Functional Evolution of the FRUITFULL Gene Lineage in the Tomato Family (Solanaceae)

因为植物扎根于土地，它们必须有办法让后代离开家园，开拓新的领域。 种子通常在两种类型的容器中生产，以促进这一过程。 干燥的豆荚在成熟时裂开，释放出种子，所以它们可以被风带走，或者如果它们有钩子，它们可以粘在动物身上。 相反，一个肉质的水果，如苹果或黄瓜，会被动物吃掉，然后传播种子。 肉质水果为所有动物提供重要的营养来源，包括人类;人类饮食和经济的很大一部分是基于水果，如西红柿，辣椒，甜瓜，南瓜或鳄梨。 许多不同的开花植物群体经历了从产生干燥豆荚到产生肉质果实的进化转变，产生了重要的生态和经济后果。 该项目的长期目标是了解决定植物是否会产生干燥豆荚或可食用的肉质果实的遗传机制。 这项工作的重点是茄科植物，其中包括豆荚生产物种，如沙漠烟草和矮牵牛，以及肉质水果生产物种，如番茄，茄子和辣椒。 这些实验着眼于一组基因的作用，这些基因似乎经历了与肉质水果起源相关的功能变化。 这些结果可以识别特定的基因或基因的变化，使一个物种能够生产出可食用的营养水果，这可能有助于作物的改良或发展。 该项目还将成为关于茄科植物果实结构和多样性的两个植物园展览的基础，并将为代表性不足的少数民族的高中生和大学生以及一名研究生和一名博士后研究员提供培训。MADS盒转录因子FRUITFULL（FUL）通过确定果实伸长和正常裂开以释放种子所需的细胞分化模式在拟南芥果实的发育中起关键作用。FUL直向同源物也被证明是一些肉质果实中适当成熟所需的，在果实发育中显示出保守的功能，但具有实质上不同的结果。 茄科（茄科）的果实祖先是干燥和开裂的，但随着茄亚科（Solanoideae）的起源，果实转向肉质。 FUL基因进化枝在某些物种中发生了重复，导致四个拷贝，该项目的第一部分将使用转录组和靶向PCR方法的组合生成基因树，以确定何时发生重复。这些数据还将用于确定不同的旁系同源分支是否经历了不同的进化模式（中性，纯化等），这将与第二部分收集的功能数据相关联。 第二部分利用CRISPR技术比较了四个FUL旁系同源物在沙漠烟草和番茄中的功能，以确定在茄科进化过程中每个旁系同源物的功能如何变化。 还将评估双突变体和四突变体，并产生转录组以确定下调对干果实和肉质果实发育中下游靶标的影响。 重点将放在发展的早期阶段，成熟和开裂之前，当定义的特征，如果皮厚度和细胞类型的身份是指定的。 这些数据将有助于我们理解产生肉质水果所需的机制，并将阐明一个关键进化现象的过程，即从干果生产到肉质水果生产的转变。 所有数据将通过GenBank、Sol Genomics Network和Dryad存储库公开发布。 根据研究者的要求，将提供突变株系和种子。

Because plants are rooted in the ground, they must have ways for their offspring to move away from home, to colonize new areas. Seeds are usually produced in one of two types of vessels to facilitate this process. A dry pod splits open at maturity to release the seeds, so they can be carried on the wind or, if they have hooks, they can stick to an animal. In contrast, a fleshy fruit such as an apple or cucumber will be eaten by an animal, which will then disperse the seeds. Fleshy fruits provide an important source of nutrition to all animals, including humans; a large part of the human diet and economy is based on fruits such as tomatoes, peppers, melons, squash, or avocados. Many different groups of flowering plants underwent an evolutionary shift from producing a dry pod to a fleshy fruit, with important ecological and economic consequences. The long-term goal of this project is to understand the genetic mechanisms that determine if a plant will produce a dry pod or an edible, fleshy fruit. The work focuses on the nightshade family, which includes pod-producing species such as desert tobacco and petunia, as well as fleshy-fruit-producing species such as tomato, eggplant, and pepper. These experiments look at the role of a group of genes that appears to have undergone a change in function associated with the origin of fleshy fruit. The results may identify specific genes or changes in genes that allow a species to make an edible, nutritious fruit, which could contribute to crop improvement or development. This project also will form the basis of two botanical garden exhibits on fruit structure and diversity in the nightshade family, and will provide training for high school students and undergraduates from under-represented minorities, as well as for a graduate student and a post-doctoral researcher. The MADS-box transcription factor FRUITFULL (FUL) plays a key role in the development of the Arabidopsis fruit by determining the patterns of cell differentiation that are required for the fruit to elongate and split open normally to release the seeds. FUL orthologs have also been shown to be required for proper ripening in some fleshy fruits, showing a conserved function in fruit development, but with a substantially different outcome. Fruits in the nightshade family (Solanaceae) are ancestrally dry and dehiscent, but there was a shift to fleshy fruit with the origin of the Solanoideae clade. The FUL gene clade has undergone duplications leading to four copies in some species, and the first part of this project will generate a gene tree using a combination of transcriptome and targeted PCR approaches to identify when duplications occurred. The data will also be used to determine whether different paralogous clades have undergone different modes of evolution (neutral, purifying, etc), which will be correlated with the functional data collected in the second part. The second part uses CRISPR technology to compare the function of the four FUL paralogs in desert tobacco and tomato to determine how the function of each paralog changed during Solanaceae evolution. Double and quadruple mutants will also be evaluated and transcriptomes generated to determine the effect of downregulation on downstream targets in both dry and fleshy fruit development. The focus will be on early stages of development, prior to ripening and dehiscence, when defining characteristics such as pericarp thickness and cell type identity are specified. The data will contribute to our understanding of the mechanisms required to produce a fleshy fruit, and will elucidate the processes underlying a key evolutionary phenomenon, the shift from dry to fleshy fruit production. All data will be publicly available upon publication through GenBank, Sol Genomics Network, and the Dryad repository. Mutant lines and seed will be available upon request from the investigators.