NSF Postdoctoral Fellowship in Biology: Overcoming Barriers to Wild Species Improvement through Genetic Analysis of an Evolutionary Novelty in the Solanum

本行动资助2023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。James Satterlee的这项研究和培训计划的题目是“通过对茄属植物的一种进化新物种的基因分析，克服野生物种改良的障碍”。该奖学金的主办机构是冷泉港实验室，赞助科学家是Zachary Lippman博士。遗传差异是如何导致在生命之树上观察到的进化上的新特征的，比如开花植物的花朵或脊椎动物的四肢？本研究将利用茄属植物作为模型系统来解决这一问题。茄属植物包括常见的主要作物品种，如西红柿、土豆和茄子。然而，与西红柿和土豆不同的是，产生茄子的谱系在其表面进化出了尖锐的刺，以阻止食草动物。在茄子和其他密切相关的区域重要作物的驯化过程中，育种者选择了没有刺的品种。以这种性状变异为出发点，这项工作将首先确定控制刺发育的基因，然后寻求解决哪些类型的遗传变化发生，使这些基因承担新的功能。实际上，对刺发育的遗传控制的理解将允许在农业上有用的茄属植物中快速地设计出理想的无刺系。该项目将包括一个公共宣传部分，包括用于社交媒体传播的短格式科学视频，以及每年向公众开放的基因组编辑和作物改良课程。引起表型新颖性的潜在遗传变化仍然知之甚少。新基因功能的进化可以通过基因编码序列周围的顺式调控DNA序列的变化来驱动。这样的序列改变可能使基因具有新的表达模式，在新的地点或时间赋予功能，同时避免编码序列突变的潜在多效效应。通过这种方式，假设祖先基因功能可能在新的环境中重新部署，以产生具有保守分子工具包的形态新颖性。本研究将通过对刺进化的遗传基础的调查来验证这一假设，刺是农业上重要的茄属植物中一个相对较新的（约16年前）形态创新。新的高质量基因组组装将被用于绘制和鉴定多个物种中与刺发育有关的基因。接下来，这项工作将旨在通过单细胞转录组学、开放染色质谱分析和比较基因组分析相结合，将刺相关基因表达模式与其潜在的调控基础联系起来，了解这些基因是如何被招募到刺发育途径中的。基因组编辑将用于验证候选基因及其顺式调控序列的功能。最后，刺发育候选驱动因子的异源表达将决定它们的充分性和与新颖性进化出现的相关性。总之，这项工作将促进对进化中创新特征出现的理解，并可能为新形态的合成工程提供途径。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 2023. 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 James Satterlee is ‘Overcoming barriers to wild species improvement through genetic analysis of an evolutionary novelty in the Solanum’. The host institution for the fellowship is the Cold Spring Harbor Laboratory and the sponsoring scientist is Dr. Zachary Lippman.How do genetic differences result in the evolutionarily novel traits observed across the tree of life, such as flowers in flowering plants or limbs in vertebrate animals? This research will address this question using the plant genus Solanum as a model system. Solanum contains familiar major crop species such as tomato, potato, and eggplant. Unlike tomato and potato however, the lineage that gave rise to eggplant evolved sharp prickles on their surface to deter herbivores. During the domestication of eggplant and other closely related regionally important crops, breeders selected cultivars lacking prickles. Using this trait variation as a starting point, this work will first identify the genes that control the development of prickles and then seek to address which types of genetic changes occurred to allow these genes to take on their new function(s). Practically, an understanding of the genetic control of prickle development will allow the rapid engineering of desirable prickle-less lines in agriculturally useful Solanum species. This project will include a public outreach component involving short-form scientific videos for social media dissemination as well as a yearly course open to the public on genome editing and crop improvement. The underlying genetic changes that give rise to phenotypic novelty remain poorly understood. Evolution of new gene function can be driven by changes in the cis-regulatory DNA sequence surrounding the gene coding sequence. Such sequence changes may allow a gene to take on a new expression pattern, conferring function in a new place or time while avoiding potential pleiotropic effects of coding sequence mutations. In this way, it is hypothesized that ancestral gene functions may be redeployed in a new context to produce morphological novelty with a conserved molecular toolkit. This research will test this hypothesis through an investigation of the genetic basis for the evolution of prickles, a relatively recent (~16 My old) morphological innovation, in the agriculturally important genus Solanum. New high-quality genome assemblies will be leveraged to map and identify genes involved in prickle development in multiple species. Next, this work will aim to understand how these genes were recruited into the prickle developmental pathway using a combination of single-cell transcriptomics, open chromatin profiling, and comparative genomic analysis to link prickle-associated gene expression patterns to their underlying regulatory basis. Genome editing will be used to verify the functions of candidate genes and their cis-regulatory sequences. Finally, heterologous expression of candidate drivers of prickle development will determine their sufficiency and relevance to the evolutionary emergence of novelty. Together, this work will advance understanding of the emergence of innovative traits in evolution and may suggest routes for the synthetic engineering of novel morphologies.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.