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United States Department of Agriculture

Agricultural Research Service

Title: New Dinucleotide and Trinucleotide Microsatellite Resources for Cotton Genome Research

Authors
item Reddy, O. - TEXAS A&M UNIVERSITY
item Pepper, A - TEXAS A&M UNIVERSITY
item Abdurakmonov, I. - TEXAS A&M UNIVERSITY
item Saha, Sukumar
item Jenkins, Johnie
item Brooks, T. - TEXAS A&M UNIVERSITY
item El-Zik, K - TEXAS A&M UNIVERSITY

Submitted to: Journal of Cotton Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 6, 2000
Publication Date: May 1, 2000
Citation: REDDY, O.U., PEPPER, A.E., ABDURAKMONOV, I., SAHA, S., JENKINS, J.N., BROOKS, T., BOLEK, Y., EL-ZIK, K.M. NEW DINUCLEOTIDE AND TRINUCLEOTIDE MICROSATELLITE RESOURCES FOR COTTON GENOME RESEARCH. JOURNAL OF COTTON SCIENCE. 2000. V.5.P.103-113.

Interpretive Summary: Microsatellites are highly informative DNA based molecular markers. Identification of additional loci is of critical importance to the development of an integrated framework genetic map for cotton and has great potential value for marker assisted selection and utilization of comparative genomic tools in cotton improvement. A multi-institutional collaboration streamlined the process of microsatellite capture, characterization, development into informative molecular markers, and dissemination. Microsatellites were identified and primers were designed for 307 sequences that contained microsatellites of at least five repeat units. Primers were synthesized for 152 of these sequences and used to amplify DNA from two upland and two G. barbadense cultivars. Sixty-nine of the 152 primers had detectable polymorphism, including several intraspecific ones. Redundancy with two other previously derived microsatellite marker sets (BNL and CM) was low which implies that cotton genome has ample microsatellites to satisfy the requirements of extensive genome mapping and marker assisted selection. Publication of the primer information on these 307 microsatellites in a referred electronic journal format such as the Journal of Cotton Science will make the information rapidly and directly accessible to researchers around the world and will expedite cotton genome mapping.

Technical Abstract: Microsatellites are a highly informative DNA-based molecular marker. Additional microsatellite loci is of critical importance to the development of an integrated, framework genetic map for cotton and has potential value for marker-assisted selection and the utilization of comparative genomic tools in cotton improvement. A collaborative multi-institutional program was initiated to streamline the process of microsatellite capture, characterization, development into informative molecular markers, and discrimination of marker information to the cotton research community. A simple and efficient biotin capture method of microsatellite identification was optimized. Primers were developed to amplify identified repeat sequences. A subset of the resulting captured sequences were analyzed for polymorphism within and between the tetraploid cotton species, Gossypium hirsutum, and G. barbadense using a set of simple, low cost microsatellite analysis methods. Out of 588 microsatellite loci sequenced, almost all contained some form of repeat structure. Primers were designed for 307 sequences that contained microsatellites of at least five repeat units. Several repeat types were present (AGA, GA, CA, and ACA) (in order of decreasing abundance). Primers were synthesized from 152 of these sequences and used to amplify DNA. Sixty-nine of the 152 primers tested (45.4%) had detectable interspecific polymorphism, including several with intraspecific polymorphism. Redundancy with two previously derived microsatellite marker sets (BNL, CM) was low.

Last Modified: 4/25/2014
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