title: Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array.
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%.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA. kshpaulo@yahoo.co.kr
authors.forename: Sung-Hyun
authors.initials: SH
authors.lastname: Kim
authors.forename: Prasanna R
authors.initials: PR
authors.lastname: Bhat
authors.forename: Xinping
authors.initials: X
authors.lastname: Cui
authors.forename: Harkamal
authors.initials: H
authors.lastname: Walia
authors.forename: Jin
authors.initials: J
authors.lastname: Xu
authors.forename: Steve
authors.initials: S
authors.lastname: Wanamaker
authors.forename: Abdelbagi M
authors.initials: AM
authors.lastname: Ismail
authors.forename: Clyde
authors.initials: C
authors.lastname: Wilson
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Close
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D015870:Gene Expression; D005819:Genetic Markers; D018745:Genome, Plant; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012275:Oryza / Q000235:genetics*; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci; D018749:RNA, Plant / Q000235:genetics; D055051:Salt-Tolerant Plants / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers; D018749:RNA, Plant