Comparative Genomics of Phenotypic Variation in the Compositae

PI: Loren Rieseberg（印第安纳大学）CoPIs: Richard Michelmore和Kent Bradford（加州大学）？Davis), Richard Kesseli（马萨诸塞大学-波士顿分校），John Burke和Steven Knapp（佐治亚大学），David Still（加州州立理工大学-波莫纳分校）高级人员：Zhao Lai（印第安纳大学）菊科（也被称为Asteraceae）是最大，最多样化，最重要的经济植物家族之一。虽然莴苣、向日葵和红花是这个家族中最有价值的三种成员，但已有40多种植物被驯化用于各种各样的用途。菊科还含有一些世界上最有害的杂草，据估计，美国每年要为此付出350亿美元的代价。该项目的主要目标是为这一重要植物科的进一步研究开发基因组资源。这项工作将包括：(1)对莴苣、向日葵和红花基因组的基因丰富区域进行测序；（ii）新增25个分类群的“基因目录”，包括6种作物、3种杂草、10种作物和杂草的野生祖先、该科中5个重要亚科的代表以及一个外群（即该科的近亲）；（iii）基因拷贝数变异与核苷酸变异的普遍性分析；（四）分析全基因组复制对家庭内多样化率的影响；(v)鉴定作物/杂草谱系间的平行遗传变化；（六）莴苣、向日葵、菊苣超高密度遗传图谱的构建；（vii）为关键复合科物种的遗传作图而开发永久居群；（viii）鉴定和验证潜在重要作物和杂草相关性状的候选基因。这项研究将为菊科研究界带来永久的资源，并将通过其对作物和杂草科学的贡献产生重大的经济影响。该项目还将培养遗传学、生物化学、生理学、比较基因组学和生物信息学等各个层次的学生。该项目将通过生产永久的、公开的基因组资源，对作物和杂草科学产生重大而持久的影响。所有结果将通过在同行评议期刊上发表、在国内和国际会议上发表的方式进行传播，结果数据将通过项目网站（http://compgenomics.ucdavis.edu）以及通过GenBank和其他可免费访问的在线数据库公开提供。此外，所有产生的种质资源将根据要求免费分发给有兴趣的各方。这个项目还有一个重要的外联部分。它不仅将直接支持多个博士后研究人员、研究生和本科生，而且还将为包括高中实习生在内的许多其他人的培训做出贡献。外联工作将专门针对传统上代表性不足和/或处境不利群体的成员。少数族裔服务机构加州州立理工大学波莫纳分校和马萨诸塞大学波士顿分校将作为辅助机构，识别和安置少数族裔学生到合作实验室。所有参与学校的推广工作也将利用现有的本地项目，以确保最大的效果。项目成员还将与正在开发植物基因组学讲习班以培训高中教师的同事直接互动。最后，该项目将产生适合高级本科生和/或研究生课程的植物基因组学文本。

PI: Loren Rieseberg (Indiana University)CoPIs: Richard Michelmore and Kent Bradford (University of California ? Davis), Richard Kesseli (University of Massachusetts - Boston), John Burke and Steven Knapp (University of Georgia), David Still (California State Polytechnic University - Pomona)Senior Personnel: Zhao Lai (Indiana University)The Compositae (also known as the Asteraceae) is one of the largest, most diverse, and most economically important plant families. While lettuce, sunflower, and safflower are the three most valuable members of this family, over 40 species have been domesticated for a wide variety of uses. The Compositae also contains some of the world's most noxious weeds, which cost the United States an estimated $35 billion annually. The primary goal of this project is to develop genomic resources for the continued study of this important plant family. This work will include: (i) sequencing the gene-rich regions of the lettuce, sunflower, and safflower genomes; (ii) generation of "gene catalogs" for 25 additional taxa, including six crops, three weeds, the wild progenitors of ten crops and weeds, representatives of five taxonomically important subfamilies within the family, and an outgroup (i.e., a close relative of the family); (iii) analyses of the prevalence of variation in gene copy number versus nucleotide variation; (iv) analyses of the effects of whole genome duplications on diversification rates within the family; (v) identification of parallel genetic changes across crop/weed lineages; (vi) construction of ultra-high density genetic maps of lettuce, sunflower, and chicory; (vii) development of permanent populations for genetic mapping in key Compositae species; and (viii) the identification and validation of candidates for genes underlying important crop- and weed-related traits. This research will result in the generation of permanent resources for the Compositae research community and will have a significant economic impact through its contributions to both crop and weed science. This project will also result in the training of students at all levels in genetics, biochemistry, physiology, comparative genomics, and bioinformatics.Broader Impacts This project will have a major, lasting impact on both crop and weed science through the production of permanent, publicly available genomics resources. All results will be disseminated via publication in peer-reviewed journals, presentations at national and international meetings, and the resulting data will be made publicly available through the project website (http://compgenomics.ucdavis.edu) and via deposition in GenBank and other freely-accessible, online databases. In addition, all resulting germplasm resources will be freely distributed to interested parties upon request. This project also has a significant outreach component. Not only will it directly support multiple postdoctoral researchers, graduate students, and undergraduates, but it will also contribute to the training of many others, including high school interns. Outreach efforts will be specifically targeted at members of traditionally underrepresented and/or disadvantaged groups. Minority-serving institutions California State Polytechnic University - Pomona and the University of Massachusetts - Boston will serve as feeder institutions for identifying and placing minority student in collaborating labs. Outreach efforts on all participating campuses will also leverage existing, local programs to ensure maximum effectiveness. Project members will also interact directly with colleagues who are developing a plant genomics workshop to train high school teachers. Finally, this project will result in the production of a plant genomics text suitable for advanced undergraduates and/or graduate courses.