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United States Department of Agriculture

Agricultural Research Service

Title: Harnessing the annotated EST information in molecular marker development for crop improvement

Author
item Hu, Jinguo

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: January 20, 2007
Publication Date: March 28, 2007
Citation: Hu, J. 2007. Harnessing the annotated EST information in molecular marker development for crop improvement. 2nd International Conference on Plant Molecular Breeding, March 23-27, 2007, Sanya, Hainan, China. Molecular Plant Breeding. 5(2):251.

Technical Abstract: Marker-assisted selection has become an integral component of many crop breeding programs in both the private and public sectors throughout the world. Various markers, such as RFLP, RAPD, AFLP and SSR are being used by the crop breeding community. The advent of high throughput sequencing technology has generated an enormous amount of DNA sequence information for the genomes of many species of economic importance. This includes the draft genome sequences of two subspecies of rice, one of the most important food crops of the world and more than 40 million expressed sequence tags (EST) in the public databases. This wealth of information provides the opportunity to develop novel approaches to discover markers such as single nucleotide polymorphism (SNP) and targeted local lesions in genomes (TILLING) techniques, which are being applied to different crops at a fast pace. The TRAP (targeted region amplification polymorphism) marker technique is a fairly new, relatively high throughput, persuasively reliable, and broadly applicable fingerprinting technique. TRAP harnesses existing sequence information and leverages bioinformatics tools to design fixed primers against known sequences of annotated ESTs, and uses the fixed primers in combination with other primers of arbitrary sequence to trap polymorphism in a targeted genomic region. Since the fixed primer is targeting the candidate gene sequence, the probability of amplifying markers linked to the phenotype under investigation is substantially higher than that of RAPD and AFLP, which generate random polymorphic markers across the genome. As anticipated, we have had success with this technique in finding marker-trait associations for three important agronomic traits of sunflower: 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. An example of applying TRAP to identify markers linked to the fertility restoration (Rf1) gene for marker-assisted selection in sunflower germplasm enhancement will be presented.

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