An undergraduate laboratory exercise to study the effect of darkness on plant gene expression using DNA microarray

Abstract

DNA microarrays are microscopic arrays on a solid surface, typically a glass slide, on which DNA oligonucleotides are deposited or synthesized in a high-density matrix with a predetermined spatial order. Several types of DNA microarrays have been developed and used for various biological studies. Here, we developed an undergraduate laboratory exercise using an Arabidopsis DNA microarray to study the gene expression of Brassica rapa, Wisconsin Fast Plant. Genes involved in senescence, cell wall loosening/degradation, and sugar transport were the most upregulated, while those involved in photosynthesis, the elimination of reactive oxygen intermediates associated with photooxidative stress and auxin synthesis, were the most downregulated. Students were able to complete the experiment successfully. Throughout the exercise, they learned various important molecular techniques including RNA isolation, quantification, reverse transcription, cRNA synthesis, labeling and purification, and microarray hybridization, washing, scanning, and feature extraction. The exercise can be integrated into a college-level molecular biology laboratory. The procedure used can be adapted to examine other effects on other organisms.

Identification of candidate genes for leaf scorch in Populus deltoids by the whole genome resequencing analysis

“…Sugar transporter family ERD6-like homologs (At1g08920 and At1g08930) could be involved in anthocyanin pigmentation in a Ca 2+ signal-dependent manner 19 . Chang et al ., (2007) found that the dark-treated plants, with no photosynthetic assimilates, have to alter their carbohydrate chemistry and this may require an increased expression of the sugar-transporter gene 20 . Therefore, those two genes might be pivotal candidate genes associated with leaf scorch in JHP.…”