Doctoral Dissertation Research: Characterization and Functional Validation of the Genetic Architecture of Skin Pigmentation

研究人类皮肤色素沉着的进化包括表征这一特征的潜在遗传变异。最近的研究表明，与皮肤色素沉着相关的基因数量在不同的人群中有所不同，而且由于在人类基因研究中某些人群的代表性不足，这种遗传变异的大部分仍未确定。本博士论文项目通过表征和功能验证在此类研究中代表性不足的人群中皮肤色素沉着的遗传结构，为模拟人类皮肤色素沉着进化奠定了必要的基础。从这个项目中产生的数据可以为色素沉着的几个研究目标提供信息，包括理解自然选择在形成这种人类特征中的作用。该项目还可以作为研究其他复杂遗传特征的模型，并可能为包括生物考古学和法医人类学在内的其他领域提供信息。此外，该项目通过湿实验、计算和实地工作训练，有助于本科生和研究生的技能发展。研究小组进行了实地调查，从具有高水平祖先等位基因和比其他现存人类群体更高水平遗传多样性的人群中收集成对遗传和色素沉着数据。这项研究提供了一个机会来研究可能存在于祖先人群中的色素沉着变异，因此有可能扩大我们对全球色素沉着遗传学的理解。新收集的样本将进行基因分型，然后使用全基因组关联（GWA）方法进行评估。来自四个不同血统群体的数据将进行荟萃分析，以增加检测低效应大小基因座的能力。在GWA研究中确定的区域不一定是导致色素沉积的位点，因此有必要进行功能验证。因此，在斑马鱼（一种研究人类皮肤色素沉积的有效模式生物）中，通过CRISPR（聚集规律间隔的短回文重复序列）基因编辑鉴定和功能评估了顶级候选基因的因果关系。使用快速自动化表型平台对幼虫进行成像，比较CRISPR镶嵌“敲除”鱼与“模拟”注射的同胞对照鱼的色素沉着。该策略可以从功能上验证来自GWAS的新相关基因是否为导致色素沉着的基因。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。

Research on the evolution of human skin pigmentation includes the characterization of this characteristic's underlying genetic variation. Recent studies have shown that the number of genes associated with skin pigmentation differs across populations and that much of this genetic variation is still unidentified due to underrepresentation of some populations in human genetic research. This doctoral dissertation project lays the groundwork necessary to model human skin pigmentation evolution by characterizing and functionally validating the genetic architecture of skin pigmentation in a population that has been underrepresented in such research. Data generated from this project can inform several pigmentation research objectives, including understanding the role of natural selection in shaping this human trait. The project can also be used as a model for research on other complex genetic traits and may inform other fields including bioarchaeology and forensic anthropology. Additionally, this project contributes to the skill development of undergraduate and graduate students through wet lab, computational, and fieldwork training.The research team conducts fieldwork to collect paired genetic and pigmentation data from individuals in a population with high levels of ancestral alleles and higher levels of genetic diversity than other extant human populations. The research presents an opportunity to research pigmentation variation that may have been present in ancestral human populations, and therefore potentially broadens our understanding of pigmentation genetics globally. Newly collected samples will be genotyped and then evaluated using a genome-wide association (GWA) approach. Data from four different descent populations will be meta-analyzed to increase power to detect low-effect size loci. Regions identified in the GWA study are not necessarily causal pigmentation loci, rendering functional validation necessary. Top candidate genes are therefore identified and functionally evaluated for causality with CRISPR (clustered regularly interspaced short palindromic repeats) gene editing in zebrafish, an effective model organism to study human skin pigmentation. Using a rapid automated phenotyping platform to image larvae, pigmentation is analyzed comparing CRISPR- mosaic “knockout” fish with “mock” injected sibling controls. This strategy can functionally verify whether novel associated genes from the GWAS are causal pigmentation genes.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.