Sequencing of Chromosome 3 Short Arms From the AA, BB, CC, BBCC Genomes of Wild Relatives of Rice for Comparative Functional and Evolutionary Genomics
水稻野生近缘种 AA、BB、CC、BBCC 基因组的 3 号染色体短臂测序,用于比较功能和进化基因组学
基本信息
- 批准号:0638541
- 负责人:
- 金额:--
- 依托单位:
- 依托单位国家:美国
- 项目类别:Continuing Grant
- 财政年份:2006
- 资助国家:美国
- 起止时间:2006-10-01 至 2010-09-30
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
PI: Rod A. Wing (University of Arizona)Co-PIs: Scott A. Jackson (Purdue University), Steven D. Rounsley (University of Arizona), Lincoln D. Stein (Cold Spring Harbor Laboratory)Comparative genomics is a powerful tool to understand how genes and genomes function and evolve yet limited studies have been done comparing the genomes of species within a genus. Such comparisons are critical for a deeper understanding of speciation, polyploidization, domestication and gene regulation. The two most advanced genus level comparative systems available for higher eukaryotes are the Drosophila comparative genome sequencing project where 12 wild Drosophila genomes are being sequenced, assembled and compared to the reference D. melanogaster genome, and the Oryza map alignment project (OMAP) were physical maps of 12 wild rice genomes have been made and aligned to the reference O. sativa genome.The long term goal of this project is to create a freely available comparative sequence resource with broad utility that can be interrogated to ask fundamental questions in genome biology, evolution and domestication in the genus Oryza. To accomplish this goal, BAC tiling paths of the short arm of rice chromosome 3 across three diploid genomes (AA, BB and CC) and their allotetraploid progeny (BBCC) will be sequenced and rigorously annotated. The sequence generated from this project will have broad utility to the scientific community in the following ways: 1) The sequence will provide comparative information on all genes and transposable elements that are common between the AA, BB, CC, BBCC genomes (e.g. allelic diversity, conserved non-coding sequences).2) The sequence will permit the identification of genes and transposable elements that are unique to cultivated rice as well as to the other wild species. For cultivated species, the unique genes may play important roles in domestication and would be prioritized for functional analysis. With respect to the wild rice accessions, the unique genes may play important roles for survival and adaptation to particular environments where they originated.3) The sequence will also provide an unprecedented data set in regions of the short arm of chromosome 3 that have undergone rearrangements (e.g. insertions, deletions, inversions and translocations). By integrating these rearrangements with genetic maps we will be able ask fundamental questions on the role that rearrangements, expansions and contractions play in chromosome speciation, genome size maintenance and the evolution of new genes.In addition to the scientific broader impacts of this proposal, a summer genomics outreach training program will be offered targeting under-represented college students and faculty to apply and extend knowledge gained in the classroom to practical experience. Students will have the opportunity to view careers in biology and will be encouraged to continue their education through the M.S. and Ph.D. levels. Interns will participate full-time in a PI lab during eight-week summer sessions. Each student will be paired with a mentor who will help develop a research project that is in alignment with the intern's particular area of interest and expertise.Access to project outcomesProject outcomes will be available in the form of publications in peer-reviewed journals and the Gramene public cereal database (http://www.gramene.org). All sequence and trace file data will deposited in Genbank (http://www.ncbi.nlm.nih.gov/).
PI:罗德·A·荣(亚利桑那大学)合作伙伴:斯科特·A·杰克逊(普渡大学)、史蒂文·D·朗斯利(亚利桑那大学)、林肯·D·斯坦(冷泉港实验室)比较基因组学是了解基因和基因组如何发挥作用和进化的强大工具,但对属内物种的基因组进行比较的研究有限。这种比较对于更深入地理解物种形成、多倍化、驯化和基因调控至关重要。高等真核生物可用的两个最先进的属水平比较系统是果蝇比较基因组测序计划,其中12个野生果蝇基因组正在进行测序、组装并与参考黑腹果蝇基因组进行比较,而水稻图谱比对计划(OMAP)是已经制作的12个野生水稻基因组的物理图谱,并与参考水稻基因组进行比对。该项目的长期目标是创建一个可自由获得的具有广泛实用价值的比较序列资源,该资源可以被询问以提出关于水稻属基因组生物学、进化和驯化的基本问题。为了实现这一目标,将对水稻3号染色体短臂跨越三个二倍体基因组(AA、BB和CC)及其异源四倍体后代(BBCC)的BAC平铺路径进行测序和严格注释。该项目产生的序列将在以下方面对科学界具有广泛的实用价值:1)该序列将提供关于AA、BB、CC、BBCC基因组之间共同的所有基因和转座元件的比较信息(例如,等位基因多样性、保守的非编码序列)。2)该序列将允许识别栽培水稻以及其他野生物种特有的基因和转座元件。对于栽培物种,独特的基因可能在驯化过程中发挥重要作用,并将优先用于功能分析。对于野生稻材料,独特的基因可能在它们起源的特定环境的生存和适应方面发挥重要作用。3)该序列还将在经历了重排(例如插入、缺失、倒置和易位)的3号染色体短臂区域中提供前所未有的数据集。通过将这些重排与基因图谱相结合,我们将能够就重排、扩展和收缩在染色体物种形成、基因组大小保持和新基因进化中所起的作用提出基本问题。除了这项提议的科学更广泛的影响外,我们还将提供夏季基因组学外展培训计划,目标是未被充分代表的大学生和教职员工,以将课堂上学到的知识应用于实践经验。学生将有机会了解生物学的职业,并将被鼓励继续他们的教育,直到硕士和博士水平。实习生将在为期八周的暑期课程期间全职参加PI实验室。每个学生将与一名导师配对,导师将帮助开发与实习生特定兴趣领域和专业知识相一致的研究项目。获取项目成果项目成果将以发表在同行评议期刊和Gramene公共谷物数据库(http://www.gramene.org).)的形式提供所有序列和轨迹文件数据将保存在基因库(http://www.ncbi.nlm.nih.gov/).
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Rod Wing其他文献
Rod Wing的其他文献
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{{ truncateString('Rod Wing', 18)}}的其他基金
Generation and Analysis of a Reference Sequence for the West African Cultivated Rice - Oryza Glaberrima (CG14)
西非栽培稻 - Oryza Glaberrima (CG14) 参考序列的生成和分析
- 批准号:
0822284 - 财政年份:2009
- 资助金额:
-- - 项目类别:
Standard Grant
Conference: 2nd International Symposium on Rice Functional Genomics, Tucson, AZ, November 2004
会议:第二届水稻功能基因组学国际研讨会,亚利桑那州图森,2004 年 11 月
- 批准号:
0441208 - 财政年份:2004
- 资助金额:
-- - 项目类别:
Standard Grant
The Oryza BAC Library Project: A Fundamental Public Resource to Study Monocot Plant Evolution, Development, and Physiology
Oryza BAC 图书馆项目:研究单子叶植物进化、发育和生理学的基本公共资源
- 批准号:
0208329 - 财政年份:2002
- 资助金额:
-- - 项目类别:
Standard Grant
Collaborative Research: The Green Plant BAC Library Project
合作研究:绿色植物BAC图书馆项目
- 批准号:
0211661 - 财政年份:2002
- 资助金额:
-- - 项目类别:
Cooperative Agreement
Molecular Analysis of Abscission Zone Development
脱落区发育的分子分析
- 批准号:
9796127 - 财政年份:1997
- 资助金额:
-- - 项目类别:
Continuing Grant
Acquisition of Major Multiuser Research Instrumentation for the Study of Plant, Fungal and Insect Genomics
采购用于植物、真菌和昆虫基因组学研究的主要多用户研究仪器
- 批准号:
9724557 - 财政年份:1997
- 资助金额:
-- - 项目类别:
Standard Grant
Molecular Analysis of Abscission Zone Development
脱落区发育的分子分析
- 批准号:
9418400 - 财政年份:1995
- 资助金额:
-- - 项目类别:
Continuing Grant
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低成本、用户友好的 DNA 制备试剂盒的商业化,可通过传统的短读长测序产生染色体跨度连续性,适用于广泛的应用
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Molecular studies on the pathogenesis of idiopathic short stature : Analysis of a growth gene(s) on the X chromosome short arm.
特发性身材矮小发病机制的分子研究:X 染色体短臂上生长基因的分析。
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04454280 - 财政年份:1992
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