Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/26/2008
Publication Date: 5/10/2008
Citation: Coram, T., Settles, M.L., Wang, M., Chen, X. 2008. Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus. TAG 117:401-411. Interpretive Summary: In this study, we used a novel combination of functional genomics, statistics, and molecular genetics to identify quantitative differences in the expression of genes involved in wheat resistance to the stripe rust pathogen. We used the microarray data of two wheat lines differing at the locus of Yr5, an effective gene against all races of stripe rust identified so far in the United States to identify expression level polymorphisms (ELPs) and single feature polymorphisms (SFPs). We identified 91 ELP probe sets and 118 SFP-containing probe sets between the two wheat lines, and only nine ELP probe sets also contained SFPs. The proportion of the expression difference represented by ELPs and SFPs was very similar to the estimated proportion of the genome that was incorporated from the resistance donor parent in the two wheat lines. Using the wheat-rice genomic similarities, we were able to determine that the majority of ELPs/SFPs likely occurred in the same chromosome as the stripe rust resistance locus and that there was a strong correlation between the physical location of the ELPs and SFPs. This study represents the first array-based polymorphism survey in near-isogenic wheat lines, and the results are applied to stripe rust resistance, an agriculturally important trait.
Technical Abstract: DNA polymorphisms are valuable for several applications including genotyping, molecular mapping and marker-assisted selection. The Affymetrix Wheat GeneChip was used to survey expression level polymorphisms (ELPs) and single-feature polymorphisms (SFPs) between two near-isogenic wheat genotypes (BC7:F4) that differ for the Yr5 stripe rust resistance locus, with the objective of developing genetic markers linked to Yr5. Ninety-one probe sets showing ELPs and 118 SFP-containing probe sets were identified between isolines, of which just nine ELP probe sets also contained SFPs. The proportion of the transcriptome estimated to be variable between isolines from this analysis was 0.30% for the ELPs and 0.39% for the SFPs, which correlated to the theoretical genome difference between isolines of ~0.39%. Using wheat-rice synteny, both ELPs and SFPs mainly clustered on long arms of rice chromosomes four and seven, which are syntenous to wheat chromosomes 2L (Yr5 locus) and 2S, respectively. The strong physical correlation between the two types of polymorphism indicated that the ELPs may be regulated by cis-acting DNA polymorphisms. Twenty SFPs homologous to rice 4L were used to develop additional genetic markers for Yr5. Physical mapping of the SFP probe sets to wheat chromosomes identified nine on the target chromosome 2BL, thus wheat-rice synteny greatly enhanced the selection of SFPs that were located on the desired wheat chromosome. Of these nine, four were converted into polymorphic cleaved amplified polymorphic sequence (CAPS) markers between Yr5 and yr5 isolines, and one was mapped within 5.3 cM of the Yr5 locus. This study represents the first array-based polymorphism survey in near-isogenic genotypes, and the results are applied to an agriculturally important trait.