2006 Annual Report 4d.Progress report. This report serves to document research conducted under a Specific Cooperative Agreement between ARS and Texas A&M 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 Chromosome Substitution (CS-B) Lines Developed: Four new CS-B lines were developed and these 4 plus 5 previously developed lines were evaluated in crosses with TM-1 for agronomic and fiber traits by the Genetics and Precision Agriculture Research Unit in cooperation with Texas A&M University. This addresses the need for better ways to introgress genes from G. barbadense into upland cotton. We discovered chromosomal association of important fiber and agronomic traits in these germplasms. We have previously developed 17 CS-B lines. Together these represent unique germplasm useful for introgression of genes from G. barbadense into upland cotton in practical breeding programs. Progress was made in developing new chromosome substitution lines with chromosomes from G. tomentosum. These CS-B lines provide a unique and useful way to improve agronomic and fiber properties in applied cotton breeding.