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Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

Author

Listed:
  • Keyan Zhao

    (Cornell University
    Stanford University)

  • Chih-Wei Tung

    (Cornell University)

  • Georgia C. Eizenga

    (USDA ARS, Dale Bumpers National Rice Research Center)

  • Mark H. Wright

    (Cornell University)

  • M. Liakat Ali

    (Rice Research and Extension Center, University of Arkansas)

  • Adam H. Price

    (Institute of Biological and Environmental Sciences, University of Aberdeen)

  • Gareth J. Norton

    (Institute of Biological and Environmental Sciences, University of Aberdeen)

  • M. Rafiqul Islam

    (Bangladesh Agricultural University)

  • Andy Reynolds

    (Cornell University)

  • Jason Mezey

    (Cornell University)

  • Anna M. McClung

    (USDA ARS, Dale Bumpers National Rice Research Center)

  • Carlos D. Bustamante

    (Cornell University
    Stanford University)

  • Susan R. McCouch

    (Cornell University)

Abstract

Asian rice, Oryza sativa is a cultivated, inbreeding species that feeds over half of the world's population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability of rice. Here we show the results of a genome-wide association study based on genotyping 44,100 SNP variants across 413 diverse accessions of O. sativa collected from 82 countries that were systematically phenotyped for 34 traits. Using cross-population-based mapping strategies, we identified dozens of common variants influencing numerous complex traits. Significant heterogeneity was observed in the genetic architecture associated with subpopulation structure and response to environment. This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement.

Suggested Citation

  • Keyan Zhao & Chih-Wei Tung & Georgia C. Eizenga & Mark H. Wright & M. Liakat Ali & Adam H. Price & Gareth J. Norton & M. Rafiqul Islam & Andy Reynolds & Jason Mezey & Anna M. McClung & Carlos D. Busta, 2011. "Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa," Nature Communications, Nature, vol. 2(1), pages 1-10, September.
    • Handle: RePEc:nat:natcom:v:2:y:2011:i:1:d:10.1038_ncomms1467
    DOI: 10.1038/ncomms1467
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    Cited by:

    1. Shin-Fu Tsai & Chih-Chien Shen & Chen-Tuo Liao, 2021. "Bayesian Optimization Approaches for Identifying the Best Genotype from a Candidate Population," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 26(4), pages 519-537, December.
    2. Hiroyoshi Iwata & Kaworu Ebana & Yusaku Uga & Takeshi Hayashi, 2015. "Genomic Prediction of Biological Shape: Elliptic Fourier Analysis and Kernel Partial Least Squares (PLS) Regression Applied to Grain Shape Prediction in Rice (Oryza sativa L.)," PLOS ONE, Public Library of Science, vol. 10(3), pages 1-17, March.
    3. Scutari Marco & Mackay Ian & Balding David, 2013. "Improving the efficiency of genomic selection," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 12(4), pages 517-527, August.
    4. Cécile Grenier & Tuong-Vi Cao & Yolima Ospina & Constanza Quintero & Marc Henri Châtel & Joe Tohme & Brigitte Courtois & Nourollah Ahmadi, 2015. "Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding," PLOS ONE, Public Library of Science, vol. 10(8), pages 1-25, August.
    5. Rijsberman, Frank, 2012. "KEYNOTE ADDRESS: The scramble for natural resources: How can science help?," 2012: The Scramble for Natural Resources: More Food, Less Land?, 9-10 October 2012 152416, Crawford Fund.
    6. Yongqi He & Shan Sun & Jia Zhao & Zhibo Huang & Liling Peng & Chengwei Huang & Zhengbin Tang & Qianqian Huang & Zhoufei Wang, 2023. "UDP-glucosyltransferase OsUGT75A promotes submergence tolerance during rice seed germination," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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