2006 Annual Report 4d.Progress report. This report serves to document research conducted under a Specific Cooperative Agreement between ARS and Mississippi State University. Additional details of research can be found in the report for the inhouse research project 6406-21000-010-00D, Germplasm Enhancement and Genetic Improvement of Cotton. New Genetic Models and Software for Analysis of Genetics and Plant Breeding Experiment: Four manuscripts describing genetic models, software, and data analysis for plant breeding experiments were published through cooperative research between the Genetics and Precision Agriculture Research Unit and Mississippi State University. These address the need for better statistical models to partition genetic variances in plant breeding. These methodologies describe a recursive approach to detect multivariable conditional variance components, compare two statistical models for evaluating boll retention in cotton, provide variance component estimation using the additive, dominance, and additive by additive model when genotypes vary across environments, and an additive dominance model to determine chromosomal effects in chromosome substitution lines and other germplasm. These software, models, and data set analyses provide new and advanced techniques for plant breeders that should improve their ability to obtain maximum information from their data sets which should in turn improve their plant breeding efforts.