Distribution of Microsatellites in the Genome ofMedicago truncatula: A Resource of Genetic Markers That Integrate Genetic and Physical Maps

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 taxonspecific 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.

Isolation and characterization of genomic microsatellite markers for small cardamom (Elettaria cardamomum Maton) for utility in genetic diversity analysis

“…The genotypes were discriminated into two major clusters at 60 % similarity Physiol Mol Biol Plants (April-June 2016) 22(2):219-229 225 dataset was limited, low stringent conditions were applied to identify SSRs from sequences. The identified SSRs include both class I (C20 bp size) and class II (C 12 bp B 19 bp size) (Mun et al 2006) repeat motifs. The observed frequency of microsatellites in genomic DNA was 1.63 SSR/kbp (including hexa nucleotides with 12 bp size).…”

“…In total 140 microsatellite repeats which include di, tri, tetra, penta and hexa repeat motifs were identified out of which 12 sequences had compound SSRs and all others were perfect repeats (Table 1, Online Resource 1). Among the repeats 27 were class 1 (C20 bp in size) and remaining were class 11 (C 12 bp B 19 bp) (Mun et al 2006). The size of the repeats varied from 10 to 54 bp.…”

Evolutionary conserved lineage of Angela-family retrotransposons as a genome-wide microsatellite repeat dispersal agent

“…Comparative studies among several plant species, with a 50-fold range in genome size, revealed a positive relationship between genome size and the proportion of repetitive DNA (Morgante et al, 2002). It is interesting that SSRs were thought to be preferentially associated with the low-copy, gene-rich regions of Arabidopsis, corn, rice, soybean and wheat (Morgante et al, 2002), supported by a recent study of the model legume Medicago truncatula (Mun et al, 2006). These findings are reflected in the relatively high frequency of SSR transferability among legume species (Pandian et al, 2000;Gutierrez et al, 2005).…”

“…Microsatellites are abundant within both animal and plant genomes (Temnykh et al, 2001;Morgante et al, 2002;Mun et al, 2006) and exhibit a high mutation rate, making them attractive as multiallelic, codominant and reliably scored molecular markers. In the most commonly used approach, sequence information of microsatellite-flanking regions is employed to design locusspecific PCR primer pairs to identify amplicon size polymorphism among genotypes.…”

Development of highly polymorphic EST-SSR markers and segregation in F1 hybrid population of Vitis vinifera L.

“…In fact, marker applications to assist breeding are reported both for herbaceous (Huang et al, 1996) and woody plants (Gianfranceschi et al, 1994;Akkurt et al, 2007). In plants, genetic markers provide the framework in breeding programs via marker-assisted selection (Mazur and Tingey, 1995), map-based cloning (Tanksley et al, 1995), and anchoring physical maps (Mun et al, 2006;Troggio et al, 2007). Among the wood plants, poplar (Populus trichocarpa Torr.…”