Submitted to: Journal of Cotton Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/2/2009
Publication Date: 7/15/2009
Citation: Xiao, J., Wu, K., Fang, D.D., Stelley, D.M., Yu, J., Cantrell, R.G. 2009. New DNA Markers for the Use in Cotton (Gossypium spp.) Improvement. Journal of Cotton Science. 13(2):75-157 Interpretive Summary: DNA markers (very small frag 1 ments of DNA) played an important role in crop improvement during the past decade. Application of DNA markers associated with important traits such as yield can significantly enhance breeding for crop improvement either by reducing breeding time or by improving selection efficiency. Although cotton is the most important source of natural fiber and is economically important for many countries, the application of DNA markers in cotton breeding has lagged due to the complex genetic make-up (genome) of cotton, and more importantly, a shortage of informative DNA markers. Development of easily accessible DNA markers will accelerate research in cotton germplasm characterization and breeding. During the past decade, the Monsanto Company developed 3099 unique DNA markers. These markers revealed over 4000 loci (locations on the cotton chromosomes). One thousand eleven unique Monsanto DNA marker loci were located on a consensus genetic map for cotton along with 615 markers developed by public institutions. Use of these unique markers and knowledge of their position on the cotton chromosomes will provide a powerful tool for cotton researchers to improve cotton varieties.
Technical Abstract: SSR markers, also known as DNA microsatellite markers, are proving to be very useful for saturation of the large and complex upland cotton (Gossypium hirsutum genetic linkage map. Monsanto Company has invested heavily in development of cotton SSRs and has implemented molecular breeding technologies for the genetic improvement of cotton globally and the acceleration of the integration of biotechnology traits into the most elite upland cotton germplasm in the commercial pipeline. Genomic clones from microsatellite-enriched cotton DNA libraries were sequenced to identify SSR-containing target regions and SSR25 containing EST collections were searched. SSR primer pairs were successfully generated for 5,315 target sequences and utilized in molecular breeding projects to routinely amplify SSR marker loci and provide useable levels of polymorphism in interspecific and intraspecific genetic populations. Bioinformatics analysis of jcs3 these sequences and primer pairs relative to SSR sequences already present in current public databases reveal that 3,099 of these SSR primer pairs and target genomic sequences are unique and amplify over 4,000 unique marker loci in a tetraploid cotton genome depending on the germplasm analyzed. A subset of the Monsanto SSR markers were placed on a consensus genetic map along with a selected set of public anchor SSR markers (BNL and JESPR markers). Chromosome-marker bins, each 20 cM in size, were constructed on the genetic linkage map containing the two marker sources. This generated 207 marker bins for a total of about 4,140cM which is approximately the size of the tetraploid cotton genetic map. These bins contain 1,011 unique Monsanto SSR marker loci and 615 public anchor SSR markers. In order to contribute to the expanding genomic resources for cotton research and improvement, Monsanto is facilitating the uploading of the unique SSR primer sequences, their respective target clone sequence, and chromosome bin designation (if known) to Cotton DB (http://cottondb.org/) and CMD (http://cottonmarker.org) databases. These will be available for general use in the cotton research community without restriction.