Exploring conservation of cellular-level traits in shade avoidance syndrome among species 5 195 5.5.3 Phenotyping To conduct plant phenotyping, a digital caliper was employed to measure specific plant attributes, which varied depending on the plant species. For the phenotyping of O. basilicum, P. sativum, S. lycopersicum Moneymaker, Capsicum annuum, Solanum melongena and Brassica nigra each sample had 8 replicates and experiments were repeated twice. Arabidopsis measurement was conducted with 12 replicates and three times replication. 5.5.4 Microscope analysis To stain the samples, we utilized a 0.1% (w/v) safranin solution, exposing the internode samples to it for two minutes. Subsequently, the samples underwent rinsing with 70% ethanol until the ethanol became clear. The samples were then returned to a 70% ethanol solution for storage. For microscope analysis, we employed the Leica 700 Microscope in conjunction with analyzeD software to capture images. Subsequently, ImageJ was utilized to measure specific components as outlined for each species in Table 1. The images were captured at a 10X magnification. Regarding data analysis and graph generation, we employed GraphPad Prism 9. Additionally, statistical analysis, including the Student t-test, was conducted using Microsoft Excel. 5.5.5 RNA Extraction and cDNA Synthesis In the initial qPCR experiment, plants were subjected to two conditions: exposure to white light (WL) or a low R/FR ratio of 0.2 (WL+FR). The plants were harvested for whole internode or pith after 6h or 24h light treatment. Each experimental condition was replicated four times, with each replicate consisting of 8 to 12 plants. Technical replicates for qPCR were performed three times. For each biological replicate, three internodes were placed in a tube, snap-frozen using liquid nitrogen, and stored at -80 degrees Celsius. Total RNA was extracted using the RNeasy kit (Qiagen), and the RNA concentration was determined using a nanodrop spectrophotometer (Thermo Fisher Scientific). Reverse transcription was carried out using random hexamer primers with RevertAid H Minus reverse transcriptase. To facilitate comparison, the Log2FC (Logarithm of Fold Change) was employed. 5.5.6 Quantitative RT-PCR Real-time PCR was conducted using the Bio-rad CFX opus 384 system with the Bio-rad CFX Maestro software. Primers listed in Table 1 were employed along with SYBRgreen
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