Plant & Animal Genomes XIV Conference Plant & Animal Genomes XIV ConferenceJanuary 14-18, 2006
Town & Country Convention Center
San Diego, CA
The study of the genetic basis of complex traits via gene expression analysis using microarrays will uncover many hundreds of genes which will mainly be genes downstream in signalling cascades. For use in plant breeding the key elements regulating these downstream genes must be identified. Combining gene expression and QTL analysis (expression level polymorphism (ELP) analysis) has the potential to link trait analysis and phenotype with gene identification.
In order to provide proof of concept for ELP analysis in wheat it was necessary to determine the extent of variation observed in gene expression under field conditions and to determine if the expression of genes and gene clusters could be associated with mapped genetic markers. A subset of a mapping population was grown in each of two years in three locations with three replications per location in a lattice design. Immature seed from each line was collected 5 days after anthesis and immediately frozen in liquid N. RNA was isolated for expression analysis using the Affymetrix wheat GeneChip. A preliminary experiment was carried out to determine the extent of variation within a location. For all three locations the rep effect was not significant. Subsequent analysis was performed on a single rep from one location with all 42 lines subjected to expression analysis. Genes with highly significant differences in expression between genotypes were identified and subjected to clustering using K-means. The expression level of each of these genes was correlated with 330 markers mapped on the population. In many instances groups of genes which clustered together on the basis of expression analysis could be mapped to a specific chromosomal region. Preliminary results indicate a location on chromosome 5B which may regulate the expression of hardness and/or storage protein related genes. The results are encouraging that ELPs in wheat can be used to uncover the molecular basis for important traits.