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

这一行动为NSF国家植物基因组计划2017财年生物学博士后研究奖学金提供了资金。该奖学金支持在东道主实验室为该研究员制定的研究和培训计划，该研究员还提出了扩大生物学参与度的计划。该奖学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，但可持续获得粮食仍然是世界许多地区的一个主要问题。孤儿作物是区域上重要的食物来源，通常具有遗传多样性，适应恶劣的环境，但由于它们没有广泛出口，对它们的研究仍然不足。它们是旨在为可持续农业实践发展作物的新植物育种计划的重要目标。以大规模和详尽的种子库(种质数据库)的形式研究孤儿作物有大量的资源。这项研究将调查包括籽粒苋属和抗除草剂杂草亲缘关系的苋属，作为一个案例研究和资源，以展示如何使用新的大规模基因组测序方法来开发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)和网站，详细介绍协议，以及向高中生教授湿实验室和系统基因组数据分析。使用新的文库准备方法RADCap，它可以有效和经济地从数千个个体中对数千个基因组标记进行前所未有的采样，将对来自苋属植物的全面采样的基因组数据进行测序。结合这个数据集和新的系统基因组学方法，该研究员将(1)重建物种关系、驯化历史，以及不同物种和地方品种内部和之间的导入；(2)比较历史材料和当代野外收集的中性基因座和已知除草剂抗性基因座位的遗传多样性；以及(3)开发研讨会和在线资源(www.OrphanCap.org)，以演示和讲授实验室和生物信息学工作流程，以建立大规模的RADCap文库及其分析。原始数据将存放在国家生物信息学研究所序列读取档案中(http://www.ncbi.nlm.nih.gov/sra)，系统发育树将上载到TreeBase(http://treebase.org)，和代码将在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.