Wednesday, November 15, 2006 - 11:30 AM

Genetic mapping in crop plants using Affymetrix GeneChip microarrays.

John Salmeron1, Tong Zhu1, Yu Xia1, Charles Chilcott1, Molly Dunn1, Gayle Dace1, Nan Zhou1, Nykoll Long1, Allen Sessions1, Bob Dietrich1, John Arbuckle2, Laurent Grivet3, and Gilles Gay3. (1) Syngenta Biotechnology, Inc., 3054 East Cornwallis Road, Research Triangle Park, NC 27709, (2) Syngenta Seeds, Inc., Stanton, MN 55018, (3) Syngenta Seeds, Toulouse, France

Map-assisted gene cloning and marker assisted breeding in crop plants are facilitated by high-density genetic maps.  Fine genetic resolution in the target region can improve precision in map-based cloning, shorten the distance for chromosome walking, and identify tightly-linked markers to reduce linkage drag during trait introgression and breeding.  Gene-based markers have the advantage of tight linkage to the trait, high levels of conservation among related species, and possible functional relevance to the trait.  Although information is rapidly becoming available through genome sequencing efforts, mapped gene markers in crop plants are still limiting.  We developed Affymetrix GeneChip technology to detect single feature polymorphisms (SFPs) from complex plant genomes.  We scored a high resolution mapping population, intermated B73 and Mo17 (IBM), for SFPs using a custom designed maize GeneChip microarray, and genetically mapped 34,034 SFPs representing 11,427 unique genes or EST clusters.  The mapped genes are validated by sequence analyses, and supported by the macro-synteny relations between rice and maize.  In a second application, we are developing comparative microarray analysis of bulked-segregant populations to identify tightly linked trait markers.  Integration of these gene markers with other types of genetic and physical markers will facilitate marker assisted breeding and identification of genes that control complex traits.