An Integrated Web Resource for Cotton

‘‘The Cotton Diversity Database’’ (http://cotton.agtec.uga.edu) is a Web resource for cotton (Gossypium spp.) phenotypic and genomic data. A primary goal for this resource is to provide both a useful management tool for breeders and other applied scientists and a research tool for genetic and genomic scientists. The resource contains four interface suites that include displays for each of the available phenotypic or genomic data types. These display suites are accessible via the genotype portal, a search interface that allows users to begin with a cotton accession and obtain all available data. The phenotypic data displays include graphical views of overall cultivar performance with means and between group standard deviations indicated in an easy-to-interpret graphical manner for common trial measures such as lint yield, micronaire, etc. The genomic data displays include interactive graphical views of genetic map and diversity data types. Genetic map data is displayed in both traditional linear and two-dimensional comparative dot plot formats. Genetic diversity data is displayed in an interactive tree-based format showing degrees of similarity among genotypes. The data are stored in Oracle relational database (RDBMS) schemas containing tables and views for data storage, auto-calculated statistics and display parameters. The searchable RDBMS provides flexibility for a wide range of query and search options as well as integration paths amongst the various data types. WORLD cotton commerce of about $20 billion annually is made possible by the unusual ability of certain members of the Gossypium genus to produce single-celled seedborne epidermal trichomes (lint fibers) that can reach as much as 5 to 6 cm in length. In the USA alone, cotton is typically grown on about 5 million hectares per year, more than all crops except maize (Zea mays L.), wheat (Triticum aestivum L.), or soybean [Glycine max (L.) Merr.] (USDA-NASS, 2002). The value of cotton fiber grown in the USA is typically about $6 billion yr, while cottonseed oil and meal add another $500 million yr. Cotton fiber exports account for about $4 billion yr of the U.S. trade surplus (Meyer et al., 2005) and business revenue stimulated by this crop in the U.S. economy is estimated at about $120 billion (National Cotton Council, www.cotton.org/econ/world). The past decade of genomics research has yielded a cotton molecular map comprised of 3347 loci detected by 2669 probes (Rong et al., 2004). The cotton map has been linked to at least 295 QTLs, influencing 26 traits related to plant growth, development, and morphology (Wright et al., 1999; Jiang et al., 2000), reproductive biology (Lan et al., 1999); fiber yield and quality (Jiang et al., 1998; Paterson et al., 2002; Chee et al., 2005a, 2005b; Draye et al., 2005), disease resistance (Wright et al., 1998) and the preservation of productivity and quality under drought stress (Saranga et al., 2001, 2004). At least four high quality BAC libraries exist, for G. barbadense L., G. raimondii Ulbr. (A.H. Paterson, unpublished, 2004), and two strains of G. hirsutum (Tomkins et al., 2001). Genomic tools have been employed toward development of strategies for genetic improvement (El-Zik and Thaxton, 2001; Xia et al., 2001), analyses of genetic diversity (Van Esbroeck et al., 1998; Brubaker and Wendel, 2001; McCarty and Percy, 2001; Bowman and Gutierrez, 2003; Lubbers et al., 2004), and many other areas. Research efforts focused on analyses of genetic diversity and the development of genomic resources to establish the context for diversity studies are particularly important for cotton (Van Esbroeck et al., 1998; Benedict and Altman, 2001; Lubbers et al., 2004; Van Becelaere et al., 2005). The US cotton gene pool is genetically impoverished as a result of at least four genetic bottlenecks. All cottons cultivated in the USA are tetraploid, thought to have arisen in the New World about 1 to 2 million years ago as a result of an unusual hybridization event between an invasive A-genome diploid genotype and an indigenous D-genome diploid. Polyploid cottons are thought to be monophyletic, representing the first genetic bottleneck. A second bottleneck was associated with the domestication of cotton from a small subset of the wild genotypes. A third bottleneck was imposed by human sampling of tetraploid cotton genotypes from their center of diversity inMexico and Central America, and spread northward into the USA, and also to China, India, Egypt, Australia, and other countries. Finally, a fourth bottleneck results from the recent widespread deployment of transgenes in only a small number of genotypes. Growing concern about genetic vulnerability of the cotton gene pool to a wide range of biotic and abiotic hazards is exemplified by recent investigation of trends in yield improvement. A “Blue Ribbon Committee” of public and private scientists convened by the National Cotton Council (Helms, 2000) determined that indeed, U.S. cotton yields had peaked in 1992 and by 1998 had reached a disturbing rate of decline of about 16.8 kg ha yr (3.3% annual rate). Accompanying this yield decline, year-to-year variations in yield were almost four Alan R. Gingle, Hongyu Yang, Junkang Rong, and Andrew H. Paterson, Center for Applied Genetic Technologies, Univ. of Georgia, 111 Riverbend Rd., Athens, GA 30602; Peng W. Chee, O. Lloyd May, and Edward L. Lubbers, Dep. of Crop and Soil Sciences, Univ. of Georgia, Coastal Plain Experiment Station, Tifton, GA 31793; Daryl T. Bowman, College of Agriculture and Life Sciences, North Carolina State Univ., Raleigh, NC 27695-8604; J. LaDon Day, Dep. of Crop and Soil Sciences, The Univ. of Georgia, Georgia Station, Griffin Campus, Griffin, GA 30223. Received 8 Mar. 2006. *Corresponding author ([email protected]). Published in Crop Sci. 46:1998–2007 (2006). Crop Breeding & Genetics doi:10.2135/cropsci2005.09.0328 a Crop Science Society of America 677 S. Segoe Rd., Madison, WI 53711 USA R e p ro d u c e d fr o m C ro p S c ie n c e . P u b lis h e d b y C ro p S c ie n c e S o c ie ty o f A m e ri c a . A ll c o p y ri g h ts re s e rv e d . 1998 Published online September 8, 2006