revolutionizing our understanding of the relationship between genotype and phenotype in plants.

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