Genetics, Vol. 166, 1463-1502, March 2004, Copyright © 2004

A Sequence-Based Genetic Map of Medicago truncatula and Comparison of Marker Colinearity with M. sativa

Hong-Kyu Choia,b, Dongjin Kima, Taesik Uhmb, Eric Limpensc, Hyunju Lima, Jeong-Hwan Muna, Peter Kalod,e, R. Varma Penmetsaa, Andrea Seresd, Olga Kulikovac, Bruce A. Roef, Ton Bisselingc, Gyorgy B. Kissd,e, and Douglas R. Cooka
a Department of Plant Pathology, University of California, Davis, California 95616,
b Molecular and Environmental Plant Sciences Program, Texas A&M University, College Station, Texas 77843,
c Department of Plant Sciences, Wageningen University, 6703HA Wageningen, The Netherlands,
d Biological Research Center, Institute of Genetics, H-6701 Szeged, Hungary,
e Agricultural Biotechnology Center, Institute of Genetics, H-2100 Godollo, Hungary
f Advanced Center for Genome Technology, University of Oklahoma, Norman, Oklahoma 73019

Corresponding author: Douglas R. Cook, University of California, 1 Shields Ave., Davis, CA 95616., drcook{at}ucdavis.edu (E-mail)

Communicating editor: A. H. PATERSON

A core genetic map of the legume Medicago truncatula has been established by analyzing the segregation of 288 sequence-characterized genetic markers in an F2 population composed of 93 individuals. These molecular markers correspond to 141 ESTs, 80 BAC end sequence tags, and 67 resistance gene analogs, covering 513 cM. In the case of EST-based markers we used an intron-targeted marker strategy with primers designed to anneal in conserved exon regions and to amplify across intron regions. Polymorphisms were significantly more frequent in intron vs. exon regions, thus providing an efficient mechanism to map transcribed genes. Genetic and cytogenetic analysis produced eight well-resolved linkage groups, which have been previously correlated with eight chromosomes by means of FISH with mapped BAC clones. We anticipated that mapping of conserved coding regions would have utility for comparative mapping among legumes; thus 60 of the EST-based primer pairs were designed to amplify orthologous sequences across a range of legume species. As an initial test of this strategy, we used primers designed against M. truncatula exon sequences to rapidly map genes in M. sativa. The resulting comparative map, which includes 68 bridging markers, indicates that the two Medicago genomes are highly similar and establishes the basis for a Medicago composite map.




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