Genetics. Published Articles Ahead of Print: February 19, 2006, Copyright © 2006
doi:10.1534/genetics.105.054791


A more recent version of this article appeared on April 1, 2006.

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Distribution of microsatellites in the genome of Medicago truncatula: A resource of genetic markers that integrate genetic and physical maps

JeongHwan Mun 1, Dong-Jin Kim 1, Hong-Kyu Choi 1, John Gish 1, Frederic Debelle 2, Joanne Mudge 3, Roxanne Denny 3, Gabriella Endre 4, Oliver Saurat 2, Anne-Marie Dudez 2, Gyorgy Kiss 5, Bruce Roe 6, Nevin Young 3 and Douglas Cook 7*

1 University of California-Davis
2 INRA-CNRS
3 University of Minnesota
4 Biological Research Center
5 Institute of Genetics
6 University of Oklahoma
7 University of California

* To whom correspondence should be addressed. E-mail: drcook{at}ucdavis.edu.

Submitted on December 15, 2005
Revised on February 9, 2006
Accepted on 9 February 2006


Abstract

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 turnover 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 non-redundant transcript sequences, 20 Mbp of random whole genome shotgun sequence, 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. 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. 378 genetic markers could be integrated with sequenced BAC clones, anchoring 274 physical contigs that represent 174 Mbp of the genome and comprising an estimated 70% of the euchromatic gene space.

Key Words: Medicago truncatula, gene-rich BACs, genetic mapping, microsatellite, sequence-tagged site genetic marker