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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #168119


item Yu, John

Submitted to: Plant Breeding News
Publication Type: Research Notes
Publication Acceptance Date: 7/11/2004
Publication Date: 7/11/2004
Citation: Yu, J. 2004. A standard panel of Gossypium genotypes established for systematic characterization of cotton microsatellite markers. Plant Breeding News. p. 148. Available:

Interpretive Summary:

Technical Abstract: Cotton Incorporated (CI) has organized and currently is supporting a cotton breeding and genetics research initiative across the U.S. Cotton Belt. Among the funded projects are those on developing and utilizing PCR-based DNA markers including microsatellite or simple sequence repeat (SSR) markers that seem to be abundant in the cotton genome (Gossypium spp.). The source materials for cotton SSR discovery include large insert BAC clones or physical contigs, random enriched small genomic clones, and expressed sequence tags (ESTs). To make significant and timely advances in the genetic improvement of cotton, many thousands of portable DNA markers are needed for the tetraploid genome of cultivated cottons. Such new markers need to be characterized systematically prior to various applications. After consultation and discussion with many cotton researchers, a manageable panel of 12 diverse genotypes is selected from cultivated and exotic cottons. The cotton genotype panel consists of G. hirsutum (AD1) TM-1, the genetic standard, and, Acala Maxxa, DPL 458BR, PM 1218BR, FM 832, and Stoneville 4892BR, cultivars; G. barbadense (AD2) 3-79, the genetic standard, and Pima S-6, a cultivar; G. arboreum (A2-8); G. raimondii (D5-3); G. tomentosum (AD3); and G. mustelinum (AD4). This panel represents a balanced diversity of the core Gossypium germplasm that includes genetic standards, base mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and four contemporary Upland cottons each with significant acreage. Three to five individual plants are maintained for each of 12 cotton genotypes in a USDA-ARS greenhouse in College Station, Texas. Only one single plant for each genotype is flagged for tissue harvest and DNA extraction, and standard protocols are followed for DNA purification and evaluation, providing the best uniformity of DNA stocks for cotton researchers with ongoing SSR marker development. Polymorphism arising from easily assayed variation in SSR numbers show great utility in crop genetic mapping and other applications. With this standard genotype panel, cotton SSR markers derived from different sources or groups can be evaluated in a systematic way to minimize the potential redundancy and to determine the markers Polymorphic Information Content (PIC) values for ready applications. The standardized information on the clones, sequences, primers, amplification conditions in addition to the PIC values will be placed in the public domain via Cotton Microsatellite Database (CMD) (, a dedicated database that is being set up at Clemson University. An Advisory Committee is formed to guide the development of CMD and to coordinate it with CottonDB (, a comprehensive cotton genome database that serves the international cotton research community (