Consortium for Maize Genomics

玉米基因组学联盟

• 批准号: 0221536
• 负责人: Karel Schubert
• 金额: $ 592.88万
• 依托单位: Donald Danforth Plant Science Center
• 依托单位国家: 美国
• 项目类别: Cooperative Agreement
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-09-01 至 2005-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0221536&HistoricalAwards=false
• 关键词: Consortium; Maize; Genomics

Maize is both a classical genetic model for plant research and an economically important crop. Having a sequence of the genes of maize will have a fundamental impact on maize genetics and crop improvement. However, the maize genome is large and complex, comprising a sea of highly repetitive DNA containing islands of genes. Current estimates indicate that the gene islands only make up 15-20% of the genome. Selective sequencing of just the gene islands would thus be a rapid and cost-effective alternative to sequencing the whole genome. The overall goal of this project is to develop and evaluate high-throughput and robust strategies to isolate and sequence maize genes. Two promising approaches will be tested. The first, termed "methylation-filtering", is based on the finding that the highly repetitive DNA is modified (methylated) while the genes are largely free of such modification. The second, termed "high Cot selection", exploits the relatively low abundance of the gene sequences, which are present in a small number of copies in the genome. Each method yields a fraction of the genome highly enriched for the genes. Libraries of these DNA fragments will be sequenced and the sequences assembled and annotated to give a first picture of the sequence and organization of maize genes. All sequence information will be released immediately into GenBank and project data analyses will be available through web-based resources. The outcomes of this project will provide the research community with a powerful resource for maize genetics, biology, and breeding. They will also facilitate determination of the best strategy for attempting large-scale sequencing of maize genes.Deliverables:Maize LibrariesContact Karel Schubert at the Danforth Center (www.danforthcenter.org) for information on the libraries. Contact Dr. Rod Wing at AGI (www.genome.arizona.edu) for access to the clones from the methylation filtered and high CoT libraries of maize.Maize Sequencing Results:Sequence reads will be submitted to the HTGS division of GenBank and the trace files submitted to the NCBI trace database on a weekly basis. Concomitant with submission to NCBI both the sequence data and trace files will accessible from the Donald Danforth Plant Science Center maize website for use by the broader Maize research community.Bioinformatics:At a minimum, assemblies of the sequence will be released every three months, with the goal of providing monthly updates. Assembled sequences will be available from the TIGR website.

玉米是植物研究的经典遗传模型，也是重要的经济作物。获得玉米基因序列将对玉米遗传学和作物改良产生根本性影响。然而，玉米基因组是大而复杂的，包括含有基因岛的高度重复DNA的海洋。目前的估计表明，基因岛只占基因组的15-20%。因此，仅对基因岛进行选择性测序将是对整个基因组进行测序的快速且具有成本效益的替代方案。该项目的总体目标是开发和评估高通量和稳健的策略来分离和测序玉米基因。两种有希望的方法将得到检验。第一种称为“甲基化过滤”，是基于这样的发现：高度重复的DNA被修饰（甲基化），而基因基本上没有这种修饰。第二种称为“高Cot选择”，利用基因序列的相对低丰度，其在基因组中以少量拷贝存在。每种方法都产生了一部分高度富集基因的基因组。这些DNA片段的文库将被测序，序列组装和注释，以给出玉米基因的序列和组织的第一张图片。所有序列信息将立即发布到基因库，项目数据分析将通过网络资源提供。该项目的成果将为研究界提供玉米遗传学，生物学和育种的强大资源。它们还将有助于确定尝试大规模玉米基因测序的最佳策略。www.danforthcenter.org 联系AGI（www.genome.arizona.edu）的Rod Wing博士，获取来自玉米的甲基化过滤和高CoT文库的克隆。玉米测序结果：每周将序列读数提交给GenBank的HTGS部门，并将跟踪文件提交给NCBI跟踪数据库。 在提交给NCBI的同时，序列数据和追踪文件都可以从唐纳德·丹福斯植物科学中心玉米网站访问，供更广泛的玉米研究界使用。生物信息学：至少每三个月发布一次序列组装，目标是提供每月更新。 组装序列将可从TIGR网站获得。