KNOTTED-like homeobox genes are thought to be critical in plant morphogenesis, apparently being involved in meristem initiation and/ or maintenance. Sequence variation in this potentially important gene family is, however, poorly documented. In grasses, for example, published knowledge of sequence variation among Kn1 homologues is based on data from as few as three species (barley, maize and rice). In order to gain a broader understanding of variation among Kn1 homologues in grasses, we designed primers to amplify an 800bp portion of this gene family across a phylogenetically-diverse array of grasses. This sequence excludes the homeodomain and spans two introns that have a total length of about 300bp. In this paper we compare levels of sequence variation between coding and non-coding regions and evaluate how changes in the former influence protein primary and secondary structure. Finally, using the GPWG phylogeny of the grass family as a baseline, we use character optimization methods to identify in which lineages major levels of change have taken place.

Key words: homeobox genes, KNOTTED, Poaceae