BMC Plant Biology (2009-05-01)

Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array

  • Ismail Abdelbagi M,
  • Wanamaker Steve,
  • Xu Jin,
  • Walia Harkamal,
  • Cui Xinping,
  • Bhat Prasanna R,
  • Kim Sung-Hyun,
  • Wilson Clyde,
  • Close Timothy J

Journal volume & issue
Vol. 9, no. 1
p. 65


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Abstract Background A large number of genetic variations have been identified in rice. Such variations must in many cases control phenotypic differences in abiotic stress tolerance and other traits. A single feature polymorphism (SFP) is an oligonucleotide array-based polymorphism which can be used for identification of SNPs or insertion/deletions (INDELs) for high throughput genotyping and high density mapping. Here we applied SFP markers to a lingering question about the source of salt tolerance in a particular rice recombinant inbred line (RIL) derived from a salt tolerant and salt sensitive parent. Results Expression data obtained by hybridizing RNA to an oligonucleotide array were analyzed using a statistical method called robustified projection pursuit (RPP). By applying the RPP method, a total of 1208 SFP probes were detected between two presumed parental genotypes (Pokkali and IR29) of a RIL population segregating for salt tolerance. We focused on the Saltol region, a major salt tolerance QTL. Analysis of FL478, a salt tolerant RIL, revealed a small ( Conclusion Recombinant inbred line FL478 contains a small (Saltol region. The Affymetrix rice genome array provides a satisfactory platform for high resolution mapping in rice using RNA hybridization and the RPP method of SFP analysis.