Gene expression analysis in leaves of sugarcane genotypes contrasting in biomass production

We collected leaves of genotypes from a panel of sugarcane genotypes selected from groups contrasting in biomass traits - high and low biomass. Genotypes of the high biomass group were IN84-58, IN84-88, Krakatau, SES205A, IJ76-318 and US85-1008. In the low biomass group, we selected White Transparent, Criolla Rayada, TUC71-7, RB72454, SP80-3280 and RB855156. Replicates of each biomass group consisted in one leaf from each genotype. Additionally, we sampled clonal replicates by collecting three leaves from six genotypes (IN84-58, SES205A, US85-1008, White Transparent, RB72454 and SP80-3280). Portions of the first visible dewlap leaves (+1) were collected from six months old sugarcane plants. We collected the middle section of each leaf, removing the midrib. We used the RNeasy Plant Mini Kit (Qiagen) with roughly 50 mg of starting leaves to extract total RNA from each sample. All samples used for sequencing had a RNA Integrity Number (RIN) greater than 8. Libraries were prepared with the TruSeq Stranded kit and sequenced in an Illumina HiSeq 2500. We pooled the 24 libraries and sequenced this pool in two lanes, in paired-end mode (2 × 100 bp).