A supplement to the rye (Secale cereale L.) reference transcriptome. Secale cereale cultivar:R1620 x R347/1

Mapping and quantifying the rye transcriptome was performed to better understand the genetic control of gene expression in semi-dwarf rye as well as the relationship between genotype and phenotype.Gene expression was assessed by a modified RNA-seq variant, Massive Analysis of cDNA Ends (MACE) on total RNA from each of 96 F6:7 recombinant inbred inbred lines (RIL) in either wild type (WT) or Ddw1 mutant (MT) near-isogenic bulks (NIB) established from six different tissues collected at five developmental stages. The following tissues were harvested at distinct developmental stages: roots, seeds as well as coleoptiles after germination, leaves when two leaves were unfolded, stems (i.) at the end of tillering, (ii.) during stem elongation and (iii.) at begin of heading, as well as ears when inflorescence emerged. RNA was isolated using the NucleoSpin® miRNAkit (Macherey Nagel, Düren, Germany). The fraction of the total RNA >200 bp and the small RNA were isolated and used separately for the preparation of the MACE libraries. The quality of the RNA samples was analyzed running the electrophoretic assay “Plant RNA nano” on an Agilent2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The preparation of MACE libraries, the sequencing using an Illumina Hiseq2000 (Illumina Inc, San Diego, CA, USA) with 1x100 bps and the quantification of mRNA expression was performed at GenXPro GmbH (Frankfurt am Main, Germany) as described in Zawada et al. (2014), Epigenetics 9:161-172.