Functional Structural Diversity among Maize Haplotypes

玉米单倍型之间的功能结构多样性

• 批准号: 1027527
• 负责人: Patrick Schnable
• 金额: $ 300万
• 依托单位: Iowa State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-03-15 至 2014-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1027527&HistoricalAwards=false
• 关键词: Functional; Structural; Diversity; among; Maize

PI: Patrick S. Schnable (Iowa State University) CoPIs: Brent Buckner (Truman State University), Carolyn J. Lawrence (Iowa State University/USDA-ARS) and Dan Nettleton (Iowa State University) Maize exhibits levels of structural variation (SV) of non-repeat sequences that are unprecedented among higher eukaryotes. This SV includes hundreds of copy number variants (CNVs) and thousands of presence/absence variants (PAVs). Many of the PAVs contain intact, expressed, single-copy genes that are present in one haplotype but absent from another. The goal of this project is to test the hypothesis that differences in gene copy number (both gains and losses) contribute to the extraordinary phenotypic diversity and plasticity of maize. Maize is a good model for these studies because it exhibits a rapid decay of linkage disequilibrium (LD) and because a draft genome sequence of the B73 inbred and mapping populations are available. In this project, the "Zeanome", a near-complete set of genes present in B73, other maize lines and the wild ancestor of maize (teosinte), will be defined using existing genomic sequence data and newly generated transcriptomic data. SV among maize and teosinte lines will be identified relative to the Zeanome. By mapping these CNVs and PAVs to phenotyped RILs it will be possible to test whether SV contributes to phenotypic variation. The hypothesis that SV contributed to the domestication of maize and the success of long-term selection will be tested. The studies will inform crop improvement. A finding that changes in gene copy number contribute to genetic gain would be transformative to the breeding industry. To help adapt crops to climate change it may be desirable to reintroduce into breeding germplasm stress resistance genes (PAVs) and genetic diversity inadvertently lost during domestication. Enhanced understanding of PAVs may help breeders develop improved hybrids. The analyses of yield components may lead to the discovery of genes with relevance to crop improvement. The resulting understanding of domestication may assist with the domestication of new bioenergy crops. The annotated "Zeanome" may be used to address a wide variety of biological investigations. All sequence data will be deposited in GenBank. All project data will be made available to the community via several existing databases, including MaizeGDB (www.maizegdb.org), Gramene (www.gramene.org) and Panzea (www.panzea.org). Tools will be developed so that MaizeGDB can better serve the community. Consistent with the current 5 year plan for the National Plant Genome Initiative (NPGI), the research will provide numerous and diverse training opportunities that will contribute to the development of an internationally competitive scientific workforce. Because the activities will occur at the interface of plant genomics, bioinformatics, and statistics, they will provide cross-disciplinary training. A variety of proven mechanisms will be used to provide large numbers of undergraduates from research universities, predominately undergraduate institutions (PUI) and underserved institutions with mentored research experiences. A teacher-scholar from a PUI will spend one month immersed in a laboratory at a research-intensive university. A postdoctoral teacher-scholar will be mentored in skills needed to excel at a PUI. Additional outreach will occur in partnership with an NSF-funded video-sharing community and via a novel video-based approach to inform students and the public about the lives of scientists.

Pi：Patrick S.Schnable(爱荷华州立大学)Copis：Brent Buckner(杜鲁门州立大学)，Carolyn J.Lawrence(爱荷华州立大学/USDA-ARS)和Dan Nettleton(爱荷华州立大学)玉米展示了在高等真核生物中前所未有的非重复序列的结构变异(SV)水平。该SV包括数百个拷贝数变体(CNV)和数千个存在/缺失变体(PAV)。许多PAV含有完整的、表达的、单拷贝的基因，这些基因存在于一种单倍型中，而在另一种单倍型中缺失。该项目的目的是验证这样一种假设，即基因拷贝数的差异(包括获得和丢失)有助于玉米的非凡表型多样性和可塑性。玉米是这些研究的一个很好的模型，因为它表现出连锁不平衡(LD)的快速衰减，并且因为B73自交系和作图群体的基因组草图序列是可用的。在这个项目中，将使用现有的基因组序列数据和新产生的转录组数据来定义“Zeanome”，即存在于B73、其他玉米品系和玉米野生祖先(Teosinte)中的一套近乎完整的基因。玉米和Teosinte品系中的SV将被鉴定为与Zeanome相关。通过将这些CNV和PAV映射到表型RIL，将有可能测试SV是否对表型变异有贡献。关于SV对玉米的驯化和长期选择的成功有贡献的假设将得到检验。这些研究将为作物改良提供信息。基因拷贝数的变化有助于遗传增益的发现将对育种行业产生革命性的影响。为了帮助作物适应气候变化，可能需要在育种种质中重新引入在驯化过程中无意中丢失的抗逆基因(PAV)和遗传多样性。提高对PAV的理解可能有助于饲养者开发改良的杂交品种。对产量构成因素的分析可能导致发现与作物改良相关的基因。由此产生的对驯化的理解可能有助于驯化新的生物能源作物。注解的“Zeanome”可用于各种生物学研究。所有序列数据将保存在GenBank中。所有项目数据将通过几个现有的数据库提供给社区，包括MaizeGDB(www.maizegdb.org)、Gramene(www.gram ene.org)和Panzea(www.panzea.org)。将开发工具，以便MaizeGDB能够更好地服务于社区。与国家植物基因组倡议(NPGI)目前的五年计划一致，这项研究将提供大量和多样化的培训机会，有助于发展一支具有国际竞争力的科学劳动力队伍。由于这些活动将发生在植物基因组学、生物信息学和统计学的交界处，他们将提供跨学科的培训。将使用各种行之有效的机制，为研究型大学、主要是本科院校(PUI)和服务不足的机构的大量本科生提供指导研究经验。PPI的一名教师兼学者将在一所研究密集型大学的实验室里沉浸一个月。博士后教师兼学者将接受在PPI方面出类拔萃所需技能的指导。将与NSF资助的视频共享社区合作，并通过一种新颖的基于视频的方法，向学生和公众宣传科学家的生活，从而开展更多的推广活动。