NSF Postdoctoral Fellowship in Biology FY 2015

本行动资助2015财年美国国家科学基金会国家植物基因组计划生物学博士后研究奖学金。该奖学金支持奖学金获得者在主办实验室的研究和培训计划，该奖学金获得者还提出了扩大生物学参与的计划。Michael S. Campbell奖学金的研究和培训计划的标题是“水稻和人类：推进基因组辅助作物改良的基于图表的工具和资源”。该奖学金的主办机构是冷泉港实验室和EMBL-EBI，赞助科学家是Doreen Ware博士和Paul Kersey博士。自从一万多年前农业开始以来，人类就一直在驯化农作物以提高产量和生产力。在过去的十年中，基因组测序为挖掘作物的新性状和改进育种方法提供了前所未有的资源。这些DNA序列现在可以用来指导未来的植物育种，这一过程被称为基因组辅助作物改良。基因组辅助作物改良的核心是使用单一共识或“参考”DNA序列来代表整个物种的基因组。遗憾的是，这些参考序列并没有捕捉到每个群体的序列变异特征。因此，如果不能充分了解基因变异的多样性，育种就会受到阻碍。最近，人类基因组学社区已经开始试验一种很有前途的解决方案，称为“变异图”，其中使用图结构来表示参考基因组方法丢失的序列变异。在这个项目中，变异图将被开发为水稻作为一种模式作物，将有助于识别新的性状变异，并最终适用于任何作物物种。研究结果将为植物育种者提供重要信息，从而对作物改良工作的速度和效果产生重大影响，有助于确保安全和持续的粮食供应。该项目将开发方法并探索变体图方法的实用性，以创建水稻的泛基因组参考和结构注释资源，从三个不同水稻品系的基因组开始，然后扩展到3000个。基于生物信息学和统计学的基因组表示和注释方法将为植物育种者提供可获得的变异材料的种群水平视图，并将提供每个个体基因组的清晰图像。研究工作是针对水稻基因组的，但是所开发的工具和技术与所有的农业植物和动物有关。将建立基础设施，将这种资源复制到其他农业植物中，并通过iPlant Collaborative （iplantcollaborative.org）提供。水稻资源将通过Gramene网站（gramene.org）公开提供。

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 Michael S. Campbell is "Of Rice and Men: Graph-Based Tools and Resources for Advancing Genome Assisted Crop Improvement " The host institutions for the fellowship are Cold Spring Harbor Laboratories and EMBL-EBI and the sponsoring scientists are Dr. Doreen Ware and Dr. Paul Kersey.Humans have been domesticating crop plants to increase yield and productivity ever since agriculture began over 10,000 years ago. Genome sequencing in the last decade now provides unprecedented resources for mining crops for new traits and for advancing breeding methods. These DNA sequences can now be used to guide the future of plant breeding through a process called genome assisted crop improvement. Central to genome assisted crop improvement is the use of a single consensus, or 'reference' DNA sequence to represent the genome of an entire species. Unfortunately, these reference sequences do not capture sequence variation characteristic of every population. Breeding is therefore hampered without full access to the diversity of gene variants. Recently, the human genomics community has begun to experiment with a promising solution to this problem called a 'Variant Graph', wherein a graph structure is used to represent sequence variation that is lost with the reference-genome approach. In this project, Variant Graphs will be developed for rice as a model crop plant, will help to identify new trait variants and will ultimately be applicable to any crop species. The outcomes will provide essential information to plant breeders and therefore significantly impact the speed and performance of crop improvement efforts, helping to ensure a secure and constant food supply. This project will develop methods for, and explore the utility of, a Variant Graph approach to create a pan-genome reference and structural annotation resource for rice, starting with the genomes of three diverse rice strains and then expanding to 3,000. The bioinformatics and statistically based approach to genome representation and annotation will give a population level view of the variant material available to plant breeders and will provide a clear picture of the genome of each individual accession. The research efforts are directed towards rice genomes, but the tools and techniques developed are relevant to all agricultural plants and animals. The infrastructure to replicate this resource for other agricultural plants will be established and made available through the iPlant Collaborative (iplantcollaborative.org). The rice resources will be publicly available through the Gramene website (gramene.org).