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United States Department of Agriculture

Agricultural Research Service

Title: The Development and Evaluation of Consensus Chloroplast Ssrs for Chloroplast Genetic Analysis

Authors
item Chung, Sang-Min - UNIV OF WISCONSIN
item STAUB, JACK

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: October 1, 2002
Publication Date: January 1, 2003
Citation: CHUNG, S., STAUB, J.E. THE DEVELOPMENT AND EVALUATION OF CONSENSUS CHLOROPLAST SSRS FOR CHLOROPLAST GENETIC ANALYSIS. PLANT AND ANIMAL GENOME ABSTRACTS. 2003. ABSTRACT P. 119.

Technical Abstract: Universal or consensus chloroplast primers are available. However, they are limited by their number and genomic distribution. In order to increase the number of consensus chloroplast SSRs (ccSSRs) beyond that previously reported, the target sequences for chloroplast SSR motifs were set at A or T (n > 6) mononucleotide repeats from tobacco (Nicotiana tabacum L.) chloroplast sequences. Twenty-three putative marker loci that possessed conserved flanking sequence spans were selected for consensus primer pair construction. All primer pairs produced amplicons after PCR employing genomic DNA from members of the Chenopodiaceae, Cucurbitaceae, and Solanaceae. Sixteen, 22, and 19 of the 23 primer pairs were successively amplified by PCR using template DNA from species of the Apiaceae, Brassicaceae, and Fabaceae, respectively. Twenty of 23 primer pairs were also functional in three monocot species of the Liliaceae and Poaceae. The agreement of cluster anal! ysis groupings with previously determined biological relationships suggests that these ccSSRs might have utility for determining genetic relationships among closely related taxa. In order to provide for a marker system having significant coverage of the chloroplast genome, ccSSR primers were strategically "recombined" and named recombined consensus chloroplast primers (RCCP) for PCR analysis. Successful amplification after extended-length PCR of 16 RCCP primer pairs from cucumber (Cucumis sativus L.) DNA suggested that the amplicons detected may be representative of the cucumber chloroplast genome. Furthermore, these RCCP pairs could have utility as a molecular tool for broad-based chloroplast genetic analysis, especially in plant species for which chloroplast genome sequence information is not now available.

Last Modified: 9/29/2014
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