Collaborative Research: RoL-Rules for Dynamic-Light Environmental Sculpting of Genomes

在嘈杂的环境中获得清晰的信号不仅是人类必须解决的问题，也是自然界所有生物都要面对的问题。这项研究的目的是确定植物对嘈杂和可变的光信号作出反应的规则。研究人员假设，在不同的时间段内，在低光和高光之间切换会改变植物对光的感知方式。为了研究这个问题，我们选择了草，因为草已经进化到可以在许多类型的光环境中生长，比如在森林地面上，光线闪烁和阴影很常见；在开阔的田野上，除了云层和一天中的时间，光线变化很少。研究人员假设，草在这些不同的光环境中茁壮成长的能力是在它们的基因组中编码的。该项目将研究基因组编码感知适应动态和恒定的光环境如何影响草的生理、发育、遗传和进化。研究人员将交叉培训研究生和博士后，特别是那些来自最先进的分子生物学、生理学和基因组学领域代表性不足的群体的学生。研讨会将汇集国际知名的植物生态学、进化生物学、植物生理学和遗传学专家，以及希望应用这些观点来了解植物如何对动态环境做出反应的学生和科学家。多达60名新的学士学位后分析师将参加国际培训讲习班。在几个组织尺度上，增加个体适应度的基因组元素的变化被维持，而那些降低适应度的变化则被反选择用于繁殖。相对于维持它们的能量消耗，对适应性中性的基因组元素被过滤掉。这些规则在基因的尺度上已经很好地建立起来了，但还没有扩展到基因组。该项目采用综合的方法，通过表征来自厄瓜多尔的一组表型多样但单系的草的全基因组来解决这个问题。这些草生长在不同的栖息地，从加拉帕戈斯群岛、帕拉莫（高山苔原）、雨林、河岸和沿海地区。这些草也有广泛的习性（分蘖vs藤蔓vs灌木vs树状），自养代谢（C3 vs C4碳固定）和生存策略（多年生vs一年生）。需要解决的具体问题是，与稳定的光环境相比，哪些基因/等位基因在动态光环境中形成形态/生理表达。该项目汇集了两个基本学科：植物学和基因组学，但将其扩展到细胞生物学、发育生物学、进化和系统学。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

The problem of getting a clear signal in a noisy environment is a problem that not only humans must resolve but one that all organisms in nature experience. The goal of this research is to determine the rules by which plants respond to noisy and variable light signals. The investigators hypothesize that switching between low and high levels of light over varying periods of time changes how light is detected by plants. To study this problem, grasses were chosen because grasses evolved to grow in many types of light environments such as on the forest floor where light flickering and shadows are common to open fields where the light changes very little except for clouds and time of day. The investigators hypothesize that the ability for grasses to thrive in these different light environments is encoded in their genomes. The project will examine how genomically encoded sensing adaptations to dynamic and constant light environments shapes the physiology, development, genetics, and evolution of grasses. Investigators will cross train graduate students and post-docs, especially those from underrepresented groups in state-of-the-art molecular biology, physiology and genomics. Seminars will bring together internationally recognized experts in plant ecology, evolutionary biology, plant physiology and genetics with students and scientists who want to apply these perspectives to understand how plants respond to dynamic environments. Up to 60 new post-baccalaureate analysts will participate in international training workshops. Changes in genomic elements at several scales of organization that increase the fitness of an individual are maintained while those changes that decrease fitness are counter selected for propagation. Genomic elements that are neutral to fitness are filtered away relative to the energy cost of maintaining them. These rules are well established at the scale of genes but not yet scalable to genomes. This project takes an integrative approach to this question by characterizing the full genomes of a phenotypically diverse, yet monophyletic, set of grasses from Ecuador. These grasses live in diverse habitats ranging from the Galapagos Islands, the Paramo’ (alpine tundra), the rain forest, and riparian and littoral zones. These grasses also have a wide range of habits (tillering vs vines vs. bushy vs. tree-like), autotrophic metabolism (C3 vs. C4 carbon fixation), and survival strategies (perennial vs. annual). The specific question to be addressed is what genes/alleles shape morphologies/physiologies expressed in dynamic light environments as opposed to stable light environments. This project brings together two basic disciplines: botany and genomics but extends the connections into cell biology, developmental biology, evolution, and systematics.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.