Split-plot microarray design allows sensitive detection of expression differences after ultraviolet radiation in the inbred parental lines of a key maize mapping population

Gene expression levels were quantified after ultraviolet radiation treatment in the parental inbred lines of the maize mapping (IBM) population. This allows us to take advantage of natural variation between maize lines to analyse variation in gene expression. Using a statistically sound split-plot experiment cDNAs were identified with differently regulated expression in B73 and Mo17 after UV treatment. Fewer genes were down-regulated in B73; this global strain difference in the number of genes up- and down-regulated does not appear to reflect general hybridization differences. Contrary to our expectation, there was a higher proportion of highly expressed genes (based on EST recovery) that were differently expressed by UV between lines. Genes affected by UV (but not significantly different between B73 and Mo17) include gene types proposed to function in UV acclimation and adaptation based on experiments in other species or other experiments in maize. Several new functional classes were identified as UV-regulated, including genes encoding proteins that modulate chromatin structure.