, Volume 139, Issue 11–12, pp 1383–1398 | Cite as

Genetic variation and association mapping of silica concentration in rice hulls using a germplasm collection

  • R. Bryant
  • A. Proctor
  • M. Hawkridge
  • A. Jackson
  • K. Yeater
  • P. Counce
  • W. Yan
  • A. McClung
  • R. Fjellstrom


An association analysis on the genetic variability for silica concentration in rice hulls was performed using a “Mini-Core” set of 174 accessions representative of the germplasm diversity found in the USDA world collection of rice. Hull silica concentration was determined in replicated trials conducted in two southern states in the USA and was analyzed for its association with 164 genome-wide DNA markers. Among the accessions, the average silica concentration ranged from 120 to 251 mg g−1. Ample variation was seen within each of the five sub-populations of rice, as well as the 14 geographic regions that the accessions originated from. There was also an effect due to location and accession × location (G × E) interaction demonstrating the importance of assessing silica concentration across multiple environments. Twelve markers on ten chromosomes were significantly associated with hull silica concentration. Six markers (RM5644, RM5371, RM1335, RM283, RM263, and RM178) corroborated quantitative trait locus for silica concentration identified in other mapping studies. Our results provide germplasm and genetic markers that will assist breeding efforts to develop cultivars that have either high or low hull silica concentration. High silica hulls are good raw material for silica based industrial compounds, while low silica hulls are more biodegradable.


Silica Association mapping Germplasm Grain quality Oryza sativa 



The authors thank J. Neil Rutger (Research Geneticist, retired) at the Dale Bumpers National Rice Research Center for providing seeds of Wells brittle, Heather Howe for technical assistance in silica concentration analysis, Tiffany Sooskaserm, Yao Zhou, Biaolin Hu, Yuemei Huang, Jodie Cammack, Kip Landry, Carl Henry, Jason Bonnette, Piper Roberts, LaDuska Simpson, and Sarah Hendrix for assistance in conducting the field studies, and Melissa Jia for genotyping. The XRD results were generated at the University of Arkansas using the Electron Optics Facility, partly funded by the NSF.


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Copyright information

© Springer Science+Business Media B.V. (outside the USA)  2012

Authors and Affiliations

  • R. Bryant
    • 1
  • A. Proctor
    • 2
  • M. Hawkridge
    • 3
  • A. Jackson
    • 1
  • K. Yeater
    • 4
  • P. Counce
    • 5
  • W. Yan
    • 1
  • A. McClung
    • 1
  • R. Fjellstrom
    • 1
  1. 1.USDA-ARS, Dale Bumpers National Rice Research CenterStuttgartUSA
  2. 2.Department of Food ScienceUniversity of ArkansasFayettevilleUSA
  3. 3.Department of PhysicsUniversity of ArkansasFayettevilleUSA
  4. 4.USDA-ARS, Southern Plains AreaCollege StationUSA
  5. 5.University of Arkansas Rice Research and Extension CenterStuttgartUSA

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