title: Red clover (Trifolium pratense) is used worldwide as a fodder plant due its high nutritional value. In response to mowing, red clover exhibits specific morphological traits to compensate the loss of biomass. The morphological reaction is well described, but knowledge of the underlying molecular mechanisms are still lacking. Here we characterize the molecular genetic response to mowing of red clover by using comparative transcriptomics in greenhouse conditions and agriculturally used field. The analysis of mown and control plants revealed candidate genes possibly regulating crucial steps of the genetic network governing the regrowth reaction. In addition, multiple identified gibberellic acid (GA) related genes suggest a major role for GA in establishing the regrowth morphology of red clover. Mown red clover plants showing this regrowth morphology were partially rescued by exogenous GA application, demonstrating the influence of GA during regrowth. Our findings provide insights into the physiological and genetic processes of mowing, a common land use practice, in red clover, to serve as a base for red clover yield improvement.
design: RNA was extracted using NucleoSpin RNA Plant Kit (Macherey-Nagel GmbH & Co. KG, Dren, Germany) according to the manufacturers instructions. Preparation of the cDNA libraries and the strand-specific sequencing was conducted by Eurofins Genomics (Ebersberg, Germany). The RNAs of four individuals were pooled for each RNA-Seq library and sequenced on an Illumina Hiseq2000 platform with chemistry v3.0, creating 2x 100 bp paired end reads.