OrphanCap: Massive-scale Evolutionary Study of Germplasm Databases Using the Orphan Crop Amaranthus as a Case Study

该行动资助了2017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。该研究金的主办机构是哥伦比亚大学，赞助科学家是德伦·伊顿博士。尽管农业技术取得了进步，但可持续地获得粮食仍然是世界许多地区的一个主要问题。孤生作物是区域重要的粮食来源，往往具有遗传多样性，适应恶劣环境，但由于没有广泛出口，对孤生作物的研究仍然不足。它们是新植物育种计划的重要目标，旨在开发可持续农业实践的作物。以大规模和详尽的种子收集（种质数据库）形式存在的巨大资源可用于研究孤儿作物。本研究将调查苋属，其中包括籽粒苋和抗除草剂的杂草亲戚，作为一个案例研究和资源，展示如何新的大规模基因组测序方法可以用来利用和了解种质数据库中的孤儿作物的多样性。 更广泛的影响包括开发一个研讨会（OrphanCap）和详细介绍该协议的网站，以及向高中生教授湿实验室和系统基因组数据分析。 使用新的文库制备方法，RADcap，它可以有效地和经济地允许前所未有的采样数以千计的基因组标记从数以千计的个人，基因组数据从一个全面的抽样苋物种将被测序。将该数据集与新的基因组学方法相结合，研究员将（1）重建物种关系，驯化历史，以及不同物种和苋属地方品种之间的基因渗入;（2）比较历史加入与当代实地收集的中性位点样本的遗传多样性，以及从已知除草剂抗性基因中取样的位点;（3）开发研讨会和在线资源（www.OrphanCap.org），以展示和教授实验室和生物信息学工作流程，用于开发大规模RADcap文库及其分析。原始数据将保存在NCBI序列读取档案（http：//www.ncbi.nlm.nih.gov/sra）中，系统发育树将上传至TreeBASE（http：treebase.org），代码可在www.OrphanCap.org上获得。

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2017. 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 host institution for the fellowship is Columbia University and the sponsoring scientist is Dr. Deren Eaton.Despite advances in agricultural technology, sustainable access to food remains a major problem throughout many parts of the world. Orphan crops are regionally important food sources that are often genetically diverse and adapted to harsh environments, yet remain understudied because they are not exported widely. They are important targets for new plant breeding programs aimed at developing crops for sustainable agricultural practices. Vast resources exist for studying orphan crops in the form of large-scale and exhaustive seed collections (germplasm databases). This research will investigate the genus Amaranthus, which includes grain amaranths and herbicide-resistant weedy relatives, as a case-study and resource for demonstrating how new massive-scale genomic sequencing methods can be used to exploit and understand the diversity of orphan crops in germplasm databases. Broader impacts include developing a workshop (OrphanCap) and website detailing the protocol, and teaching wet-lab and phylogenomic data analysis to high school students. Using the novel library preparation method, RADcap, which can efficiently and economically allow for unprecedented sampling of thousands of genomic markers from thousands of individuals, genomic data from a comprehensive sampling of Amaranthus species will be sequenced. Combining this dataset with new phylogenomic methods, the Fellow will (1) Reconstruct species relationships, the history of domestication, and introgression within and between different species and landraces of Amaranthus; (2) Compare genetic diversity in historical accessions versus contemporary field-collected samples at neutral loci, and at loci sampled from known herbicide resistance genes; and (3) Develop a workshop and online resource (www.OrphanCap.org) to demonstrate and teach the laboratory and bioinformatic workflow for developing massive-scale RADcap libraries and their analysis. Raw data will be deposited in the NCBI sequence read archive (http://www.ncbi.nlm.nih.gov/sra), phylogenetic trees will be uploaded to TreeBASE (http://treebase.org), and code will be available at www.OrphanCap.org.