Distribution of microsatellites in the genome of Medicago truncatula: a resource of genetic markers that integrate genetic and physical maps.
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., > or = 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.
Mun
Jeong-Hwan
JH
Department of Plant Pathology, University of California, Davis 95616, USA.
Kim
Dong-Jin
DJ
Choi
Hong-Kyu
HK
Gish
John
J
Debellé
Frédéric
F
Mudge
Joanne
J
Denny
Roxanne
R
Endré
Gabriella
G
Saurat
Oliver
O
Dudez
Anne-Marie
AM
Kiss
Gyorgy B
GB
Roe
Bruce
B
Young
Nevin D
ND
Cook
Douglas R
DR
D000483:Alleles; D002874:Chromosome Mapping / Q000379:methods*; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D005819:Genetic Markers; D016678:Genome; D018745:Genome, Plant; D046913:Medicago truncatula / Q000235:genetics*; D018895:Microsatellite Repeats; D020161:Physical Chromosome Mapping / Q000379:methods*
D005819:Genetic Markers