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

植物能够适应环境的变化，因为它们可以被农业土地利用所调用，并因基因表达和遗传适应的差异而具有惊人的形态灵活性。然而，关于生物对土地利用的反应，关于潜在的分子遗传过程和遗传多样性的变化，我们的知识很少。在拟议的项目中，我们的目标是调查生物对环境扰动(草原系统的割草和施肥)的遗传反应。红三叶(Trifolium Pratense)是一种重要的草原农业牧草，具有丰富的蛋白质来源，并因固氮而降低了氮肥的需求。这两个属性都有助于减少草原农业的生态足迹。草地早熟禾存在于所有生物多样性探索草地站点上，在Tratsch I中，我们发现：(I)草地早熟禾对割草的反应具有特定的形态变化；(Ii)我们确定了在样地和其他草地之间差异表达的基因，表现出割草特有的反应；(Iii)建立了允许更广泛的采样方案和与环境变量关联的mRNA-SEQ指纹图谱协议。因此，我们现在能够将景观遗传学与景观基因组学相互联系起来，以更好地了解物种基因组在环境背景下的功能。我们建议将我们的数据收集和分析扩展到所有的探索，以调查如何地点/处理/环境特异性的转录变化。我们进一步建议将草地早熟禾差异基因表达与环境数据相关联。对割草反应基因的功能分析将提高我们对差异表达的发育调控因子的理解，这些调控因子在割草处理中协调生物量的表型和再生。我们测试了不同的管理制度，以实现高蛋白含量和尽可能低的施肥制度，以最大限度地减少草地农业的环境足迹。最后，我们假设表观遗传修饰参与了对修剪反应的形态变化的调节，为了验证这一假设，我们将观察发育基因基因组座位甲基化模式的定量和时间变化。

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.