Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

TASSEL 2.0: A Software Package For Association And Diversity Analyses In Plants And Animals.

Zhiwu Zhang¹ , Peter J Bradbury² , Dallas E Kroon¹ , Terry M Casstevens³ , Edward S Buckler⁴

¹  Institute of Genetic Diversity, Cornell University, 175 Biotechnology Bldg, Ithaca, NY 14853-2703

²  USDA-ARS Cornell University, 741 Rhodes Hall, Ithaca, NY 14853-2703

³  Department of Genetics, North Carolina State University, Raleigh, NC 27695

⁴  USDA-ARS Cornell University, 159 Biotechnology Bldg, Ithaca, NY 14853-2703

TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) is a software package which performs a variety of genetic analyses. The analyses include association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information. These new analyses should permit association analysis in a wide range plant and animal species. In addition to these association tools, TASSEL permits the analysis of diversity estimates include average pairwise divergence and segregating sites. Linkage disequilibrium is estimated by the standardized disequilibrium coefficient, D’, as well as r², and P-values. One of the convenient features of TASSEL is allowing users to use GDPC (Genomic Diversity and Phenotype Connection) to select data sources, retrieve and filter data and export data to chosen formats. TASSEL also has a variety of data extraction utilities and visualization tools, such as alignment viewer, extraction of SNPs and indels from alignments, neighbor-joining cladogram, K-nearest neighbor missing data imputation, and miscellaneous data graphing. TASSEL is open source software written in Java. The application and source code can be downloaded from http://www.maizegenetics.net or http://sourceforge.net/projects/tassel.