Figure 1

Experimental design. Seven sequential developmental stages during seedling development were defined during the time of the study: Stage 1: Imbibed, underground seed for 48 hrs, pre-emerging hypocotyls. Stage 2: Yellow cotyledons, underground, radicle is between 10–15 mm long. Stage 3: Yellow cotyledons, underground, radicle is between 16–25 mm long. Stage 4: Cotyledons start emerging from the ground. They are mostly yellow with green edges. Hypocotyls are 40–50 mm long, green where close to the hypocotyls and yellow where deep in the ground. Stage 5: Cotyledons are yellow and green, above the ground and hanging on the curvature of the hypocotyl. Primary roots are developed. Stage 6: Cotyledons are above ground, mostly green, growing straight from the hypotocyl. Primary roots are developed. Stage 7: Cotyledons are above ground and fully green. Plants are 7–8 cms long with full roots and unifoliolates developed. No trifoliolates. Two technical replicates of 70-mer Oligo chips containing 19,200 features were hybridized to observe differential transcript abundance profile between each of stages 2 through 7 in relation to the imbibed seed (stage 1). The dyes were swapped in two experimental replicates to avoid potential dye bias for a total of 4 Oligo chips per biological replicate. Since two biological replicates were set up, a total of 8 chips were used to compare transcript abundance per germination stage defined.