Functional Structural Diversity among Maize Haplotypes

Iowa State University, Ames IA

Investigators

Abstract

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.