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

对环境变异和变化的反应可以通过调节生物体-环境相互作用的适应性遗传基础来促进或限制。本研究旨在了解和解释功能适应性生物多样性的遗传学整合分析在多个层次的功能性状变异（DNA序列，基因表达，表型）与数据的环境，生态和进化历史的一个完整的物种：茄节番茄（野生番茄）。该项目侧重于对植物与环境相互作用至关重要的两个特征：叶生态生理学（影响植物对水，光和二氧化碳的反应）和组成性和诱导性防御反应（影响植物与其天敌之间的相互作用）。这两种性状在茄属物种内部和之间都有差异，可能是快速适应性变化的结果。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，该项目有三个组成部分：1）比较转录组学（即，基因表达谱），这将提供一个进化的基因组学框架，以了解遗传变异的群体，并确定候选基因的重要生态过渡物种; 2）实验转录组学的基因表达反应，以良性（非胁迫;非诱导）和胁迫（干旱压力;诱导防御）条件，这将识别对生态相关环境的分子反应，并评估对生物体与环境相互作用至关重要的当前和未来进化反应的遗传约束;和3）将本研究的结果与现有数据整合，以产生支持对非生物和生物环境变化的功能反应的核心基因座组，并对整个物种群的自然适应性性状变异进行综合了解。全球环境变化预计将从根本上改变生物多样性的格局，但预测这种变化的方向和幅度是极其困难的。这项研究旨在了解目前的生物多样性是如何形成的，并对环境变化作出反应。揭示的序列和性状数据将有助于理解植物如何应对和科普物理环境和捕食者施加的压力。该项目还将通过培训研究人员在实验遗传学、基因组学和生物信息学方面的广泛技能来促进人力资源。这项研究的重点是野生番茄，这是经济上重要的茄属中的一组安第斯物种。揭示多样化的遗传基础在安第斯生物热点地区尤为重要，土地使用和气候变化的影响威胁着生物多样性的摇篮，据估计，该地区拥有全球开花植物多样性的12%。此外，通过研究几种重要作物物种的野生亲缘植物，包括番茄、马铃薯和辣椒，这项研究有可能确定有价值的自然变异，赋予植物对关键环境胁迫的耐受性。

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.