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United States Department of Agriculture

Agricultural Research Service

Title: High Potential of Trap Markers in Sunflower Genome Mapping

Authors
item Hu, Jinguo
item Chen, Junfang - NORTH DAKOTA STATE UNIV.
item Berville, Andre - INRA, FRANCE
item Vick, Brady

Submitted to: Sunflower International Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: May 20, 2004
Publication Date: June 15, 2004
Citation: Hu, J., Chen, J., Berville, A., Vick, B.A. 2004. High potential of TRAP markers in sunflower genome mapping. International Sunflower Conference Proceedings. 16th International Sunflower Conference, August 29-September 2, 2004, Fargo, ND. p. 665-671.

Interpretive Summary: A genetic linkage map is useful for the identification of DNA markers associated with genes and QTLs (quantitative trait locus) governing the traits of economic importance in a segregating population. Collaborating with Dr. A. Berville of INRA (National Institute of Agricultural Research, France), we are constructing a linkage map for fine mapping QTLs controlling the oleic content in sunflower oil. A segregating population, 129 recombinant inbred lines (RILs) derived from the cross of 83HR4 x RHA345, was developed by A. Berville in France to investigate the oleic content in sunflower seed oil. DNA samples of the RILs were shipped to Fargo for marker analysis. We utilized the TRAP marker technique to generate markers for linkage map construction. One hundred and seventy-six polymorphic markers were generated with 38 primer combinations in 23 PCR reactions, producing an average of 4.6 markers per primer combination. The MapMaker program mapped 160 of the 176 markers in 17 linkage groups (corresponding to the 17 chromosome pairs) covering a total length of 1140 centiMorgans (cM). This preliminary result suggested that TRAP has high potential in genome mapping.

Technical Abstract: We constructed a linkage map with a set of 129 RILs (recombinant inbred lines) derived from the cross of 83HR4 x RHA345. Twenty oligos, selected from 61 oligos used in a preliminary screening between the two parental lines for the higher level of polymorphism, and three oligos of published SSR (simple sequence repeat) were used as fixed primers in combination with six infrared fluorescence dye-labeled arbitrary primers in the TRAP reactions. All the fixed primers were designed against sunflower EST (expressed sequence tag) sequences. One hundred and seventy-six polymorphic markers were generated with 38 primer combinations in 23 PCR reactions, producing an average of 4.6 markers per primer combination. A linkage map was constructed with the MapMaker program using a LOD score of 5.0 and a maximum recombination fraction of 0.25. The resulting map consisted of 160 markers in 17 linkage groups plus four pairs of linked markers, and covered a total length of 1140 centiMorgans (cM). These TRAP markers were well distributed throughout the genome; the number of markers per linkage group ranged from three to 28, and the average interval between two markers was 9 cM. Since TRAP can detect a high level of polymorphic markers that segregate in expected genetic ratios, it will be useful as a high throughput mapping method to develop ultra-high density linkage maps and tag important agronomic traits in segregating populations.

Last Modified: 9/21/2014
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