Project Presentations

• Molecular And Functional Diversity In The Maize Genome
  
  John Doebley, Edward Buckler, Theresa Fulton, Brandon Gaut, Major Goodman, Jim Holland, Stephen Kresovich, Michael McMullen, Lincoln Stein, Doreen Ware, Wei Zhao, Payan Canaran, Stephen Wright
  
  Plant & Animal Genomes XIII Conference, January 15-19, 2005, San Diego, CA
  
  In 2001, maize became the number one production crop in the world. Maize is also the single most diverse crop species, containing tremendous variation in morphological and physiological traits and extensive DNA sequence polymorphism. We have previously determined the genetic relationships among maize and teosinte germplasm, examined how average loci evolve, and developed methods for relating nucleotide diversity to phenotypic effects. Our new objective is to understand how selection has shaped molecular diversity in maize and then relate molecular diversity to functional phenotypic variation. How has selection shaped molecular diversity? To address this, 4000 loci will be screened for selection evidence, and then 1000 loci will be studied extensively by doing SNP surveys across diverse maize and teosinte. A range of tests of selection will be used to identify genes showing positive, diversifying and purifying selection. The identified genes will be those involved in domestication, agronomic improvement, and local adaptation. How does this molecular diversity relate to functional trait variation? A wide range of maize and maize-teosinte linkage and association mapping populations will be created that capture a tremendous range of diversity. These populations will be genotyped for SNPs and candidate genes and phenotyped for domestication, agronomic and developmental traits. This will permit high-power and high-resolution dissection of a wide range of traits, and relate the molecular diversity to functional variation. Further information and data produced by the project can be obtained at the project website, www.panzea.org.
  
  
• An Interactive Web-Based Multiple Sequence Alignment Viewer With Polymorphism Analysis Support
  
  Payan Canaran, Doreen Ware, Lincoln D. Stein
  
  Plant & Animal Genomes XIII Conference, January 15-19, 2005, San Diego, CA
  
  Making sequence data from genotyping assays available to the public in a web environment requires visualization tools for displaying alignments and polymorphism-related information. We developed an interactive web-based viewer for displaying multiple sequence alignments. The viewer provides a set of features for assisting nucleotide polymorphism analysis. These include highlighting and providing statistics on positions of variation, displaying base-pair quality scores and a utility to filter out sequences of poor quality or low similarity to other sequences in the alignment. The viewer also provides general features such as search utilities and formatters for generating text dumps of sequences. Initially designed to support visualization needs of the maize diversity web site Panzea (www.panzea.org) and based on the Genomic Diversity and Phenotype Data Model (www.maizegenetics.net/gdpdm), viewer can be configured to retrieve sequence and related data from other sources with moderate or no additional coding. The viewer is written in Perl and doesn't have demanding dependencies. Many of its features can be customized to fit individual web site needs through a simple configuration file. It provides a utility for pre-caching displays and allows faster response times for large alignment sets that would otherwise respond slowly. The viewer is publicly available. Downloading information and a live installation can be accessed at the Panzea web site (www.panzea.org/db/snp_alignment/snp_cgi.dev.pl).
  
  
• Molecular And Functional Diversity In The Maize Genome
  
  John Doebley, Ed Buckler, Brandon Gaut, Major Goodman, Jim Holland, Steve Kresovich, Mike McMullen, Lincoln Stein, Doreen Ware, Jianming Yu, Gael Pressoir
  
  Plant & Animal Genomes XIV Conference, January 14-18, 2006, San Diego, CA
  
  Maize is the number one production crop in the world and is the most diverse crop species. We are examining two questions in this model species, How has selection shaped molecular diversity? and How does this molecular diversity relate to functional trait variation? To answer these we are performing SNP discovery in 4000 genes. The sequence data from our SNP discovery panel are being used to determine the proportion of genes influenced by artificial selection during the domestication and crop improvement phases of maize evolution. The SNPs will be used to genetically characterize the comprehensive germplasm base of maize, and to perform QTL and association mapping both in maize (Zea mays ssp. mays) and in its wild relative (teosinte, Zea mays ssp. parviglumis) for traits of evolutionary, developmental and agronomic importance. Our project will generate several key resources for the maize research community: (i) validated SNP markers from 4000 genes, (ii) a maize QTL mapping population of 5000 fully genotyped RILs from crosses between diverse maize inbred lines and B73, (iii) a maize association mapping population consisting of 281 diverse maize inbred lines, (iv) a teosinte association mapping population, and (v) a maize-teosinte QTL mapping population of backcross RILs. We expect the maize QTL and association mapping populations to be of greatest interest to the maize community. Seed will become available from all of our germplasm resources, and collaborators are invited to contribute candidate genes and trait data for association mapping. For further information, see the project website: www.panzea.org.