Comparative transcriptome analysis and phenotypic monitoring of Trifolium pratense (Fabaceae) under land use scenarios (TRATSCH II - Trifolium pratense RNA analysis to screen character heterogeneity)

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Plants adapt to changes in the environment as they can be invoked by agricultural land use with an astonishing morphological flexibility caused by differential gene expression and genetic adaptation. However, our knowledge about organismal responses to land use with regard to underlying molecular genetic processes and changes in genetic diversity is scarce. In the proposed project, we aim to investigate the organisms genetic responses to environmental perturbations (mowing and fertilization on grassland systems). Red clover (Trifolium pratense) is an important agricultural forage species in grasslands, as it is a rich protein source, and has reduced nitrogen fertilization requirements due to N2-fixation. Both attributes contribute to reduce the ecological footprint of grassland based agriculture. T. pratense occurs on all Biodiversity Exploratory grassland sites and in TRATSCH I we showed that T. pratense (i) responds to mowing with specific morphological changes; (ii) we identified genes that are differentially expressed between plots and others, that show a mowing-specific response, and (iii) established a mRNA-seq fingerprinting protocol which allows for a broader sampling scheme and associations with environmental variables. Thus, we are now able to interrelate landscape genetics towards landscape genomics to better understand a species genome functioning in an environmental context. We propose to extend our data collection and analyses to all Exploratories to investigate how site/treatment/environmental specific transcriptional changes of T. pratense are. We further propose to correlate T. pratense differential gene expression with environmental data. Functional analysis of the mowing-response genes will improve our understanding of differentially expressed developmental regulators that coordinate the phenotype and regrowth of biomass upon mowing treatments. We test different management regimes to achieve high protein content with the lowest possible fertilization regime to minimize the environmental footprint in grassland based agriculture. Last, we hypothesize that epigenetic modifications are involved in the regulation of morphological changes in response to mowing, and to test the hypothesis we will observe quantitative and temporal shifts in methylation pattern of the developmental genes genomic loci.