EAGER: Establishing the genetic basis of hibernation by building and utilizing a next-generation genomics resource for the model hibernator, the thirteen-lined ground squirrel

哺乳动物的冬眠是非常动态和极端的。为了尽量减少寒冷季节的能量消耗，哺乳动物冬眠时进入一种休眠状态，新陈代谢、呼吸和心率等生理过程急剧减少，体温降至接近或甚至低于冰点。然而，在整个冬眠期间，冬眠并不是持续的，而是被短暂的、但代谢强烈的唤醒打断，回到基础生理状态。除了每年冬眠周期的组成部分之外，驱动这些休眠和觉醒周期的分子机制仍然知之甚少。为了更好地识别驱动冬眠的遗传因素，该项目将开发一个高质量的基因组资源，用于模型冬眠者，13线地松鼠。一旦完成，研究人员将利用这些资源来检测与冬眠特征相关的遗传变异，从而对这些生理极端的遗传学产生新的见解。该项目通过培训和教育下一代科学家并建立新的合作伙伴关系，使NSF的更广泛目标保持一致。研究人员将与斯坦福大学计算、进化和人类基因组学中心合作，开发一门针对冬眠的课程，旨在教育和鼓励来自社会经济弱势和种族代表性不足背景的中学生进入STEM职业。该项目还将培养1名女博士后和1名本科研究员。最后，该项目将与美国国家标准与技术研究所建立伙伴关系，并与其他哺乳动物基因组的研究人员进行比较分析。本研究的目的是建立一个基因组学框架，以建立冬眠的遗传基础。研究人员将首先为冬眠动物模型——13纹地松鼠（Ictidomys tridecemlineatus）开发一种高质量的从头组装。目前的地鼠组合是草稿质量，包含数千个contigs和scaffold，这使得性状的遗传定位具有挑战性。使用尖端的基因组学技术，将生成远程和长读数据，这将增加组合和支架的长度，并缩小两者之间的间隙。这些产生的支架将通过连锁定位组装到染色体上。将使用基因型测序策略创建连锁图谱，以在全兄弟姐妹家庭中生成单核苷酸多态性（SNP）标记，这些标记将被分配到连锁组中，并用于定位和排序支架。最后，研究人员将验证与冬眠相关的特征是遗传的假设。遗传变异将在150+ 13列地松鼠中得到表征。从体温遥测记录中测量的冬眠相关性状的狭义遗传力将利用基因型数据对相关松鼠进行估计。通过基因组和连锁图谱的完成，将进行定量性状位点分析，以确定与遗传可遗传性状相关的特定变异。研究结果将发表在同行评议的期刊上，并在科学会议上发表。

Hibernation is extraordinarily dynamic and extreme for mammals. To minimize energy expenditures during cool seasons, mammalian hibernators enter into a state of torpor, whereby physiological processes, including metabolic, respiratory and heart rates, are dramatically reduced, and body temperature is lowered to near or even below freezing. However, torpor is not continuous for the whole of hibernation but is instead punctuated by brief, but metabolically intense, arousals back to basal physiology. The molecular mechanisms that drive these cycles of torpor and arousal, in addition to the components underlying the annual cycle of hibernation, remain poorly understood. To better identify the genetic elements driving hibernation, this project will develop an enabling high-quality genomics resource for the model hibernator, the 13-lined ground squirrel. Once completed, the investigators will use this resource to detect genetic variants associated with hibernation traits, leading to new insight about the genetics of these physiological extremes. This project aligns the broader goals of the NSF by training and educating the next generation of scientists and establishing new partnerships. Collaborating with Stanford's Center for Computational, Evolutionary and Human Genomics, the investigators will develop a hibernation-specific lesson aimed at educating and encouraging STEM career entrance for middle school students from socioeconomically disadvantaged and ethnically underrepresented backgrounds. This project will also train a female postdoctoral scholar and an undergraduate researcher. Finally, this project will develop a partnership with the National Institute of Standards and Technology and enable comparative analyses with researchers assembling genomes of other mammals. The goal of this study is to build a genomics framework to establish the genetic basis hibernation. The investigators will first develop a high quality de novo assembly for the model hibernator, the 13-lined ground squirrel, Ictidomys tridecemlineatus. The current ground squirrel assembly is of draft quality, containing thousands of contigs and scaffolds, which makes genetic mapping of traits challenging. Using cutting-edge genomics techniques, both long-range and long-read data will be generated, which will increase the lengths of, and close gaps between, both contigs and scaffolds. These resulting scaffolds will be assembled onto chromosomes via linkage mapping. The linkage map will be created using a genotype-by-sequencing strategy to generate Single Nucleotide Polymorphic (SNP) markers in full-sibling families, which will be assigned into linkage groups and used to orient and order the scaffolds. Finally, the investigators will test the hypothesis that hibernation-related traits are genetically heritable. Genetic variation will be characterized in 150+ 13-lined ground squirrels. Narrow sense heritability of hibernation-related traits, measured from body-temperature telemetry records, will be estimated from related squirrels using genotype data. A quantitative trait loci analysis, enabled by the completion of the genome and linkage map, will be performed to identify specific variants associated with genetically heritable traits. Study results will be published in peer-reviewed journals and presented at scientific meetings.