Sample Preparation of Arabidopsis thaliana Shoot Apices for Expression Studies of Photoperiod-Induced Genes

Plants produce new organs from a population of pluripotent cells which are located in specific tissues called meristems. One of these meristems, the shoot apical meristem (SAM), gives rise to leaves during the vegetative phase and flowers during the reproductive phase. The transition from vegetative SAM to an inflorescence meristem (IM) is a dramatic developmental switch, which has been particularly well studied in the model species Arabidopsis thaliana. This developmental switch is controlled by multiple environmental signals such as day length (or photoperiod), and it is accompanied by changes in expression of hundreds of genes. A major interest in plant biology is to identify and characterize those genes which are regulated in the stem cells of the SAM in response to the photoperiodic signals. In this sense, techniques such as RNA in situ hybridization (RNA ISH) have been very successfully employed to detect the temporal and spatial expression patterns of genes in the SAM. This method can be specifically optimized for photoperiodic-flowering studies. In this chapter, we describe improved methods to generate plant material and histological samples to be combined with RNA ISH in flowering-related studies.