Poster: Genomic & proteomic resources

Abs # 893: Comparative genome analysis in legumes

Presenter:	Choi, Hong-Kyu , hchoi@ucdavis.edu
Authors	Choi, Hong-Kyu  (A)   Kim, Dong-Jin  (A)   Zhu, Hongyan  (A)   Mun, Jeong-Hwan  (A)   Baek, Jong-Min  (A)   Roe, Bruce  (B)   Young, Nevin  (C)   Doyle, Jeff  (D)   Ellis, Noel  (E)   Kiss, Gyorgy  (F)   Cook, Douglas  (A)
Affiliations:	(A): University of California, Department of Plant Pathology (B): University of Oklahoma, Department of Chemistry and Biochemistry (C): Unversity of Minnesota, Department of Plant Pathology (D): Cornell University, Department of Plant Biology (E): John Innes Centre (F): Biological Research Center, Institute of Genetics

For purposes of establishing a comparative genetic map among crop and model legumes we analyzed the position of conserved genetic markers in five legume species, including Medicago truncatula, Medicago sativa, Pisum sativa, Vigna radiata, and Glycine max. These species encompass the phylogenetic distribution of most of the agronomically important legumes. The basis for this comparative mapping study is a sequence-based genetic map of Medicago truncatula. The markers we have used are exclusively genes, or gene-containing BAC clones, which greatly facilitates a phylogenetic approach for prediction of orthologous elements between species. The majority of these genes were mapped based on single nucleotide polymorphisms that were converted to CAPS markers, or small insertion-deletions that could be scored as length polymorphisms. To enhance the success of cross-species, gene-specific markers we used a comparative approach involving multiple sequence alignments of legume genes. Alignment to the closest Arabidopsis homolog was used to infer intron position and oligonucleotide primers were designed to anneal within conserved exon regions and to amplify across the more polymorphic intron regions. In addition to their application as comparative phylogenetic and genetic markers within the five target genomes, we also assessed twelve cross-species primer pairs for their potential as phylogenetic tools across the breadth of the Fabaceae. Towards this end we amplified and sequenced loci from 96 diploid legume species and outrgoup controls, and used the sequence information to construct gene phylogenies. The data provide general support for this strategy to sample orthologous sequences across the Fabaceae