floral phenotypes (Fig. 2.1H). In addition, we have identified numerous hybrid populations between taxa with different flower colors (Fig. 2.2). All such populations offer research opportunities to increase the precision of genotype/phenotype correlations, and perhaps even allow definitive verification of specific genes underlying color variation in Aquilegia.
Despite identification of the likely players in flavonoid pathway function and evolution in Aquilegia (Table 2.1), following the expression and sequence variation in all of these genes in natural or laboratory populations is daunting. With advances in DNA sequencing, such analyses may nonetheless soon become possible in Aquilegia and other natural systems. First, genome sequencing provides a scaffold for mapping variation and identifying the candidate genes that underlie QTL. The Aquilegia genome is currently in production for 8× sequencing (at the Joint Genome Institute), and as sequencing costs decline, similar genomic resources should become available for many additional natural systems. Second, next-generation sequencing techniques open the prospects for sequencing whole transcriptomes from population samples (Kahvejian et al., 2008; Shendure and Ji, 2008). As we have shown here, even without a whole-genome sequence, characterization of ESTs can provide the necessary scaffolds for analyzing the short reads these technologies produce. Thus, if such population-level analysis becomes a reality, then it will be possible to quickly obtain both expression and sequence data for genes underlying flower color (Gilad et al., 2008) in a large number of populations.
Genomic resources will also greatly aid in our ability to dissect traits about which we currently understand little in terms of underlying biochemistry and genetics. Although traits such as petal spur length and flower orientation have strong effects on pollinator visitation and resulting pollen transfer (Hodges et al., 2004), our knowledge of how these traits are genetically influenced and biochemically expressed is meager. Genes affecting cell size or cell number may cause spur-length differences between species. Variation in flower orientation among species is the result of heterochrony as all flowers of Aquilegia go through a similar pattern of orientation during development (Hodges et al., 2002). Early developmental stages of buds are upright; they then become pendent and ultimately become upright again. Differences between species arise because of differences when anthesis occurs in this sequence (Hodges et al., 2002). Little is known about the types of genes that may affect such floral differences and thus the genetic dissection of these traits is more challenging. However, as noted above, the existence of hybrid zones between species that differ in these traits offers the possibility that genomic techniques, such as