Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.)

Chih Wei Tung, Keyan Zhao, Mark H. Wright, M. Liakat Ali, Janelle Jung, Jennifer Kimball, Wricha Tyagi, Michael J. Thomson, Kenneth McNally, Hei Leung, Hyunjung Kim, Sang Nag Ahn, Andy Reynolds, Brian Scheffler, Georgia Eizenga, Anna McClung, Carlos Bustamante, Susan R. McCouch

Research output: Contribution to journalArticlepeer-review

60 Scopus citations


We present an overview of a research platform that provides essential germplasm, genotypic and phenotypic data and analytical tools for dissecting phenotype-genotype associations in rice. These resources include a diversity panel of 400 Oryza sativa and 100 Oryza rufipogon accessions that have been purified by single seed descent, a customdesigned Affymetrix array consisting of 44,100 SNPs, an Illumina GoldenGate assay consisting of 1,536 SNPs, and a suite of low-resolution 384-SNP assays for the Illumina BeadXpress Reader that are designed for applications in breeding, genetics and germplasm management. Our longterm goal is to empower basic research discoveries in rice by linking sequence diversity with physiological, morphological, and agronomic variation. This research platform will also help increase breeding efficiency by providing a database of diversity information that will enable researchers to identify useful DNA polymorphisms in genes and germplasm of interest and convert that information into cost-effective tools for applied plant improvement.

Original languageEnglish (US)
Pages (from-to)205-217
Number of pages13
Issue number4
StatePublished - Dec 2010

Bibliographical note

Funding Information:
Acknowledgment We thank Teresa Hancock and Heather Maupin for their valuable assistance in phenotyping of the rice diversity panel, Daniel Wood, Fumio “Gen” Onishi and Kazi Akther for crossing and genotyping during CSSL development, and Dr. Rolfe Bryant (USDA-ARS Stuttgart, AR) for help with chemical analyses. This project is funded by the National Science Foundation Award 0606461 (to SMc; GE; AM; CB), the Crop Functional Genomics Center of the 21st Century Frontier Research Program (Project no. CG3113), Republic of Korea (to S-N. Ahn), and USAID Linkage Program and the Government of Japan (to IRRI).


  • Chromosome segment substitution lines
  • Genome-wide association mapping
  • Linkage disequilibrium
  • Oryza rufipogon
  • Oryza sativa
  • Rice phenotyping
  • SNP genotyping

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