Gene diversity is the foundation upon which plant breeders can improve a crop. Genetic diversity shown in diverse cultivars can also be useful in a regional setting to buffer the crop against abiotic and biotic stresses such as drought and pests. Coefficient of parentage analyses have indicated that a high degree of diversity exists among U.S. cotton cultivars. However, the commercial breeding programs rely largely upon protocols that seem likely to lead to loss of genetic diversity. The recent stagnation in yield and fiber quality improvement suggests that many of the favorable genes have been fixed in the gene pool that is commonly used by the commercial breeders.
To address the status of the genetic diversity in the U.S. cotton germplasm, we collaborated with the Plant Genome Mapping Laboratory (Dr. Andrew Paterson, UGA, Athens, GA) and the TAES Cotton Breeding Program (Dr. John Gannaway, TX Agric. Expt. Sta., Lubbock, TX) to study the genetic diversity in a large collection of historically important cultivars and germplasm lines that was developed from about 1900 to the early 1990s. More than 330 cultivars/lines were selected and surveyed with 360 genetically mapped DNA markers. 
The initial results from this work showed that 1) the coefficient of parentage overestimated diversity in cotton, 2) there was little to no diversity for much of the cotton genome, 3) many genes (alleles) observed in the older germplasm were no longer present in the modern cultivars, and 4) the use of secondary gene pools remains largely uncapitalized in cotton improvement. This information could enable cotton breeders to more accurately select parental combinations that simultaneously increase the opportunity for selecting superior progenies and maintain genetic diversity in a breeding program. Additional research on regional and international gene diversity is being conducted as well as looking into temporal depletion of genetic diversity of Upland cotton from 1900 to present.