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United States Department of Agriculture

Agricultural Research Service

Title: Indentification of 700 new microsatellite loci from cotton (G. hirsutum)

item Hoffman, Steven
item Yu, John
item Grum, Daniel
item Xiao, Jinhua
item Kohel, Russell
item Pepper, Alan

Submitted to: Journal of Cotton Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/11/2007
Publication Date: 12/31/2007
Citation: Hoffman, S.M., Yu, J., Grum, D.S., Xiao, J., Kohel, R.J., Pepper, A.E. 2007. Indentification of 700 new microsatellite loci from cotton (G. hirsutum). Journal of Cotton Science. 11:208-241.

Interpretive Summary: Molecular markers offer powerful tools in crop improvement of the new century. In cotton, recent development of portable DNA markers such as microsatellites in Upland cotton species contributes an expanded research in germplasm characterization and molecular breeding. This report describes 700 pairs of microsatellite markers that were developed from Upland cotton cultivar Tamcot Sphinx genomic DNA. This set of microsatellite markers were characterized from 1,059 pairs of primers designed from 4,512 sequenced clones. The characterization reveals 28.7% DNA polymorphism between TM-1 and 3-79, the genetic standards of two major cotton species. The polymorphic markers are used to map the cotton genome and provide new information for cotton genetic research.

Technical Abstract: Microsatellite markers, also known as SSRs, comprise a keystone technology for genetic linkage analysis, QTL mapping, marker-assisted breeding, and genome analysis. In order to contribute to a growing body of molecular marker resources for cotton research and improvement, we developed primers to amplify 700 new microsatellite markers, designated Gh for Gossypium hirsutum. These primers were designed using microsatellite sequences that were isolated from Gossypium hirsutum cultivar Tamcot Sphinx genomic DNA by a biotinylated-oligonucleotide capture method. A total of 4,512 clones, from (GA)n, (AGA)n, and (CA)n microsatellite-enriched libraries were sequenced. From these, 1,059 primer pairs were developed. Of the first 700 primer-pairs to be characterized, 602 primer pairs (86%) produced one or more distinct PCR amplification products within the expected size range in at least one of the test cotton genotypes G. hirsutum cultivar TM-1 and G. barbadense cultivar 3-79. Further, 201 primer pairs (28.7%) yielded size polymorphisms between TM-1 and 3-79 that were easily resolved using high-resolution agarose electrophoresis. A subset of 165 polymorphic markers was fully genotyped on the TM-1 x 3-79 interspecific recombinant inbred (RI) of 191 individuals. In this analysis, segregation distortion was low (10.3% of loci) and functional redundancy of marker loci was low (1.2% of loci). Data from these markers are being incorporated in an integrated SSR map from the TM-1 x 3-79 recombinant inbred population. Future updates regarding sequence, primer, polymorphism, and linkage information from the remainder of the Gh microsatellite collection will be uploaded directly to CottonDB and CMD databases.

Last Modified: 10/15/2017
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