Functional Structural Diversity among Maize Haplotypes

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）玉米表现出非重复序列的结构变异（SV）水平，这在高等真核生物中是前所未有的。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，而不存在于另一种单倍型中。该项目的目的是验证基因拷贝数的差异（包括增益和损失）有助于玉米非凡的表型多样性和可塑性的假设。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自交系的基因组序列草图和定位群体是可用的。在这个项目中，将利用现有的基因组序列数据和新生成的转录组数据来定义“Zeanome”，这是B73、其他玉米品系和玉米的野生祖先（teosinte）中存在的一套近乎完整的基因。玉米和大刍草系之间的SV将被鉴定为相对于Zeanome。通过将这些cnv和pav映射到表型ril，将有可能测试SV是否有助于表型变异。SV有助于玉米驯化和长期选择成功的假设将得到验证。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，可能需要在育种中重新引入种质抗逆性基因（pav）和在驯化过程中无意中丢失的遗传多样性。加深对pav的了解可以帮助育种者培育出更好的杂交品种。对产量成分的分析可能导致与作物改良有关的基因的发现。由此产生的对驯化的理解可能有助于新的生物能源作物的驯化。注释的“Zeanome”可用于解决各种各样的生物学调查。所有序列数据将存入GenBank。所有项目数据将通过几个现有数据库向社区提供，包括MaizeGDB （www.maizegdb.org）、Gramene （www.gramene.org）和Panzea （www.panzea.org）。将开发工具，以便MaizeGDB能够更好地为社区服务。与国家植物基因组计划（NPGI）当前的5年计划一致，该研究将提供大量和多样化的培训机会，这将有助于发展具有国际竞争力的科学劳动力。因为活动将发生在植物基因组学，生物信息学和统计学的界面，他们将提供跨学科的培训。将采用各种行之有效的机制，为研究型大学（主要是本科院校）和服务不足的院校的大量本科生提供指导研究经验。来自PUI的教师学者将在研究型大学的实验室中沉浸一个月。博士后教师学者将获得在PUI中脱颖而出所需的技能指导。此外，还将与nsf资助的视频分享社区合作，通过一种新颖的基于视频的方法，向学生和公众介绍科学家的生活。

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.