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Speed-mapping quantitative trait loci using microarrays

Nature Methods volume 4, pages 839–841 (2007)Cite this article

Abstract

We developed a rapid, economical method for high-resolution quantitative trait locus (QTL) mapping using microarrays for selective genotyping of pooled DNA samples. We generated 21,207 F2 flies from two inbred Drosophila melanogaster strains with known QTLs affecting lifespan, and hybridized DNA pools of young and old flies to microarrays. We used changes of gene frequency of 2,326 single-feature polymorphisms (SFPs) to map previously identified and additional QTLs affecting lifespan.

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Figure 1: Hybridization intensities of F2 Young DNA pool and means of two parental DNA populations.
Figure 2: QTLs on the X chromosome affecting variation in male and female lifespan between Oregon and 2b strains.

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Acknowledgements

We thank R. Wilson for help with the fly work. This work was supported by contracts 53-K06-5-10 and 58-1950-9-001 from the US Department of Agriculture's Agriculture Research Service and by National Institutes of Health grants GM45344 and GM45146.

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Author notes

  1. Jeff Leips, Wei Zou & Kurt R Wollenberg

    Present address: Present addresses: Department of Biological Sciences, 1000 Hilltop Circle, University of Maryland Baltimore County, Baltimore, Maryland 21250, USA (J.L.), PGxHealth, LLC, 5 Science Park, New Haven, Connecticut 06511, USA (W.Z.) and Bioinformatics and Scientific IT Program, Office of Technology Information Systems, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA (K.R.W.).,

Authors and Affiliations

  1. Jean Mayer–US Department of Agriculture Human Nutrition Research Center on Aging, Nutrition and Genomics, Tufts University, 711 Washington Street, Boston, 02111, Massachusetts, USA

    Chao-Qiang Lai, Jessica F Roberts, Laurence D Parnell & Jose M Ordovas

  2. Department of Genetics and W.M. Keck Center for Behavioral Biology, Campus Box 7614, North Carolina State University, Raleigh, 27695, North Carolina, USA

    Jeff Leips & Trudy F C Mackay

  3. Bioinformatics Research Center, North Carolina State University, 840 Main Campus Drive, Raleigh, 27695, North Carolina, USA

    Wei Zou & Zhao-Bang Zeng

  4. Tufts-New England Medical Center, Tufts University, 750 Washington Street, Boston, 02111, Massachusetts, USA

    Kurt R Wollenberg

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  1. Chao-Qiang Lai
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Corresponding author

Correspondence to Chao-Qiang Lai.

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Competing interests

A patent application associated with techniques used in this article is being prepared.

W.Z. is an employee of PGxHealth.

Supplementary information

Supplementary Text and Figures

Supplementary Figure 1–3, Supplementary Tables 1, 3–5, Supplementary Methods (PDF 322 kb)

Supplementary Table 2

Positional candidate genes within QTL regions. (XLS 121 kb)

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Lai, CQ., Leips, J., Zou, W. et al. Speed-mapping quantitative trait loci using microarrays. Nat Methods 4, 839–841 (2007). https://doi.org/10.1038/nmeth1084

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