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

Author
item KIM, SUNG-HYUN - University Of California
item BHAT, PRASANNA - University Of California
item CUI, XINPING - University Of California
item WALIA, HARKAMAL - University Of California
item XU, JIN - University Of California
item WANAMAKER, STEVE - University Of California
item ISMAIL, ABDELBAGI - University Of California
item Wilson, Clyde
item CLOSE, TIMOTHY - University Of California

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/29/2009
Publication Date: 5/29/2009
Citation: Kim, S., Bhat, P.R., Cui, X., Walia, H., Xu, J., Wanamaker, S., Ismail, A.M., Wilson, C., Close, T.J. 2009. Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array. Biomed Central (BMC) Plant Biology. 9(65)1-10.

Interpretive Summary: Along with wheat and corn, rice is one of the great cereals whose cultivation made human civilization possible. In 2005, the complete genetic sequence, or genome, was compiled and placed in computer banks around the world. Recently, a large number of genetic variations have been identified in rice. It is thought that some of these variations might be responsible for certain traits such as yield, tillering, disease resistance, and stress tolerance among others. In this study, a specialized technique (SFP markers) was used to answer a lingering question about the source of salt tolerance in a particular rice variety, FL478, bred from cross between a salt-tolerant (Pokkali) and salt-sensitive parent (IR29). Surprisingly, earlier genetic work suggested that a large part of a region of the chromosome that is thought to be involved with salt tolerance (Saltol region) in FL478 came from the salt-sensitive parent, not the salt-tolerant parent. However, this work revealed that a small segment in the Saltol region from the salt-tolerant parent and might important in conveying salt tolerance to FL478. These results help give the rice breeders a rational basis on which to breed for salt tolerance in rice. Specifically, this work may have isolated a portion of genome which may be involved in salt tolerance.

Technical Abstract: 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.