Microsatellites: consensus and controversy

Chambers, Geoffrey K.; MacAvoy, Elizabeth S.

doi:10.1016/s0305-0491(00)00233-9

Cited by 262 publications

(196 citation statements)

References 100 publications

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“…[28][29][30] At the CD4 locus, a detailed study of LD between a microsatellite and a neighbouring stable marker (an Alu deletion) has been reported in African and non-African populations. 27 The CD4 microsatellite is also a pentanucleotide repeat, a rare occurrence in the human genome, 59 with a structure similar to that of the NOS2A À2.6 microsatellite (TTTTC and CCTTT, respectively) and a similar distribution of repeats (4-15 and 6-18, respectively). The CD4 microsatellite is located B10 kb from the Alu insertion/deletion.…”

Section: Discussionmentioning

confidence: 99%

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Haplotypic relationship between SNP and microsatellite markers at the NOS2A locus in two populations

et al. 2003

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The density of genetic markers required for successful association mapping of complex diseases depends on linkage disequilibrium (LD) between non-functional markers and functional variants. The haplotypic relationship between stable markers and potentially unstable but highly informative markers (e.g. microsatellites) indicates that LD might be maintained over considerable genetic distance in non-African populations, supporting the use of such 'mixed marker haplotypes' in LD-based mapping, and allowing inferences to be drawn about human origins. We investigated sequence variation in the proximal 2.6 kb of the inducible nitric oxide synthase (NOS2A) promoter and the relationship between SNP haplotypes and a pentanucleotide microsatellite (the 'NOS2A À2.6 microsatellite') in Gambians and UK Caucasians. UK Caucasians exhibited a subset of sequence diversity observed in Gambians, sharing four of 11 SNPs and a similar haplotypic structure. Five SNPs were found in the sequence of interspersed repetitive DNA elements. In both populations, there was dramatic loss of LD between SNP haplotypes and microsatellite alleles across a very short physical distance, suggesting a high intrinsic mutation rate of the NOS2A À2.6 microsatellite, the SNP haplotypes are relatively ancient, or that this was a region of frequent recombination. Understanding locus-and population-specific LD is essential when designing and interpreting genetic association studies.

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Section: Discussionmentioning

confidence: 99%

“…Alternatively, the microsatellite alleles could themselves be the diseasecausing variants. Although some preliminary functional data are reported for the diabetic association, 41 there are few precedents for direct functional effects of promoter microsatellites in the literature 59 and this therefore seems unlikely.…”

Section: Discussionmentioning

confidence: 99%

Haplotypic relationship between SNP and microsatellite markers at the NOS2A locus in two populations

et al. 2003

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“…Microsatellite loci are useful markers for genetic mapping (see Reviews, Chamvers and MacAvoy, 2000). In the genus Anguilla, several authors have reported a 15 number of microsatellite markers that have been mainly used for population studies (Daemen et al, 1997;Ishikawa et al, 2001;Tseng et al, 2001;Wirth and Bernatchez, 2001); however, the existent number of markers is still too small to construct a linkage map.…”

Section: Introductionmentioning

confidence: 99%

Microsatellite–centromere mapping in the Japanese eel (Anguilla japonica) by half-tetrad analysis using induced triploid families

et al. 2006

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Genetic improvement of the Japanese eel (Anguilla japonica) can be achieved by artificially controlling its life cycle using recent advances in reproductive biology. In this study, we developed 43 microsatellite loci to confirm Mendelian inheritance at 10 5 of them as well at 16 previous reported in two full-sib families produced by artificial insemination. In order to establish a base for aquaculture genetics of this species in the near future, these microsatellite loci were mapped in relation to the centromere by half-tetrad analysis using four artificially induced triploid families. The second division segregation frequency (y) of the microsatellite loci ranged from 0.008 to 0.968 (mean ± 10 SD = 0.645 ± 0.298). These results suggest the presence of strong chiasma interference in the eel. Significant differences were observed for the map distances of microsatellite loci between the two isolation procedures. Microsatellites isolated using the enrichment procedure were mapped to various sites starting from the centromere to the telomere, whereas those from the conventional size-selected library showed a tendency to be 15 distributed in the telomeric region.

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“…Based on interruptions of microsatellites, they are classified as interrupted, pure, compound, interrupted compound, complex and interrupted complex (14). The present study also focused on compound microsatellites, which are composed of two or more microsatellites adjacent to each other.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Simple and Imperfect Microsatellites in Ebolavirus Species and Other Genomes of Filoviridae Family

2015

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Background:Microsatellites have evoked the interest of researchers owing to their applications in different fields such as DNA fingerprinting, genetic mapping, population genetics, forensics, paternity studies and evolution. Objectives: The present study focused on the analysis of simple sequence repeats (SSRs) in genomes of seven species from three genera of the Filoviridae family. Materials and Methods: Genome sequences of seven species from the Filoviridae family were assessed by the National Center for Biotechnology Information (NCBI), microsatellites were extracted using the IMEx software, and statistical analysis was performed Microsoft Office Excel 2007. Results: A total of 516 microsatellites and 14 Compound Simple Sequence Repeats (cSSR) (also known as compound microsatellites) were extracted. Evidently, the conversion of SSRs to cSSR was low. Mononucleotide A/T was the most prevalent followed by dinucleotide AC/CA and trinucleotide AAC/CAA. Highest incidence of SSRs (mon-/di-nucleotide motif) was observed in RNA Dependent RNA Polymerase (RDRP) gene whereas tri-nucleotide motif was maximally localized in nucleoproteins (NP). Conclusions:The salient features of simple and compound microsatellites in Filoviridae family have been highlighted herein. Microsatellite regions with higher mutation rates compared to the rest of the genome play a crucial role in genome evolution by acting as a source of quantitative genetic variation. The SSR mutation rate is known to be affected by motif length, motif sequence, and number of repeats and purity of repetition. The functional role of tandem repeats in viruses, remains to be fully elucidated. However, with the repetitive sequence allegedly acting as a hot spot for recombination, we postulate their involvement in genetic events such as recombination, replication, and repair mechanisms that drive sequence diversity leading to the formation of the genetic basis of adaptation.

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Microsatellites: consensus and controversy

Cited by 262 publications

References 100 publications

Haplotypic relationship between SNP and microsatellite markers at the NOS2A locus in two populations

Haplotypic relationship between SNP and microsatellite markers at the NOS2A locus in two populations

Microsatellite–centromere mapping in the Japanese eel (Anguilla japonica) by half-tetrad analysis using induced triploid families

Analysis of Simple and Imperfect Microsatellites in Ebolavirus Species and Other Genomes of Filoviridae Family

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