ARS | Publication request: Detecting Single-Feature Polymorphisms On The 7E Thinopyrum Chromosome Using the Wheat Oligonucleotide Array

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: December 1, 2006
Publication Date: January 13, 2007
Citation: Buescher, E., Cui, X., Anderson, J.M. 2007. Detecting Single-Feature Polymorphisms On The 7E Thinopyrum Chromosome Using the Wheat Oligonucleotide Array. Plant and Animal Genome Conference.

Technical Abstract: Wheatgrass species such as Thinopyrum and Lophopyrum have become important sources of useful traits particularly disease resistance to Barley and Cereal Yellow Dwarf viruses, leaf rust and Fusarium head blight. Molecular markers derived from wheat have been used to identify and characterize wheatgrass-wheat translocations. However, most wheat-derived PCR markers do not identify wheatgrass specific polymorphisms and consequently typically are used as negative (wheat DNA fragment missing) markers. In order to identify single feature polymorphisms that are either codominant for wheatgrass and wheat or are dominant for wheatgrass, wheat oligonucleotide arrays were hybridized with labeled cRNA isolated from five wheat-wheatgrass substitution or addition lines each having a wheatgrass 7E chromosome and the reference wheat line Chinese Spring. These arrays were analyzed for single feature polymorphisms (SFP) using a robustified projection pursuit (RPP) algorithm (Cui et al, 2005) as well as a false discovery rate (FDR) based modified t-test (Rostoks et al, 2005). SFPs can be single nucleotide polymorphisms (SNPs), insertion/deletions (InDels) or explained by alternative splicing. Comparisons of the translocation perfect match (PM) probes and probesets yielded approximately 44 putative 7E SFPs using the RPP algorithm after any already known SNPs were removed based on wheat SNP database search (http://wheat.pw.usda.gov/GG2/blast.shtml). Future objectives are to clone and sequence the putative 7E SFPs to determine which are SNPs or InDels. The markers developed from SFP data for the 7E wheatgrass chromosome will be used to map the 7E chromosomes and as markers linked to wheatgrass-derived disease resistance traits.