NSF Postdoctoral Fellowship in Biology FY 2015

该行动资助了2015财年NSF国家植物基因组计划生物学博士后研究奖学金。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。该奖学金的研究和培训计划的标题为艾米丽约瑟夫是“调节网络中的多基因适应”该奖学金的主办机构是加州大学戴维斯分校和赞助科学家格雷厄姆库珀博士，杰弗里罗斯-伊瓦拉，和朱利安马洛夫。野生植物的驯化产生了今天的作物植物的多样性。在作物育种过程中，祖先野生基因组随着驯化特定性状的选择而逐渐改变。这个过程是一种类似于自然选择的基因组适应。该项目通过比较两种作物（玉米和番茄）及其野生亲缘植物之间的基因调控变化，研究基因组适应性。将比较基因的表达，并开发生物信息学方法来评估和比较基因组变化。这些信息将揭示作为育种计划基础的关键调控网络，从长远来看，可以为基因组辅助育种策略提供新的工具。高中研讨会，公开演讲和本科生的研究经验将从基因组的角度向不同的观众展示农业的基本知识。了解适应的遗传基础一直是研究人员通过自然选择和驯化选择研究进化的长期目标。多基因适应被认为对驯化特别重要，但目前的群体遗传学方法很难检测到。这项研究将开发方法，以检测协调的变化，基因表达系统的调控网络，由于多基因适应。这些方法将应用于两个系统：玉米的驯化，使用公开的数据，以及野生番茄的环境适应，使用将作为研究的一部分生成的基因表达数据。生成的原始番茄基因表达数据将在NCBI的Sequence Read Archive上提供，处理后的数据将在Dryad Digital Repository上存档。用于进行分析的脚本将提供给GitHub上的其他研究人员使用。

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2015. 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 Emily Josephs is "Polygenic adaptation in regulatory networks" The host institution for the fellowship is the University of California, Davis and the sponsoring scientists are Drs. Graham Coop, Jeffrey Ross-Ibarra, and Julin Maloof.Domestication of wild plants has produced the diversity of crop plants available today. During crop breeding, ancestral wild genomes gradually changed as domestication specific traits were selected. The process is a type of genome adaptation similar to natural selection. This project investigates genome adaptation in two crop species, maize and tomato, by comparing gene regulatory changes between the crops and their wild relatives. Expression of genes will be compared and bioinformatics methods will be developed to assess and compare genome change. The information will uncover key regulatory networks that are at the foundation of breeding programs and in the long run could provide new tools for genome-assisted breeding strategies. Workshops at high schools, public presentations and research experiences for undergraduates will expose diverse audiences to basic knowledge about agriculture from a genomic perspective. Understanding the genetic basis of adaptation has been a longstanding goal of researchers studying evolution through natural and domestication selection. Polygenic adaptation, which is thought to be particularly important for domestication, is difficult to detect with current population genetic methods. This research will develop methods to detect coordinated changes in gene expression systematically across regulatory networks due to polygenic adaptation. These methods will be applied to two systems: domestication in maize, using publicly available data, and environmental adaptation in wild tomatoes, using gene expression data that will be generated as part of the research. The raw tomato gene expression data generated will be available on NCBI's Sequence Read Archive and processed data will be archived on the Dryad Digital Repository. The scripts used to conduct analyses will be made available for use by other researchers on GitHub.