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United States Department of Agriculture

Agricultural Research Service

Title: DNA Sequence Information-Facilitated Molecular Marker Development for Crop Improvement

Author
item Hu, Jinguo

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: August 20, 2005
Publication Date: September 5, 2005
Citation: Hu, J. 2005. DNA sequence information-facilitated molecular marker development for crop improvement [abstract]. Huazhong Agricultural University and Univeristy of California Davis, Bilateral Symposium on Genomics and Crop Genetic Improvement, September 5-8, 2005, Wuhan, China. p. 27.

Technical Abstract: The advent of high throughput sequencing technology has generated abundant information on the DNA sequences for the genomes of many crop plant species. This includes the completion of the map-based whole genome sequence for rice, one of the most important food crops of the world and the establishment of the EST (expressed sequence tags) databases for many crop species of economic importance. The number of ESTs in the databases has been steadily increasing. In addition, powerful bioinformatics tools have annotated thousands of sequences as putative functional genes. To harness the existing sequence information for marker development, we developed a marker technique, called Targeted Region Amplification Polymorphism (TRAP), which is high throughput, reliable, and widely applicable. Unlike the two most popular marker techniques, RAPD and AFLP, which do not need prior sequence information to generate markers, TRAP exploits bioinformatics tools to design the fixed primers against known sequences of putative genes, and uses the fixed primer in combination with other primers of arbitrary sequence to trap polymorphism in the targeted genomic region. In sunflower, three genes controlling important agronomic traits have been successfully tagged with the TRAP technique. They are: a dominant gene conferring resistance to several races of downy mildew (Plasmopara halstedii), a recessive gene controlling apical branching, and a recessive gene governing complete male sterility. Using the conserved telomere sequence repeat as a fixed primer, we developed markers that defined 20 of the 34 linkage group ends of an SSR marker saturated sunflower linkage map. Results from the application of TRAP to other crop species in assessing intra- and interspecific genetic variation of germplasm collections and in mapping quantitative trait loci (QTL) will be discussed.

Last Modified: 10/1/2014
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