Chapter 3 88 3.4 ACKNOWLEDGEMENTS We express our gratitude to the Utrecht Sequencing Facility team (USEQ) for their expertise in performing sequencing, multiplexing, and mapping. Special thanks to Dr. Sara Buti, Dr. Cheyang Liao, and MSc Muthanna Biddanda Devaiah for their invaluable assistance with library preparation and troubleshooting. We also extend our appreciation to Dr. Leonardo Jo, Dr. Maria Angelica Sanclemente, and Dr. Andres Romanowski for their guidance in bioinformatics analysis. 3.5 MATERIALS AND METHODS 3.5.1 Plant materials and growth conditions We germinated Solanum lycopersicum seeds (cv Moneymaker (obtained from Intratuin B.V) and M82 (obtained from Tomato Genetics Resource Center)) for one week in sealed plastic boxes padded with a paper towel soaked with tap water. After one week, similarly sized seedlings were transferred to a 7 cm square pot filled with sieved Primasta ® soil. One week after transfer, plants were randomly separated into two groups and put into far-red or white light treatment. We grew the seedlings grown at 20°C, 70% humidity, 16/8 hour light/ dark cycle in white light conditions for 7 days before the start of the light treatments. For this experiment two treatments with different light conditions were used: white light (WL) and farred (WL+FR). WL condition light intensity was 200 PAR (photosynthetically active radiation). WL+FR condition light intensity was 200 PAR white light supplemented with additional FR to reach R:FR (red-light: far-red light = 0.21). 3.5.2 Phenotype measurements Stem and internode length were measured with digital caliper every day at 10:30am and 4:30pm. 3.5.3 Tissue harvest for RNA-seq The first internode (between the cotyledons and first true leaf) was harvested. Each group of internodes were collected at 6, 24, 30, 48 hours after treatment start. In the end, 200+ samples were collected for two light treatments (WL and WL+FR), two cultivars, four timepoints and two tissues with at least 4 biological replicates per group. Samples were placed immediately into liquid nitrogen until mRNA isolation.
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