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United States Department of Agriculture

Agricultural Research Service


item Hoffman, Steven
item Yu, John
item Kohel, Russell
item Cantrell, Roy
item Xiao, Jnhua
item Pepper, Alan

Submitted to: Plant and Animal Genome
Publication Type: Abstract only
Publication Acceptance Date: 1/14/2006
Publication Date: 1/14/2006
Citation: Hoffman, S., Yu, J., Kohel, R.J., Cantrell, R.G., Xiao, J., Pepper, A. 2006. Characterization of 656 new SSR markers developed from Gossypium hirsutum sequences [abstract]. Proceedings of Plant and Animal Genome XIV Conference. Paper No. P157.

Interpretive Summary:

Technical Abstract: In an effort to contribute valuable marker resources to the cotton research community we are making available the sequences 656 SSR markers captured from Gossypium hirsutum (GH) cultivar TAMCot Sphinx. A total of 4,512 clones, from two independent (GA)n, (AGA)n, and (CA)n microsatellite-enriched libraries were sequenced by Monsanto, Inc., yielding 3,629 finished, high-quality sequences. We used Blast to check for sequence redundancy, and have manually designed primer pairs to amplify 1,059 microsatellites. We are currently designing primer pairs to produce an amplicon size of 60-120 bp making the resolution of small expansions or contractions of SSR sites possible with High Resolution Agarose electrophoresis. Both forward and reverse primers have been designed with an average length of 24.5 bp. These markers typically exhibit very specific amplification, often amplifying single loci in the Gossypium species. Approximately 82% of the primer pairs clearly amplified one or few loci. Of the 656 markers screened 195 were polymorphic between TM-1 and 3-79 and 165 were fully genotyped on the TM-1 (G. hirsutum) x 3-79 (G. barbadense) interspecific recombinant inbred (RI) population using 3% High Resolution Agarose electrophoresis. Phenotyping of Gh markers on the TM-1 x 3-79 RI Lines revealed that 51.3% had the TM1 genotype while 44.4% had the 3-79 genotype and 4% were either ambiguous or heterozygous. 20 of the Gh Markers phenotyped on the RI population had individual genotype frequencies that were significantly different from equal contributions of TM1 and 3-79, of these 14 were biased toward TM1, and 3 toward 3-79.

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