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

Authors

Sung-Hyun Kim, University of California, RiversideFollow
Prasanna R. Bhat, University of California, RiversideFollow
Xinping Cui, University of California, RiversideFollow
Harkamal Walia, University of California, RiversideFollow
Jin Xu, University of California, RiversideFollow
Steve Wanamaker, University of California, RiversideFollow
Abdelbagi M. Ismail, International Rice Research InstituteFollow
Clyde Wilson, USDA, Agricultural Research ServiceFollow
Timothy J. Close, University of California, RiversideFollow

Date of this Version

2009

Citation

BMC Plant Biology 2009, 9:65

Comments

© 2009 Kim et al.

Open access

doi:10.1186/1471-2229-9-65

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 (< 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%. Conclusion: 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.