NSF Postdoctoral Fellowship in Biology FY 2021: Uncovering the regulatory mechanisms for a genetic switch between anthocyanin and carotenoid pigmentation in monkeyflowers

本行动资助2021财年美国国家科学基金会植物基因组生物学博士后研究奖学金。该奖学金支持奖学金获得者在主办实验室的研究和培训计划，该奖学金获得者还提出了扩大生物学参与的计划。这项研究和培训计划的题目是“揭示猴子花中花青素和类胡萝卜素色素沉着之间基因转换的调节机制”。该奖学金的主办机构是密歇根州立大学，赞助科学家是戴维·劳瑞博士。植物生物学的一个主要目标是了解调节重要色素生产的遗传机制，包括花青素（红色、紫色或蓝色）和类胡萝卜素（黄色、橙色或红色）。这项工作将使用猕猴花（Mimulus whitneyi）来确定造成这种颜色差异的调控基因。猕猴花有紫色或黄色的花，也有紫色或黄色的花。该研究还将揭示由该调节器控制的遗传网络，并评估它是否在多物种的花色转变进化中重复使用。这种综合方法将促进我们对植物色素沉着的理解，色素沉着在光合作用、抗逆性、抵御食草动物和病原体以及繁殖中至关重要。花青素和类胡萝卜素在人类健康中也起着关键作用，因此了解其调控的遗传机制对通过基因工程改善作物植物的营养具有直接的应用价值。这项研究将为研究员提供生物信息学、种群基因组学和表观基因组学方法方面的培训，以建立一个全面的研究计划。为了扩大这项工作的影响，研究员将通过为服务不足的初中和高中教室开发一个基于mimulus的教育模块，为密歇根州弗林特和底特律的学生提供STEM教育。该模块将侧重于花色素沉着，传粉者的视觉和植物适应性。本模块生成的材料将在CREATE开放科学网页上公开提供。本研究旨在确定植物色素沉着两种关键途径协调进化的调控机制。具体来说，该项目将重点研究多态猴花Mimulus whitneyi从紫色到黄色（花青素到类胡萝卜素）颜色转变的遗传基础。研究目标1将通过生成高质量的参考基因组，对11个自然种群的紫色和黄色变种进行全基因组合并测序，并进行基因分型，从而确定和验证紫黄花多态性的主调控基因。Aim 2将通过使用RNA-seq、基因网络分析和ATAC-seq来表征紫色和黄色变种的基因网络和调控元件，从而生成花青素和类胡萝卜素生物合成途径的调控和共调控模型。目的3将通过研究另外三种猴花自然种群中紫色/黄色趋同多态性的遗传基础，阐明Mimulus属植物颜色转变的进化历史。所有测序数据将通过NCBI和Phytozome公开提供，生物信息学管道和自定义脚本可通过GitHub获得。代金券标本将存放在密歇根州立大学植物标本馆，在那里它们将被数字化并记录在iDigBio和Symbiota数据库中。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。

This action funds an NSF Plant Genome Postdoctoral Research Fellowship in Biology for FY 2021. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to Lauren Stanley is “Uncovering the regulatory mechanisms for a genetic switch between anthocyanin and carotenoid pigmentation in monkeyflowers.” The host institution for the fellowship is Michigan State University and the sponsoring scientist is Dr. David Lowry.A major goal of plant biology is to understand the genetic mechanisms regulating the production of important pigments, including anthocyanins (red, purple, or blue) and carotenoids (yellow, orange, or red). This work will use the monkeyflower species Mimulus whitneyi, which has co-occurring plants with either purple or yellow flowers, to identify the regulatory gene responsible for this color difference. The research will also uncover the genetic network controlled by this regulator and assess whether it has repeated use in the evolution of flower color transitions across multiple species. This integrative approach will advance our understanding of plant pigmentation, which is crucial to photosynthesis, stress tolerance, defense against herbivores and pathogens, and reproduction. Anthocyanins and carotenoids also play a key role in human health, and thus understanding the genetic mechanisms underlying their regulation has a direct application for the nutritional improvement of crop plants via genetic engineering. This research will provide the Fellow with training in bioinformatics, population genomics, and epigenomics methods to build a comprehensive research program. To broaden the impact of this work, the Fellow will contribute to STEM education for students in Flint and Detroit, Michigan through the development of a Mimulus-based education module for underserved middle and high school classrooms. The module will focus on floral pigmentation, pollinator vision, and plant fitness. Materials generated for this module will made publicly available on the CREATE Open Science webpage.This research aims to identify the regulatory mechanisms underlying the coordinated evolution of two key plant pigmentation pathways. Specifically, the project will focus on the genetic basis for a floral purple-to-yellow (anthocyanin-to-carotenoid) color transition using the polymorphic monkeyflower species Mimulus whitneyi. Aim 1 of the research will identify and validate a master regulatory gene underlying the purple/yellow flower color polymorphism in M. whitneyi by generating a high-quality reference genome, performing whole-genome pooled sequencing of purple and yellow morphs, and genotyping across eleven natural populations. Aim 2 will generate a model for the regulation and co-regulation of the anthocyanin and carotenoid biosynthesis pathways by characterizing gene networks and regulatory elements in purple and yellow morphs using RNA-seq, gene network analysis, and ATAC-seq. Aim 3 will illuminate the evolutionary history of color transitions in the Mimulus genus by investigating the genetic basis for convergent purple/yellow flower color polymorphisms in natural populations of three additional monkeyflower species. All sequencing data will be made publicly available through NCBI and Phytozome, with bioinformatics pipelines and custom scripts available through GitHub. Voucher specimens will be deposited at the Michigan State University Herbarium, where they will be digitized and documented in the iDigBio and Symbiota databases.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.