Dimensions: Integrating dimensions of Solanum biodiversity: leveraging comparative and experimental transcriptomics to understand functional responses to environmental change

维度：茄属生物多样性的整合维度：利用比较和实验转录组学来了解对环境变化的功能反应

• 批准号: 1136707
• 负责人: Leonie Moyle
• 金额: $ 118.29万
• 依托单位: Indiana University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-12-01 至 2017-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1136707&HistoricalAwards=false
• 关键词: Dimensions; Integrating; dimensions; Solanum; biodiversity

Responses to environmental variation and change can be facilitated or constrained by the genetic basis of adaptations that mediate organism-environment interactions. This research aims to understand and interpret the genetics of functional adaptive biodiversity by integrating analyses at multiple levels of functional trait variation (DNA sequence, gene expression, phenotypes) with data on the environmental, ecological, and evolutionary history of an entire clade of species: Solanum section Lycopersicum (the wild tomatoes). The project focuses on two traits critical to plant-environment interactions: leaf ecophysiology (which influences plant responses to water, light, and carbon dioxide), and constitutive and induced defense responses (which influence the interaction between plants and their natural predators). Both traits differ within and among Solanum species, likely as the result of rapid adaptive change. Using 'next generation' sequencing technologies to quantify DNA sequence and gene expression differences among genotypes and environmental conditions, the project has three components: 1) Comparative transcriptomics (i.e., gene expression profiling) which will provide a evolutionary genomics framework for understanding genetic variation in the group, and identify candidate genes for important ecological transitions among species; 2) Experimental transcriptomics of gene expression responses to both benign (unstressed; noninduced) and stressed (drought-stressed; induced defense) conditions, which will identify molecular responses to ecologically-relevant environments, and evaluate the genetic constraints on current and future evolutionary responses critical to organism-environment interactions; and 3) Integration of results from this study with existing data to generate a core set of loci underpinning functional responses to abiotic and biotic environmental variation, and to develop an integrated understanding of natural adaptive trait variation across an entire group of species. Global environmental change is expected to fundamentally alter patterns of biodiversity, but predicting the direction and magnitude of this change is extremely difficult. This research aims to understand how current biodiversity is shaped by, and reacts to, environmental variation. The sequence and trait data uncovered will contribute to understanding how plants are able to respond to and cope with stress imposed by both their physical environment and by their predators. The project will also contribute to human resources by training researchers in a broad set of skills at the interface of experimental genetics, genomics, and bioinformatics. This research focuses on the wild tomatoes, a diverse group of Andean species within the economically important genus Solanum. Uncovering the genetic basis of diversification is particularly pertinent in the Andean biological hotspot, where the impacts of land-use and climate change threaten a cradle of biodiversity that holds an estimated 12% of global flowering plant diversity. In addition, by examining the wild relatives of several important crop species, including tomato, potato, and pepper, this research has the potential to identify valuable natural variation that confers plant tolerance to critical environmental stresses.

对环境变化和变化的反应可以促进或限制，这些适应的遗传基础介导了有机体 - 环境相互作用。这项研究旨在通过在多种水平的功能性状变化（DNA序列，基因表达，表型）以及有关物种的整个环境，生态和进化史的数据中整合功能自适应生物多样性的遗传学。该项目着重于对植物环境相互作用至关重要的两个特征：叶片生态生理学（这影响了植物对水，光和二氧化碳的反应），以及构成和诱导的防御反应（这影响植物及其自然捕食者之间的相互作用）。卵巢物种内部和之间的两个特征都可能是由于快速自适应变化而导致的。使用“下一代”测序技术来量化基因型和环境条件之间的DNA序列和基因表达差异，该项目具有三个组成部分：1）比较转录组学（即基因表达谱分析），这将提供进化基因组学基因组学框架，以了解该组中的基因变异，并确定候选基因在物种之间的候选基因； 2）基因表达反应对良性（未压力；未诱导）和压力（干旱胁迫；诱发的防御）条件的实验转录组学，这些条件将确定对与生态相关的环境的分子响应，并评估对当前和未来对生物环境相互作用至关重要的遗传约束； 3）这项研究的结果与现有数据的整合，以产生对非生物和生物环境变化的功能响应的基础核心，并在整个物种中发展对自然适应性状变化的综合理解。预计全球环境变化从根本上改变了生物多样性的模式，但是预测这种变化的方向和大小极为困难。这项研究旨在了解当前的生物多样性如何受环境变化的影响和反应。发现的序列和特征数据将有助于了解植物如何应对其物理环境和捕食者所施加的压力。该项目还将通过在实验遗传学，基因组学和生物信息学的界面上培训研究人员的广泛技能来为人力资源做出贡献。这项研究的重点是野生西红柿，野生西红柿是经济上重要的solanum属内的多样化的安第斯物种。在安第斯生物热点中，发现多样化的遗传基础尤其相关，在安第斯生物热点中，土地利用和气候变化的影响威胁着生物多样性的摇篮，估计占全球开花植物多样性的12％。此外，通过检查几种重要的农作物物种的野生亲戚，包括番茄，马铃薯和胡椒，这项研究有可能识别有价值的自然变异，从而使植物对关键环境压力的耐受性赋予了宽容。