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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #206115
Title: Panzea: A Database and Resource for Molecular and Functional Diversity in the Maize Genome

Author
item ZHAO, WEI - COLD SPRING HARBOR LAB
item CANARAN, PAYAN - COLD SPRING HARBOR LAB
item JURKUTA, REBECCA - UNIV OF WISCONSIN-MADISON
item FULTON, THERESA - CORNELL UNIVERSITY
item GLAUBITZ, JEFFREY - UNIV OF WISCONSIN-MADISON
item Buckler, Edward - Ed
item DOEBLEY, JOHN - UNIV OF WISCONSIN-MADISON
item GAUT, BRANDON - UNIV OF CALIFORNIA-IRVINE
item GOODMAN, MAJOR - NORTH CAROLINA STATE UNIV
item Holland, Jim - Jim
item KRESOVICH, STEPHEN - CORNELL UNIVERSITY
item McMullen, Michael
item STEIN, LINCOLN - COLD SPRING HARBOR LAB
item Ware, Doreen

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/31/2007
Publication Date: 2/26/2007
Citation: Zhao, W., Canaran, P., Jurkuta, R., Fulton, T., Glaubitz, J., Buckler Iv, E.S., Doebley, J., Gaut, B., Goodman, M., Holland, J.B., Kresovich, S., Mcmullen, M.D., Stein, L., Ware, D. 2007. Panzea: A Database and Resource for Molecular and Functional Diversity in the Maize Genome. Nucleic Acids Research. 34:D752-D757.

Interpretive Summary: Maize is an important crop species and also the most diverse crop species known. On average, two randomly chosen maize lines have one SNP every ~100 bp; this divergence is roughly equivalent to the differences between humans and chimpanzees. This exceptional genotypic diversity underlies the phenotypic diversity maize needs to be cultivated in a wide range of environments. Understanding the mechanisms underlying the morphological and genetic diversity that exists in maize is critical to future plant breeding and is of great interest to maize geneticists and plant breeders. The Molecular and Functional Diversity in the Maize Genome project aims to understand how selection has shaped molecular diversity in maize and then relate molecular diversity to functional phenotypic variation. The project will screen 4000 loci for the signature of selection and create a wide range of maize and maize-teosinte mapping populations. These populations will be genotyped and phenotyped, permitting high-power and high-resolution dissection of the traits and relating the molecular diversity to functional variation. Panzea (http://www.panzea.org) is the bioinformatics arm of this project and also a community resource for maize diversity. As of August 2005, Panzea provides access to 400,552 SSR data points, 551,584 SNP data points, 67,703 sequence data points, and 34,124 phenotype experiment data points produced by the project through user-friendly web-based database searches and data retrieval/visualization tools, as well as a wide variety of information and services related to maize diversity. This is useful for the maize community as well as for plant biologists and plant breeders in general.

Technical Abstract: Maize, a classical model for genetic studies, is an important agronomic crop, and the genome is known to contain many natural differences in the DNA between different strains. On average, two randomly chosen maize lines have an average of one single nucleotide polymorphism (SNP) every ~100 bp; this difference is roughly equivalent to the differences between humans and chimpanzees. This difference in the nucleotide sequences underlies provides the underlying capacity that maize needs to be cultivated in a wide range of environments. The Molecular and Functional Diversity in the Maize Genome project aims to understand how selection has shaped the differences in the DNA content of maize and then relate these differences to functional trait differences, such as flowering time, or row number on a corn cob. The project will screen 4000 different regions of the maize genome for the signature of selection and create a wide range of maize and maize-teosinte mapping populations. These populations will be genotyped and phenotyped, permitting high-power and high-resolution dissection of the traits and relating the molecular diversity to functional variation. Panzea (http://www.panzea.org) is the bioinformatics arm, or database support for this project and also a community resource for the maize community. Panzea provides access to the genotype (DNA sequence), phenotype (traits evaluated), and polymorphism data (differences in the DNA sequence between different strains) produced by the project through user-friendly web-based database searches and data retrieval/visualization tools, as well as a wide variety of information and services related to maize diversity.