| Abstract Detail
Tuesday Morning Contributed Talks Dietrich, Bob [1], Grivet, Laurent [2], Zhu, Tong [1], Chilcott, Charles [1], Dunn, Molly [1], Xia, Yu [1], Zhou, Nan [1], Long, Nykoll [1], Puddephat, Ian [3], Bontems, Sylvain [4], Bonnet, Gregori [4]. Affymetrix microarrays as tools for generating maps and markers in tomato. WE have used an Affymetrix genechip containing 250,000 features representing 23,000 tomato genes as a tool to develop an ultra-high density (UHD) map, and to identify markers targeted to a specific locus. To generate the UHD map, genomic DNA of 76 tomato introgression lines (Eshed and Zamir, Genetics 141: 1147-1162) were hybridized to individual tomato genechips. Based on differential hybridization signals, over 6,000 genes were mapped to one of 107 unique bins. The mapped gene sequences were then blasted against tomato BAC end, genome survey sequence (GSS) and unigene databases. Based on high quality blast hits, an additional 14,000 sequences were mapped to bins on the UHD map. This data set provides a large set of candidate markers mapped to specific regions of the tomato genome and also allows the alignment of the UHD map with the tomato physical map. The tomato genechips are also being used to target marker discovery to specific loci using a bulked segregant analysis (BSA) approach. The initial experiment targeted the Fusarium resistance locus Fr1. Two pools of genomic DNA were prepared, one containing 22 individuals homozygous for the resistant allele and the other containing 21 individuals homozygous for the susceptible allele. The two pools of genomic DNA and genomic DNA from the parental lines were each hybridized to tomato genechips. Chip features that gave a differential hybridization signal between the two pools were sequenced to identify SNP’s and then mapped to determine linkage to the target locus. 16 of 17 marker candidates identified in this experiment were found to be genetically linked to the target locus.
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1 - Syngenta Biotechnology, Inc., 3054 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
2 - Syngenta Seeds, 12, chemin de l\'Hobit, BP27, Saint-Sauveur, F-31790, France
3 - Syngenta Jealotts Hill Int. Research Centre, Bracknell, Berkshire, RG42 6EY, UK
4 - Syngenta Seeds, Domaine du Moulin, Sarrians, 84260, France
Keywords:
microarray
bulked segregant analysis
ultra high density map.
Session: SOL04-1
Location: Ballroom AB/Monona Terrace
Date: Tuesday, July 25th, 2006
Time: 8:10 AM
Abstract ID:466 |
