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.
The term "presence-absence variation" (PAV) describes genetic fragments that are present in one maize genome but absent from another. PAVs can potentially influence plant phenotypes or traits that are of agronomic importance. The focus of this award was to discover and characterize PAVs in the maize genome as a first step towards testing the hypothesis that PAVs contribute to the extraordinary phenotypic diversity and plasticity of this important crop and genetic model species. We also developed informatic tools so that the model organism database for maize (MaizeGDB) can display PAVs and otherwise better serve the research community in several significant ways. Making use of advances in DNA sequencing technology and other genomic tools, 11,962 PAVs that are present in 26 maize inbred lines but that are absent from the B73 reference genome were identified. 1,569 of these PAVs were genetically mapped. The chromosomal positions of only about half (76/148) of tested genetically mapped PAVs could also be determined using linkage disequilibrium (LD) mapping. Current methods of detecting associations between genotype and phenotypes rely on LD between genetic markers and causal DNA variants. Hence, our finding that not all PAVs can be positioned on chromosomes via LD mapping has important implications for association mapping, a statistical approach for identifying genes or markers that influence traits. Our results suggest that the power of association studies could be improved by the inclusion of PAV genotyping scores. This collection of genotyped and mapped PAVs will therefore enable the community to better test for associations between genotypes and phenotypic variation in yield-related traits. The current study has produced numerous resources for the maize genetics research community. RNA-sequencing data generated on 27 inbred lines from 5 tissues has been made available to the community via NCBI’s Short Reads Archive (SRA) under accessions SRA050451 and SRA050790. The PAV sequences identified from the RNA-sequencing have been used to create a commercially available Zeanome sequence capture array that contains probes designed from the B73 reference genome, PAVs, and the wild ancestor of maize, teosinte. The thousands of SNPs identified from these lines through sequencing can be used for additional genome-wide analyses. Videos describing the process used to identify PAVs and "a day in the life of" graduate students and staff members can be viewed at http://schnablelab.plantgenomics.iastate.edu/media/. NSF support provided research experience for 7 undergraduate (REU) students to encourage and prepare them for further scientific training. One of these REUs is now in a scientific graduate program. A Post-Doctoral scholar received mentoring on proposal and manuscript preparation and patent application process in additional to training that helped him become an independent researcher; he is now a tenure-track faculty member at Kansas State University. Over 50 Iowa State University undergraduates gained exposure to a research environment by helping to generate project data. A Research/Teaching Scholar was mentored to gain experience at Truman State University; she is currently a Visiting Professor of Biology at Central Methodist University. More than 10 undergraduate students worked during the academic year or summer at Truman State University to learn lab protocols and/or bioinformatics skills. Data generated from this award were used to enrich a Biology course at Truman State University; students used these data to learn methods to analyze DNA sequences.
