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

这项行动为2023财年的NSF植物基因组博士后生物学研究奖学金提供资金。该研究金支持研究员在东道实验室的研究和培训计划，研究员还提出了扩大生物学参与的计划。詹姆斯·萨特利（James Satterlee）的研究和培训计划的标题是“通过对索尔佩迪（Solpendi）中进化新奇的遗传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，赞助科学家是扎卡里·李普曼博士。遗传差异是如何导致在整个生命之树上观察到的进化上新颖的特征的，比如开花植物的花或脊椎动物的四肢？本研究以茄属植物为模型系统，探讨这一问题。茄属植物包含常见的主要作物种类，如番茄、马铃薯和茄子。然而，与番茄和土豆不同，茄子的起源是在其表面进化出尖锐的刺，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。以这种性状变异为起点，这项工作将首先确定控制刺发育的基因，然后寻求解决发生了哪些类型的遗传变化，以使这些基因承担新的功能。实际上，理解刺发育的遗传控制将允许在农业上有用的茄属物种中快速工程化所需的无刺品系。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简短科学视频，以及每年向公众开放的基因组编辑和作物改良课程。引起表型新奇的潜在遗传变化仍然知之甚少。新基因功能的进化可以由基因编码序列周围的顺式调控DNA序列的变化驱动。这样的序列变化可以允许基因采取新的表达模式，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性效应。通过这种方式，假设祖先基因功能可以在新的背景下重新部署，以产生具有保守分子工具包的形态学新奇。这项研究将通过调查刺进化的遗传基础来验证这一假设，刺是农业上重要的茄属中一种相对较新的（~16岁）形态学创新。新的高质量基因组组装将被用来绘制和识别多个物种中与刺痒发育有关的基因。接下来，这项工作的目的是了解这些基因是如何被招募到刺的发展途径，使用单细胞转录组学，开放染色质分析和比较基因组学分析的组合，以连接刺相关的基因表达模式，其潜在的监管基础。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，异源表达的候选驱动程序的刺痒发展将决定其充分性和相关性的进化出现的新奇性。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建议。该奖项反映了NSF的法定使命，并通过使用基金会的智力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.