Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Genome-wide association studies coming of age in rice

Nature Genetics volume 42, pages 926–927 (2010)Cite this article

Subjects

A new study reports the next-generation sequencing of 517 rice genomes, each to approximately onefold coverage. By leveraging sequence information across rice lines and by imputing missing genotypes, a haplotype map (HapMap) was constructed and used for genome-wide association studies in this major crop.

To meet the food needs of the human population, plant breeders select for agronomically important traits, such as crop yield. These traits typically vary continuously, and a focus for plant geneticists has been to identify quantitative trait loci (QTLs) that affect this variation. Finding the genes and DNA variants underlying these loci provides insights into genetic pathways on the one hand and on the other hand provides targets for marker-assisted selection to introduce favorable genetic variants into breeding programs. To date, most crop QTLs have been identified using biparental crosses or association studies with candidate genes. These efforts have yielded many successes1 but have sampled only a small number of genetic variants likely to be of agronomic importance2. On page 961 of this issue, Bin Han and colleagues3 now report the construction of a comprehensive HapMap for rice (Oryza sativa) that they used for genome-wide association studies (GWAS) for 14 agronomic traits. Strong associations could be identified for some traits, and compared to human GWAS, the percentage of variation explained in this study by these associations was generally much higher3,4.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Constructing a rice HapMap for GWAS with low-fold sequencing.

Marina Corral

References

  1. Harjes, C.E. et al. Science 319, 330–333 (2008).

    Article  CAS  Google Scholar 

  2. Myles, S. et al. Plant Cell 21, 2194–2202 (2009).

    Article  CAS  Google Scholar 

  3. Huang, X. et al. Nat. Genet. 42, 961–967 (2010).

    Article  CAS  Google Scholar 

  4. Manolio, T.A. et al. Nature 461, 747–753 (2009).

    Article  CAS  Google Scholar 

  5. Bentley, D.R. et al. Nature 456, 53–59 (2008).

    Article  CAS  Google Scholar 

  6. Ossowski, S. et al. Genome Res. 18, 2024–2033 (2008).

    Article  CAS  Google Scholar 

  7. Mather, K.A. et al. Genetics 177, 2223–2232 (2007).

    Article  CAS  Google Scholar 

  8. McNally, K.L. et al. Proc. Natl. Acad. Sci. USA 106, 12273–12278 (2009).

    Article  CAS  Google Scholar 

  9. Yu, J. et al. Nat. Genet. 38, 203–208 (2006).

    Article  CAS  Google Scholar 

  10. Atwell, S. et al. Nature 465, 627–631 (2010).

    Article  CAS  Google Scholar 

  11. Clark, R.M. et al. Science 317, 338–342 (2007).

    Article  CAS  Google Scholar 

  12. Hinds, D.A. et al. Science 307, 1072–1079 (2005).

    Article  CAS  Google Scholar 

  13. Weigel, D. & Mott, R. Genome Biol. 10, 107 (2009).

    Article  Google Scholar 

  14. Cronn, R. et al. Nucleic Acids Res. 36, e122 (2008).

    Article  Google Scholar 

  15. Huang, X. et al. Genome Res. 19, 1068–1076 (2009).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Richard M. Clark is at the Department of Biology, University of Utah, Salt Lake City, Utah, USA.,

    Richard M Clark

Authors
  1. Richard M Clark
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Richard M Clark.

Ethics declarations

Competing interests

The author declares no competing financial interests.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Clark, R. Genome-wide association studies coming of age in rice. Nat Genet 42, 926–927 (2010). https://doi.org/10.1038/ng1110-926

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng1110-926

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing