Characterization of maize genes that exhibit present-absent expression in different genotypes.

University of Minnesota M.S. thesis. December 2010. Major: Plant biological sciences. Advisors:Nathan M. Springer, Robert M. Stupar, Fumiaki Katagiri. 1 computer file (PDF); vii, 47 pages.Maize inbred lines exhibit high levels of gene expression diversity. Several hundred genes exhibit severe expression variation such that the transcript is detected only in one inbred and absent in another. However, the frequency, types of genes affected and potential causes for these “present-absent” (PA) expression patterns in maize inbred lines are not well characterized. Microarray analyses of gene expression patterns in 11-day old seedlings, ear, embryo, and endosperm tissues from two maize inbred lines, B73 and Mo17, identified 570 genes (out of 17000) with PA expression patterns in at least one tissue type. Over 55% of the PA genes exhibit “constitutively absent expression” in which one of the two genotypes exhibits lack of expression in all tissues tested. The remaining PA genes exhibit “tissue specific absent expression” where a gene exhibits present-absent expression in some tissues and present-present expression in at least one other tissue types studied. Many of the PA genes are maize-specific sequences that do not have orthologues in other plant species and the majority of the remaining PA genes are members of gene families. Using existing eQTL and aCGH datasets, we found that PA expression differences are primarily caused by differential regulation rather than by differences in gene content. Collectively, our analysis documented a high frequency of genes that are expressed in some maize lines but not others and suggests that many of these changes are due to trans-regulatory variation