Home LiteratureArticle Details
PMID: 21915109 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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

Nature communications ·Vol. 2 ·2011-09-13 ·Pages 467

Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR

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.

MeSH Terms
Genetic Heterogeneity Genetic Linkage Genome, Plant Genotype Oryza/genetics Polymorphism, Single Nucleotide
Authors & Affiliations
13 authors, click to expand affiliations / ORCID
Zhao Keyan
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA.
Tung Chih-Wei
Eizenga Georgia C
Wright Mark H
Ali M Liakat
Price Adam H
Norton Gareth J
Islam M Rafiqul
Reynolds Andy
Mezey Jason
McClung Anna M
Bustamante Carlos D
McCouch Susan R
References (50)
50 references, click to expand
  1. Evolutionary history of GS3, a gene conferring grain length in rice.
    Genetics. 2009 Aug;182(4):1323-34 PMID: 19506305
  2. Control of tillering in rice.
    Nature. 2003 Apr 10;422(6932):618-21 PMID: 12687001
  3. Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice.
    Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4555-60 PMID: 19246394
  4. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).
    Science. 2002 Apr 5;296(5565):92-100 PMID: 11935018
  5. Loss of function of a rice brassinosteroid insensitive1 homolog prevents internode elongation and bending of the lamina joint.
    Plant Cell. 2000 Sep;12(9):1591-606 PMID: 11006334
  6. The origin and evolution of fragrance in rice (Oryza sativa L.).
    Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14444-9 PMID: 19706531
  7. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice.
    Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12273-8 PMID: 19597147
  8. FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets.
    Development. 2003 Aug;130(16):3841-50 PMID: 12835399
  9. Efficient control of population structure in model organism association mapping.
    Genetics. 2008 Mar;178(3):1709-23 PMID: 18385116
  10. The genetic architecture necessary for transgressive segregation is common in both natural and domesticated populations.
    Philos Trans R Soc Lond B Biol Sci. 2003 Jun 29;358(1434):1141-7 PMID: 12831480
  11. Principal components analysis corrects for stratification in genome-wide association studies.
    Nat Genet. 2006 Aug;38(8):904-9 PMID: 16862161
  12. Functional markers developed from multiple loci in GS3 for fine marker-assisted selection of grain length in rice.
    Theor Appl Genet. 2011 Mar;122(5):905-13 PMID: 21107518
  13. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.
    Nature. 2010 Jun 3;465(7298):627-31 PMID: 20336072
  14. ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations.
    Bioinformatics. 2010 Dec 1;26(23):2952-60 PMID: 20926420
  15. Engineering OsBAK1 gene as a molecular tool to improve rice architecture for high yield.
    Plant Biotechnol J. 2009 Oct;7(8):791-806 PMID: 19754838
  16. Multiple introgression events surrounding the Hd1 flowering-time gene in cultivated rice, Oryza sativa L.
    Mol Genet Genomics. 2010 Aug;284(2):137-46 PMID: 20607290
  17. slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8.
    Plant Cell. 2001 May;13(5):999-1010 PMID: 11340177
  18. Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS.
    Plant Cell. 2000 Dec;12(12):2473-2484 PMID: 11148291
  19. Yield penalties of disease resistance in crops.
    Curr Opin Plant Biol. 2002 Aug;5(4):339-44 PMID: 12179968
  20. Linkage and association mapping of Arabidopsis thaliana flowering time in nature.
    PLoS Genet. 2010 May 06;6(5):e1000940 PMID: 20463887
  21. New insights into the history of rice domestication.
    Trends Genet. 2007 Nov;23(11):578-87 PMID: 17963977
  22. Generating high-yielding varieties by genetic manipulation of plant architecture.
    Curr Opin Biotechnol. 2004 Apr;15(2):144-7 PMID: 15081053
  23. Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana.
    Nat Rev Genet. 2010 Dec;11(12):867-79 PMID: 21085205
  24. Genome-wide association studies of 14 agronomic traits in rice landraces.
    Nat Genet. 2010 Nov;42(11):961-7 PMID: 20972439
  25. The OsTB1 gene negatively regulates lateral branching in rice.
    Plant J. 2003 Feb;33(3):513-20 PMID: 12581309
  26. Not just a grain of rice: the quest for quality.
    Trends Plant Sci. 2009 Mar;14(3):133-9 PMID: 19230745
  27. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome.
    PLoS One. 2010 May 24;5(5):e10780 PMID: 20520727
  28. OsLIC, a Novel CCCH-Type Zinc Finger Protein with Transcription Activation, Mediates Rice Architecture via Brassinosteroids Signaling.
    PLoS One. 2008;3(10):e3521 PMID: 18953406
  29. Complex-trait analysis in plants.
    Genome Biol. 2010;11(4):113 PMID: 20409352
  30. Analysis of the rice mutant dwarf and gladius leaf 1. Aberrant katanin-mediated microtubule organization causes up-regulation of gibberellin biosynthetic genes independently of gibberellin signaling.
    Plant Physiol. 2005 Aug;138(4):1982-93 PMID: 16040652
  31. Genetic structure and diversity in Oryza sativa L.
    Genetics. 2005 Mar;169(3):1631-8 PMID: 15654106
  32. Genomics: The search for association.
    Nature. 2010 Oct 28;467(7319):1135-8 PMID: 20981103
  33. Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping.
    PLoS Genet. 2011 Aug;7(8):e1002221 PMID: 21829395
  34. A draft sequence of the rice genome (Oryza sativa L. ssp. indica).
    Science. 2002 Apr 5;296(5565):79-92 PMID: 11935017
  35. Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities.
    Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21760-5 PMID: 20018713
  36. PLINK: a tool set for whole-genome association and population-based linkage analyses.
    Am J Hum Genet. 2007 Sep;81(3):559-75 PMID: 17701901
  37. The Rice Annotation Project Database (RAP-DB): 2008 update.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D1028-33 PMID: 18089549
  38. Discovery and utilization of QTLs for insect resistance in soybean.
    Genetica. 2005 Feb;123(1-2):181-9 PMID: 15881690
  39. Loss of function of a proline-containing protein confers durable disease resistance in rice.
    Science. 2009 Aug 21;325(5943):998-1001 PMID: 19696351
  40. Genetic and molecular bases of rice yield.
    Annu Rev Plant Biol. 2010;61:421-42 PMID: 20192739
  41. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS.
    PLoS Genet. 2010 Apr 01;6(4):e1000888 PMID: 20369019
  42. The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza.
    Genome Res. 2006 Jan;16(1):140-7 PMID: 16344555
  43. Gramene database in 2010: updates and extensions.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D1085-94 PMID: 21076153
  44. Towards the understanding of complex traits in rice: substantially or superficially?
    DNA Res. 2009 Jun;16(3):141-54 PMID: 19359285
  45. Plastid movement impaired 2, a new gene involved in normal blue-light-induced chloroplast movements in Arabidopsis.
    Plant Physiol. 2006 Aug;141(4):1328-37 PMID: 16778016
  46. The TIME FOR COFFEE gene maintains the amplitude and timing of Arabidopsis circadian clocks.
    Plant Cell. 2003 Nov;15(11):2719-29 PMID: 14555691
  47. SSD1, which encodes a plant-specific novel protein, controls plant elongation by regulating cell division in rice.
    Proc Jpn Acad Ser B Phys Biol Sci. 2010;86(3):265-73 PMID: 20228626
  48. An Arabidopsis example of association mapping in structured samples.
    PLoS Genet. 2007 Jan 19;3(1):e4 PMID: 17238287
  49. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness.
    Nat Genet. 2006 Feb;38(2):203-8 PMID: 16380716
  50. The map-based sequence of the rice genome.
    Nature. 2005 Aug 11;436(7052):793-800 PMID: 16100779
Article Info
Journal
Nature communications
Abbr.
Nat Commun
ISSN
2041-1723
DOI
10.1038/ncomms1467
Published
2011-09-13
Epub
2011-00-13
Pages
467
Language
English
Region
England
NLM ID
101528555
PMCID
PMC3195253
Subset
IM
Grants
NHGRI NIH HHS · P50 HG002790 · United States
Biotechnology and Biological Sciences Research Council · BBF0041841 · United Kingdom
External Links
PubMed source DOI: 10.1038/ncomms1467 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2