The vegetative transcriptome of Arabidopsis thaliana

Plants grow continuously and undergo numerous changes in their vegetative morphology and physiology during their life span. The molecular basis of these changes is largely unknown. To provide a more comprehensive picture of shoot development in Arabidopsis, microarray analysis was used to profile the mRNA content of shoot apices of different ages, as well as leaf primordia and fully-expanded leaves from 6 different positions on the shoot, in early-flowering and late-flowering genotypes. This extensive dataset provides a new and unexpectedly complex picture of shoot development in Arabidopsis. At any given time, the pattern of gene expression is different in every leaf on the shoot, and reflects the activity at least 6 developmental programs. Three of these are specific to individual leaves (leaf maturation, leaf aging, leaf senescence), two occur at the level of the shoot apex (vegetative phase change, floral induction), and one involves the entire shoot (shoot aging). Our results demonstrate that vegetative development is a much more dynamic process that previously imagined, and provide new insights into the underlying mechanism of this process. Samples were collected from FRI;FLC and FRI;flc-3 of four growth time points—shoot apices with all primordia under 1 mm (120 apices for days 4 and 6, 60 for day 9, and 30 for days 11 and 14, and 24 for day 21), 1 mm leaf primordia (30 primordia per replicate, 60 for leaves 1/2), fully expanded leaves (9 leaves per replicate, 18 for leaves 1/2), and leaves past full expansion (leaves 3, 5, and 7 collected at the same point as fully-expanded leaf 9). Six-day-old shoot apices were also harvested for FRI;FLC;35S::miR156mimic. To determine the point of full expansion, leaves from 8 representative plants of each genotype were measured daily until the average daily increase in total leaf length was less than 1 mm on each of two consecutive days, with the second day called the point of full expansion. Two microarray experiments were done with fully-expanded leaves of FRI;flc-3 and FRI;FLC, the first set (called experiment 1, throughout) collected from the same plants as the leaf primordia and the second (experiment 2) at the same time as the shoot apices, leaves past full expansion, and FRI;FLC;35S::mir156mimic. Equal collections were made at three different times in the day—4-5 hours, 8-9 hours, and 11.5-12.5 hours after the subjective dawn—and pooled to minimize the effects of circadian rhythms on the data. Three replicates were used for all conditions except there were only two shoot apex day 6 replicates for FRI;FLC and one for FRI;flc-3.