Open Access Research article

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

Sung-Hyun Kim1, Prasanna R Bhat1, Xinping Cui2, Harkamal Walia1, Jin Xu2, Steve Wanamaker1, Abdelbagi M Ismail3, Clyde Wilson4 and Timothy J Close1*

Author Affiliations

1 Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA

2 Department of Statistics, University of California, Riverside, CA 92521 USA

3 International Rice Research Institute, Manila, Philippines

4 United States Department of Agriculture Agricultural Research Service, George E Brown Jr, Salinity Laboratory, Riverside, CA 92507 USA

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BMC Plant Biology 2009, 9:65  doi:10.1186/1471-2229-9-65

Published: 29 May 2009



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.


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 (< 1 Mb) region carrying alleles from the presumed salt tolerant parent, flanked by alleles matching the salt sensitive parent IR29. Sequencing of putative SFP-containing amplicons from this region and other positions in the genome yielded a validation rate more than 95%.


Recombinant inbred line FL478 contains a small (< 1 Mb) segment from the salt tolerant parent in the 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.