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Originally published as Genetics Published Articles Ahead of Print on February 19, 2006.
Genetics, Vol. 172, 2541-2555, April 2006, Copyright © 2006
doi:10.1534/genetics.105.054791
Distribution of Microsatellites in the Genome of Medicago truncatula: A Resource of Genetic Markers That Integrate Genetic and Physical Maps
Jeong-Hwan Mun*,
Dong-Jin Kim*,
Hong-Kyu Choi*,
John Gish*,
Frédéric Debellé
,
Joanne Mudge
,
Roxanne Denny,
Gabriella Endré
,
Oliver Saurat,
Anne-Marie Dudez,
Gyorgy B. Kiss,**,
Bruce Roe,
Nevin D. Young and
Douglas R. Cook*,1
* Department of Plant Pathology, University of California, Davis, California 95616, Laboratoire des Interactions Plantes-Microorganismes, INRA-CNRS, 31326 Castanet-Tolosan Cedex, France, Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108, Biological Research Center, Institute of Genetics, H-6701 Szeged, Hungary, ** Institute of Genetics, Agricultural Biotechnology Center, 2100 Godollo, Hungary and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
1 Corresponding author: Department of Plant Pathology, University of California, 1 Shields Ave., Davis, CA 95616.
E-mail: drcook{at}ucdavis.edu
Microsatellites are tandemly repeated short DNA sequences that are favored as molecular-genetic markers due to their high polymorphism index. Plant genomes characterized to date exhibit taxon-specific differences in frequency, genomic location, and motif structure of microsatellites, indicating that extant microsatellites originated recently and turn over quickly. With the goal of using microsatellite markers to integrate the physical and genetic maps of Medicago truncatula, we surveyed the frequency and distribution of perfect microsatellites in 77 Mbp of gene-rich BAC sequences, 27 Mbp of nonredundant transcript sequences, 20 Mbp of random whole genome shotgun sequences, and 49 Mbp of BAC-end sequences. Microsatellites are predominantly located in gene-rich regions of the genome, with a density of one long (i.e., 
20 nt) microsatellite every 12 kbp, while the frequency of individual motifs varied according to the genome fraction under analysis. A total of 1,236 microsatellites were analyzed for polymorphism between parents of our reference intraspecific mapping population, revealing that motifs (AT)n, (AG)n, (AC)n, and (AAT)n exhibit the highest allelic diversity. A total of 378 genetic markers could be integrated with sequenced BAC clones, anchoring 274 physical contigs that represent 174 Mbp of the genome and composing an estimated 70% of the euchromatic gene space.