Regrowth and growth dynamics of crop plants after mowing and cutting influence the profitability of their use in agriculture and therefore their improvement are important economic target traits for plant breeding. However, little is known about regrowth dynamics and their underlying molecular mechanisms, especially in non-model organisms. In this study I show how molecular genetic analysis can provide explanations to unravel documented regrowth pattern of Trifolium pratense (red clover). During an introductory experiment, T. pratense was shown to exhibit specific morphogenetic changes in response to cutting, including altering leaf morphology and plant architecture. Moreover it was demonstrated that red clover plants exhibit two different growth strategies resulting in high and low performing plants, and cutting acts as an artificial trigger. This can initiate a second growth phase even in low performing plants and contributes to yield increase. Transcriptome analysis of 32 T. pratense plants, including two treatments (mown/not mown) and two conditions (field/greenhouse), was made, to investigate the molecular mechanisms of the observed phenotypic changes. This resulted in 12 high quality transcriptomes. In total the draft assembly consists of 44,643 contigs with an N50 value of 1,656 (bp). A reference based annotation of the T. pratense genome revealed 24073 known and 4051 newly identified plant specific transcripts. The identification of functional groups within the differentially expressed contigs revealed site specific structures within the transcriptomes, indicating that the plants grown in the greenhouse are less influenced by environmental stress and therefore show a stronger expression of genes related to regrowth. The results of the digital gene expression allowed the identification of candidate genes involved in the plant response during regrowth and could be partially validated via qRT-PCR. In total 14 candidate genes have been selected for further functional analysis including qRT-PCR and t-DNA insertion mutant analysis in the model plant A. thaliana. The phenotypic monitoring of these A. thaliana t-DNA mutant lines displayed gene specific individual growth and regrowth patterns. The results of the phenotypic monitoring, the transcriptome analysis, and the functional analysis, were combined in working models that hypothesizes how regrowth takes place. Therefore T. pratense plants potentially overcome the first stress response after cutting on a molecular level by reprogramming the pathways involved in immune response from inhibiting growth, to promoting growth. In addition further growth activating pathways are activated during regrowth, involving the phytohormone gibberellin. Rapid regrowth and leaf morphology changes could be achieved by expression of genes involved in cell wall modifications. The study provides a good basement to identify the mechanisms involved in regrowth and shift in growth strategies.
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