Comparative Genomics of the Compositae

这个多学科的合作研究项目将为菊科植物的功能、比较和进化基因组学开发资源，特别是莴苣（Lactucasativa）和向日葵（Helianthus annuus）。六驯化和十逃逸和归化事件正在调查，以阐明作物的驯化和杂草的进化的遗传基础和进化力量。这些数据将建立在菊科基因组计划（CGP，http://compgenomics.ucdavis.edu）的基础上，并利用为拟南芥和其他模式物种开发的丰富知识。具体地说，（i）450，000个EST序列将存放在GenBank和CGP网站上，重点是等位基因多样性（包括18种植物）;（ii）正在对七个属的表型和分子变异进行研究，以确定与驯化或杂草性状有关的选择模式和序列或表达差异，（iii）正在检测莴苣和向日葵种子油谱的数量性状和基因表达模式，以及（iv）正在表征莴苣、向日葵和拟南芥中的基因顺序和染色体重排。 这项研究将调查广泛的基因参与栽培植物和杂草的进化，并将评估基因序列变化与基因表达变化的相对重要性，以促进不同性状的进化，如开花时间，种子生产和质量以及克隆生长等。 将评估平行进化趋势的遗传基础（例如向短生命周期的变化，或从一年生长向多年生生长的变化），并为今后的功能分析提供基础，科学界将通过基因组方案的网址和克隆和基因组的商业分销商随时获得与本项目一起开发的数据和资源。 与学术界和私营部门的多个国家和国际互动将允许迅速发布农业上有用的信息和遗传多样性加入。 我们的项目是对私营部门下游项目的补充。 CGP将产生重大的经济影响，并为菊科植物产生永久性资源，菊科植物是最大的生态成功家族之一。 生菜是美国十大作物之一，向日葵在全球排名第14位。 该科还包括许多次要作物，重要杂草和具有新颖生物化学的物种。 CGP通过有效利用来自模式生物的测序和功能基因组学的信息，将基本基因组学信息汇集到作物改良中。 该项目有助于开发所有植物的遗传数据。CGP强调具有来自多所大学的专业知识的多学科团队。CGP整合了遗传学、生物化学、生理学和生物信息学，并将在这些领域提供广泛的培训。 此外，一个有效的外联方案，影响到各级学生到位。 CGP将为少数民族提供研究经验，特别是在加州理工大学波莫纳分校和美国大学。马萨诸塞州，波士顿，并介绍计算机科学专业的生物学。

This collaborative multi-disciplinary research project will develop resources for functional, comparative, and evolutionary genomics of the Compositae, particularly lettuce (Lactuca sativa) and sunflower (Helianthus annuus). Six domestication and ten escape and naturalization events are being investigated to elucidate the genetic bases and evolutionary forces underlying the domestication of crops and evolution of weeds. These data will build on the Compositae Genome Project (CGP, http://compgenomics.ucdavis.edu) as well as capitalize on the wealth of knowledge being developed for Arabidopsis and other model species. Specifically, (i) 450,000 EST sequences will be deposited in GenBank and the CGP web site with an emphasis on allelic diversity (covering 18 plant species); (ii) the study of phenotypic and molecular variation in seven genera is being examined for patterns of selection and sequence or expression differences associated with domestication or weed traits, (iii) quantitative traits and gene expression patterns for seed oil profiles in lettuce and sunflower are being detected, and (iv) gene order and chromosome rearrangements in lettuce, sunflower, and Arabidopsis are being characterized. This research will investigate a broad range of genes involved in evolution of cultivated plants and weeds and will evaluate of the relative importance of changes in gene sequence versus changes in gene expression for the evolution of different traits such as flowering time, seed production and quality and clonal growth among others. The genetic bases of parallel evolutionary trends (e.g. changes to short life cycles, or changes from annual to perennial growth) will be assessed and will provide a basis for future functional analyses.The data and resources developed with this project will be readily available to the scientific community through the CGP web site and commercial distributors of clones and arrays. Multiple national and international interactions with the academic and private sectors will allow for rapidly released agriculturally useful information and genetically diverse accessions. Our project is complementary to downstream programs in the private sector. The CGP will have significant economic impact and generate permanent resources for the Compositae, one of the largest and ecologically successful families. Lettuce is one of the top ten US crops and sunflower ranks #14 worldwide. The family also includes many minor crops, important weeds, and species with novel biochemistries. The CGP funnels basic genomics information to crop improvement by efficiently leveraging information from the sequencing and functional genomics of model organisms. The project contributes to the genetic data being developed across all plants. The CGP emphasizes multidisciplinary teams with expertise drawn from multiple universities. The CGP integrates genetics, biochemistry, physiology, and bioinformatics and will provide broad training in these areas. In addition, an effective outreach program that impacts all levels of students is in place. The CGP will provide research experience to minorities, especially at Cal Poly Pomona and U. Mass., Boston and introduce computer science majors to biology.