Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

GEMs, SFPs And eQTL; Discovery And Mapping Of Expression Level Polymorphisms In Germinating Grain Using The Barley1 Genechip

Elena Potokina¹ , Arnis Druka² , Zewei Luo¹ , Roger Wise³ , Robbie Waugh² , Mike J. Kearsey¹

¹  School of Biosciences, The University of Birmingham, Birmingham, B15 2TT, UK

²  Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK

³  Department of Plant Pathology, Iowa State University, Ames, IA 50011-1020, USA

The genetic control of gene expression during seed germination in barley was investigated using a genetical genomics approach. We carried out genome-wide linkage analysis for the expression data of 22 thousand transcripts for 139 double haploid lines derived from a cross of Steptoe and Morex genotypes with Affymetrix Barley1 GeneChip. The gene expression levels were mapped as quantitative trait loci (eQTLs). In tissues of germinating barley grain important to malting quality, we mapped regulatory control elements for expression of thousands of genes across the genome. Many of the most significantly linked eQTLs are regulated in cis and inherited as monogenic traits representing good candidate genes for previously mapped agronomic QTLs in barley. We also explored the possibility of using transcript abundance data from cRNA hybridizations to Affymetrix microarrays to reveal genetic polymorphisms that can be used as markers to genotype individuals in mapping populations. We developed a robust algorithm to distinguish a maximal number of genetic polymorphisms (AFFYs) in cRNA profiling data that can be used as markers to genotype individuals in segregation populations. For Steptoe/Morex population we identified more than 4000 separate markers which accurately predict the SNP genotype of over 98% of the DH lines. According to our estimates, 35% of the AFFY markers reveal nucleotide polymorphism of the particular gene (Single Feature Polymorphisms, SFPs) while 65% mark polymorphism resulting in extreme variation of gene expression (Genetic Expression Markers, GEMs). These latter are probably cis-acting regulators. A small proportion, ~5%, are loosely or un-linked trans regulators.