*4.2. Br135K Microarray Analysis*

The Br135K microarray (Brapa\_V3\_microarray, 30 -Tiling microarray) is a high-density DNA array prepared with Maskless Array Synthesizer (MAS) technology by NimbleGen (http://www.nimblegen. com/) [55]. Probes were designed from 41,173 genes from *Brassica rapa* accession Chiifu-401-42 (http://brassicadb.org/brad/). All three probes were 60 mers with 30 bp overlaps in 120 bp regions (60 bp of coding sequence plus 60 bp of the 3'UTR for each gene), representing 123,647 features. Fifty features from five markers (*GUS*, *GFP*, *Bar*, *Kan*, *Hyg*) were also included. Total and polysomal RNA were extracted using an RNeasy Mini kit (Qiagen, GmbH, Hilden, Germany) and the RNA protect Reagent (Qiagen), and contaminating DNA was removed by on-column DNase digestion with RNase-free DNase (Promega, Madison, WI, USA). Labeling, data processing, and background correction were performed as described previously [56]. To assess the reproducibility of the microarray analysis, the experiment was repeated using independently prepared total RNA samples from two biological replicates. To obtain insights regarding the putative biological functions and biochemical pathways of the DEGs, enrichment analysis was carried out by searching the GO [57], agriGO [58], and Kyoto Encyclopedia of Genes and Genomes [59] databases.
