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

对人类皮肤色素沉着进化的研究包括对这一特征潜在的遗传变异的表征。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，而且由于某些人群在人类遗传学研究中的代表性不足，这种遗传变异仍未被识别。这一博士论文项目通过表征和功能验证在此类研究中未被充分代表的人群中的皮肤色素沉积的遗传结构，为模拟人类皮肤色素沉着进化奠定了必要的基础。这个项目产生的数据可以为几个色素沉着研究目标提供信息，包括了解自然选择在塑造人类这一特征中的作用。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，这个项目通过湿实验室、计算和野外工作培训来促进本科生和研究生的技能发展。研究小组进行实地工作，从具有较高祖先等位基因水平和比其他现存人类群体更高水平的遗传多样性的群体中的个体收集配对的遗传和色素数据。这项研究为研究人类祖先种群中可能存在的色素变化提供了一个机会，因此有可能拓宽我们对全球色素沉积遗传学的理解。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被荟萃分析，以增加检测低效大小基因座的能力。GWA研究中确定的区域不一定是因果色素沉着基因座，因此功能验证是必要的。因此，头号候选基因被识别出来，并通过CRISPR(簇状规则间隔短回文重复)基因编辑在斑马鱼中进行因果关系的功能评估，斑马鱼是研究人类皮肤色素沉着的有效模式生物。使用快速自动表型平台对幼虫进行成像，比较CRISPR马赛克“敲除”鱼和“模拟”注射同胞对照的色素沉着。这一策略可以从功能上验证来自GWA的新的相关基因是否是因果色素沉着基因。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.