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

植物适应环境的变化，因为它们可以被农业土地利用所调用，具有由差异基因表达和遗传适应引起的惊人的形态灵活性。然而，我们的知识有机体对土地利用的基本分子遗传过程和遗传多样性的变化方面的反应是稀缺的。在拟议的项目中，我们的目标是调查生物体对环境扰动（割草和施肥草地系统）的遗传反应。红三叶草（Trifolium pratense）是草地上重要的农业牧草，具有丰富的蛋白质来源和固氮作用，减少了对氮肥的需求。这两个属性都有助于减少草地农业的生态足迹。T. Pratense发生在所有的生物多样性勘探草地网站和TRATSCH我，我们表明，T。Pratense（i）响应割草与特定的形态变化;（ii）我们确定了基因之间的差异表达的地块和其他，显示割草特异性反应，（iii）建立了一个mRNA-seq指纹协议，允许更广泛的采样方案和与环境变量的关联。因此，我们现在能够相互关联的景观遗传学对景观基因组学，以更好地了解一个物种的基因组在环境中发挥作用。我们建议将我们的数据收集和分析扩展到所有的Exploratories，以调查如何网站/治疗/环境特定的转录变化的T。普拉滕斯群岛我们进一步提出T.与环境数据的差异基因表达。割草反应基因的功能分析将提高我们的理解差异表达的发育调节协调割草处理后的表型和生物量的再生。我们测试了不同的管理制度，以实现高蛋白质含量与尽可能低的施肥制度，以尽量减少草地农业的环境足迹。最后，我们假设，表观遗传修饰参与调节的形态变化，割草，并测试的假设，我们将观察定量和时间的变化，甲基化模式的发育基因的基因组位点。

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.