This study investigates genome evolution, gene expression, and phenotypic variation in two recently formed allotetraploid species (Tragopogon miscellus and T. mirus), their diploid parents (T. pratensis, T. dubius, and T. porrifolius), and synthetic allotetraploids. Using SNPs identified from 454 and Illumina sequencing of the diploids, we designed primers for Sequenom Mass-ARRAY analysis. This study investigates gene loss and shifts in gene expression between allotetraploids and their diploid progenitors. All samples were obtained from ~700 plants grown simultaneously under controlled conditions. We are integrating the genetic knowledge obtained from the Sequenom data with phenotypic data obtained over 1.5 years of growth and development. Phenotypes scored include general size (via weight, height, and leaf number), physiological robustness (measured in photosynthetic rate), reproductive timing and fitness, and NPK values.