Many traits of economic importance in crop plants are quantitative, complicating the selection for desirable characteristics. Recent studies suggest a complex relationship between genotype and phenotype, with genetic variability often appearing as differences in gene expression rather than structural changes in proteins. In oat (Avena sativa L.), lipid and protein content are economically important traits. In the first of four studies reported here, partial sequences for eight genes involved in lipid or protein biosynthesis were obtained from ten oat cultivars with varying lipid and protein content. Phylogenetic analysis showed that these sequences clustered into families possibly corresponding to homeologous genes. Some cultivar- and family-specific polymorphisms were identified. In the second study, we surveyed differential gene expression between developing kernels of cultivars Kanota and Ogle by constructing reciprocal subtractive libraries. Of the 195 contig sequences obtained, only a minority had homology to characterized sequences. Grouping these sequences in categories based on gene ontology of their BLAST hits showed different profiles of expression for each cultivar. In the third study, we tested a method for transforming macroarray data consisting of dividing spot signal by the median array background. This reduced variation due to array exposure time. In the fourth study, gene expression levels were considered as quantitative traits in the Kanota x Ogle mapping population. Macroarrays featuring oat clones differentially expressed between both parents were hybridized with cDNA from the population lines. Among the 33 significant expression quantitative trait loci detected, most clustered to linkage group 29--43, a possible "hot-spot" of gene expression regulation.

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