Comparative Genomics of the Compositae

这个多学科合作研究项目将为菊科植物，特别是莴苣（Lactuca sativa）和向日葵（Helianthus annuus）的功能、比较和进化基因组学开发资源。研究了6个驯化事件和10个逃逸归化事件，以阐明作物驯化和杂草进化的遗传基础和进化力量。这些数据将建立在复合植物基因组计划（CGP, http://compgenomics.ucdavis.edu）的基础上，并利用拟南芥和其他模式物种的丰富知识。具体而言，(i) 45万个EST序列将存入GenBank和CGP网站，重点是等位基因多样性（涵盖18个植物物种）；（ii）正在研究7个属的表型和分子变异，以确定与驯化或杂草性状相关的选择、序列或表达差异模式；（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；（iv）正在研究莴苣、向日葵和拟南芥的基因顺序和染色体重排。本研究将研究与栽培植物和杂草进化有关的广泛基因，并将评估基因序列变化与基因表达变化对不同性状进化的相对重要性，如开花时间、种子产量和质量以及无性系生长等。将评估平行进化趋势的遗传基础（例如，从短生命周期的变化，或从一年生到多年生生长的变化），并将为未来的功能分析提供基础。这个项目开发的数据和资源将通过CGP网站和克隆和阵列的商业分销商随时提供给科学界。与学术界和私营部门的多重国家和国际互动将允许迅速发布农业有用信息和遗传多样性的加入。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，并为复合科（最大和生态成功的家庭之一）产生永久资源。莴苣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，重要杂草和具有新生物化学的物种。CGP通过有效地利用模式生物的测序和功能基因组学信息，为作物改良提供基本基因组学信息。该项目有助于开发所有植物的遗传数据。CGP强调来自多所大学的多学科团队的专业知识。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，一个有效的外展计划，影响各级学生是到位的。CGP将为少数族裔提供研究经验，特别是在加州波莫纳理工学院和马萨诸塞大学。并向计算机科学专业的学生介绍生物学。

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.