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ARS Home » Midwest Area » St. Paul, Minnesota » Plant Science Research » Research » Publications at this Location » Publication #228436
Title: Single-Feature Polymorphism Discovery by Computing Probe Affinity Shape Powers

Author
item XU, WAYNE WENZHONG - UNIVERSITY OF MINNESOTA
item CHO, SEUNGHO - UNIVERSITY OF MINNESOTA
item Yang, Suk
item Bolon, Yung Tsi
item JIA, HAIYAN - UNIVERSITY OF MINNESOTA
item XIONG, YANWEN - UNIVERSITY OF MINNESOTA
item BILGIC, HATICE - UNIVERSITY OF MINNESOTA
item BODDU, JAYANAND - UNIVERSITY OF MINNESOTA
item MUEHLBAUER, GARY - UNIVERSITY OF MINNESOTA

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/26/2009
Publication Date: 8/26/2009
Citation: Xu, W., Cho, S., Yang, S.H., Bolon, Y.E., Jia, H., Xiong, Y., Bilgic, H., Boddu, J., Muehlbauer, G. 2009. Single-feature polymorphism discovery by computing probe affinity shape powers. BioMed Central (BMC) Genetics. 10:48.

Interpretive Summary: In order to study the effect of genetic variation, a reliable method is required to discover and analyze genetic differences. Previously described methods resulted in high error rates and low sensitivity. Here, a new method with low false positive rates and increased sensitivity was developed for discovery and analysis of genetic differences within related species for a specific platform. This method was successfully tested on barley lines. These results demonstrate that this new discovery method successfully identifies genetic differences and can also be useful for genome analysis in other organisms.

Technical Abstract: Single-feature polymorphism (SFP) discovery is a rapid and cost-effective approach for plant genomic polymorphism studies. However, either a high false positive rate or low sensitivity was reported in previous SFP detection methods. An alternative method was developed for genome-wide SFP discovery by computing probe affinity differences and affinity shape powers formed between the neighboring probes of Affymetrix GeneChip and the expressed transcripts from different genotypes. A 2.05% false positive rate (FPR) and a sensitivity of 69.08% resulted from testing the published barley GeneChip data set with known SNPs and known non-polymorphic sequences. We used this method for SFP discovery in barley bowman and Bowman-uniculm2 mutant lines, and 365 SFPs were found. Fifteen SFPs out of 16 were confirmed by PCR sequencing (93.75%). Most of the SFP located genes were functionally annotated in this study. This method can be applied to other organisms for genome-scope SFP discovery.