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Steven D Tanksley - One of the best experts on this subject based on the ideXlab platform.
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abundance variability and chromosomal location of Microsatellites in wheat
Molecular Genetics and Genomics, 1995Co-Authors: M S Roder, Steven D Tanksley, J Plaschke, Susanne U Konig, A Borner, Mark E Sorrells, Martin W GanalAbstract:The potential of microsatellite sequences as genetic markers in hexaploid wheat (Triticum aestivum) was investigated with respect to their abundance, variability, chromosomal location and usefulness in related species. By screening a lambda phage library, the total number of (GA)n blocks was estimated to be 3.6 x 104 and the number of (GT)n blocks to be 2.3 x 104 per haploid wheat genome. This results in an average distance of approximately 270 kb between these two microsatellite types combined. Based on sequence analysis data from 70 isolated Microsatellites, it was found that wheat Microsatellites are relatively long containing up to 40 dinucleotide repeats. Of the tested primer pairs, 36% resulted in fragments with a size corresponding to the expected length of the sequenced microsatellite clone. The variability of 15 microsatellite markers was investigated on 18 wheat accessions. Significantly, more variation was detected with the microsatellite markers than with RFLP markers with, on average, 4.6 different alleles per microsatellite. The 15 PCR-amplified Microsatellites were further localized on chromosome arms using cytogenetic stocks of Chinese Spring. Finally, the primers for the 15 wheat Microsatellites were used for PCR amplification with rye (Secale cereale) and barley accessions (Hordeum vulgare, H. spontaneum). Amplified fragments were observed for ten primer pairs with barley DNA and for nine primer pairs with rye DNA as template. A microsatellite was found by dot blot analysis in the PCR products of barley and rye DNA for only one primer pair.
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abundance polymorphism and genetic mapping of Microsatellites in rice
Molecular Genetics and Genomics, 1993Co-Authors: Steven D TanksleyAbstract:Dinucleotide Microsatellites have been characterized and used as genetic markers in rice. Screening of a rice genomic library with poly(dG-dA)·(dC-dT) and poly(dG-dT)·(dC-dA) probes indicated that (GA)n repeats occurred, on average, once every 225 kb and (GT)n repeats once every 480 kb. DNA sequencing of ten randomly selected Microsatellites indicated that the numbers of repeats ranged from 12 to 34 and that the patterns of Microsatellites in rice were similar to those of humans and other mammals. Primers to these microsatellite loci as well as to four published microsatellite-containing sequences have been designed and degrees of polymorphism has been examined with 20 rice accessions. Multiple alleles, ranging from 5 to 11, have been observed at all the microsatellite loci in 20 rice accessions. Alleles specific to two cultivated subspecies, indica and japonica, were found in some microsatellite loci. Heterozygosity values of all the microsatellite markers were significantly higher than those of RFLP markers, based upon a parallel comparison. Ten microsatellite loci have been genetically mapped to four rice chromosomes. The genomic distribution of Microsatellites appears to be random in rice.
John Doebley - One of the best experts on this subject based on the ideXlab platform.
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Directional Evolution for Microsatellite Size in Maize
Molecular Biology and Evolution, 2003Co-Authors: Yves Vigouroux, Yoshihiro Matsuoka, John DoebleyAbstract:Directional evolution in Microsatellites is the tendency for Microsatellites either to increase or to decrease in size over time between populations. We analyzed 99 microsatellite loci in a sample of 193 maize plants representing the entire pre-Columbian range of this crop for evidence of directional evolution. We took advantage of the known phylogeographic history of maize with the independent movement of maize from its ancestral location in Mexico to North and South America. We show that there is an increase in the average allele size of Microsatellites in the geographically derived North and South American groups relative to the ancestral Mexican group. We also show that there is a negative correlation between average allele size and altitude in all three groups. Directional evolution in maize Microsatellites can be explained by changes in the mutation rate over time and space, changes in the degree of mutational bias to a larger allele, demographic differences between the ancestral and geographically derived populations, and/or scenarios involving selection on microsatellite size. The occurrence of directional evolution for microsatellite size indicates that the estimation of population parameters with microsatellite data in maize should be done with caution.
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rate and pattern of mutation at microsatellite loci in maize
Molecular Biology and Evolution, 2002Co-Authors: Yves Vigouroux, Yoshihiro Matsuoka, Jennifer S Jaqueth, O S Smith, William D Beavis, Stephen J C Smith, John DoebleyAbstract:Microsatellites are important tools for plant breeding, genetics, and evolution, but few studies have analyzed their mutation pattern in plants. In this study, we estimated the mutation rate for 142 microsatellite loci inmaize (Zea mays subsp. mays) in two different experiments of mutation accumulation. The mutation rate per generation was estimated to be 7.7 × 10 - 4 for Microsatellites with dinucleotide repeat motifs, with a 95% confidence interval from 5.2 X 10 - 4 to 1.1 X 10 - 3 . For Microsatellites with repeat motifs of more than 2 bp in length, no mutations were detected; so we could only estimate the upper 95% confidence limit of 5.1 × 10 - 5 for the mutation rate. For dinucleotide repeat Microsatellites, we also determined that the variance of change in the number of repeats (σ 2 m ) is 3.2. We sequenced 55 of the 73 observed mutations, and all mutations proved to be changes in the number of repeats in the microsatellite or in mononucleotide tracts flanking the microsatellite. There is a higher probability to mutate to an allele of larger size. There is heterogeneity in the mutation rate among dinucleotide Microsatellites and a positive correlation between the number of repeats in the progenitor allele and the mutation rate. The microsatellite-based estimate of the effective population size of maize is more than an order of magnitude less than previously reported values based on nucleotide sequence variation.
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Microsatellites in zea variability patterns of mutations and use for evolutionary studies
Theoretical and Applied Genetics, 2002Co-Authors: Yoshihiro Matsuoka, Sharon E Mitchell, Stephen Kresovich, M M Goodman, John DoebleyAbstract:To evaluate the performance of Microsatellites or simple sequence repeats (SSRs) for evolutionary studies in Zea, 46 microsatellite loci originally derived from maize were applied to diverse arrays of populations that represent all the diploid species of Zea and 101 maize inbreds. Although null phenotypes and amplification of more than two alleles per plant were observed at modest rates, no practical obstacle was encountered for applying maize Microsatellites to other Zea species. Sequencing of microsatellite alleles revealed complex patterns of mutation including frequent indels in the regions flanking microsatellite repeats. In one case, all variation at a microsatellite locus came from indels in the flanking region rather than in the repeat motif. Maize Microsatellites show great variability within populations and provide a reliable means to measure intraspecific variation. Phylogeographic relationships of Zea populations were successfully reconstructed with good resolution using a genetic distance based on the infinite allele model, indicating that microsatellite loci are useful in evolutionary studies in Zea. Microsatellite loci show a principal division between tropical and temperate inbred lines, and group inbreds within these two broad germplasm groups in a manner that is largely consistent with their known pedigrees.
Emese Meglécz - One of the best experts on this subject based on the ideXlab platform.
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microsatellite flanking region similarities among different loci within insect species
Insect Molecular Biology, 2007Co-Authors: Emese Meglécz, Armelle Coeur Dacier, S J Anderson, Denis Bourguet, R Butcher, A Caldas, A Cassellundhagen, Deborah A Dawson, N Faure, Cecile FauvelotAbstract:Although Microsatellites are ubiquitous in eukaryota, the number of available markers varies strongly among taxa. This meta-analysis was conducted on 32 insect species. Sequences were obtained from two assembled whole genomes, whole genome shotgun (WGS) sequences from 10 species and screening partial genomic libraries for Microsatellites from 23 species. We have demonstrated: (1) strong differences in the abundance of Microsatellites among species; (2) that Microsatellites within species are often grouped into families based on similarities in their flanking sequences; (3) that the proportion of Microsatellites grouped into families varies strongly among taxa; and (4) that microsatellite families were significantly more often associated with transposable elements - or their remnants - than unique microsatellite sequences.
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high similarity between flanking regions of different Microsatellites detected within each of two species of lepidoptera parnassius apollo and euphydryas aurinia
Molecular Ecology, 2004Co-Authors: Emese Meglécz, Frederic Petenian, Etienne Danchin, Jean-yves Rasplus, Armelle Coeur Dacier, Eric FaureAbstract:Microsatellite flanking regions have been compared in two butterfly species. Several microsatellite flanking regions showed high similarity to one another among different Microsatellites within a same species, but very few similarities were found between species. This can be the consequence of either duplication/multiplication events involving large regions containing Microsatellites or of Microsatellites imbedded in minisatellite regions. The multiplication of Microsatellites might also be linked to mobile elements. Furthermore, crossing over between nonhomologous Microsatellites can lead to the exchange of the flanking regions between Microsatellites. The same phenomenon was observed in both studied butterfly species but not in Aphis fabae (Hemiptera), which was screened at the same time using the same protocol. These findings might explain, at least partially, why microsatellite isolation in Lepidoptera has been relatively unsuccessful so far.
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High similarity between flanking regions of different Microsatellites detected within each of two species of Lepidoptera
Molecular Ecology, 2004Co-Authors: Emese Meglécz, Frederic Petenian, Etienne Danchin, Armelle Coeur D'acier, Jean-yves Rasplus, Eric FaureAbstract:Microsatellite flanking regions have been compared in two butterfly species. Several microsatellite flanking regions showed high similarity to one another among different Microsatellites within a same species, but very few similarities were found between species. This can be the consequence of either duplication/multiplication events involving large regions containing Microsatellites or of Microsatellites imbedded in minisatellite regions. The multiplication of Microsatellites might also be linked to mobile elements. Furthermore, crossing over between nonhomologous Microsatellites can lead to the exchange of the flanking regions between Microsatellites. The same phenomenon was observed in both studied butterfly species but not in Aphis fabae (Hemiptera), which was screened at the same time using the same protocol. These findings might explain, at least partially, why microsatellite isolation in Lepidoptera has been relatively unsuccessful so far.
Eric Faure - One of the best experts on this subject based on the ideXlab platform.
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high similarity between flanking regions of different Microsatellites detected within each of two species of lepidoptera parnassius apollo and euphydryas aurinia
Molecular Ecology, 2004Co-Authors: Emese Meglécz, Frederic Petenian, Etienne Danchin, Jean-yves Rasplus, Armelle Coeur Dacier, Eric FaureAbstract:Microsatellite flanking regions have been compared in two butterfly species. Several microsatellite flanking regions showed high similarity to one another among different Microsatellites within a same species, but very few similarities were found between species. This can be the consequence of either duplication/multiplication events involving large regions containing Microsatellites or of Microsatellites imbedded in minisatellite regions. The multiplication of Microsatellites might also be linked to mobile elements. Furthermore, crossing over between nonhomologous Microsatellites can lead to the exchange of the flanking regions between Microsatellites. The same phenomenon was observed in both studied butterfly species but not in Aphis fabae (Hemiptera), which was screened at the same time using the same protocol. These findings might explain, at least partially, why microsatellite isolation in Lepidoptera has been relatively unsuccessful so far.
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High similarity between flanking regions of different Microsatellites detected within each of two species of Lepidoptera
Molecular Ecology, 2004Co-Authors: Emese Meglécz, Frederic Petenian, Etienne Danchin, Armelle Coeur D'acier, Jean-yves Rasplus, Eric FaureAbstract:Microsatellite flanking regions have been compared in two butterfly species. Several microsatellite flanking regions showed high similarity to one another among different Microsatellites within a same species, but very few similarities were found between species. This can be the consequence of either duplication/multiplication events involving large regions containing Microsatellites or of Microsatellites imbedded in minisatellite regions. The multiplication of Microsatellites might also be linked to mobile elements. Furthermore, crossing over between nonhomologous Microsatellites can lead to the exchange of the flanking regions between Microsatellites. The same phenomenon was observed in both studied butterfly species but not in Aphis fabae (Hemiptera), which was screened at the same time using the same protocol. These findings might explain, at least partially, why microsatellite isolation in Lepidoptera has been relatively unsuccessful so far.
Martin W Ganal - One of the best experts on this subject based on the ideXlab platform.
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abundance variability and chromosomal location of Microsatellites in wheat
Molecular Genetics and Genomics, 1995Co-Authors: M S Roder, Steven D Tanksley, J Plaschke, Susanne U Konig, A Borner, Mark E Sorrells, Martin W GanalAbstract:The potential of microsatellite sequences as genetic markers in hexaploid wheat (Triticum aestivum) was investigated with respect to their abundance, variability, chromosomal location and usefulness in related species. By screening a lambda phage library, the total number of (GA)n blocks was estimated to be 3.6 x 104 and the number of (GT)n blocks to be 2.3 x 104 per haploid wheat genome. This results in an average distance of approximately 270 kb between these two microsatellite types combined. Based on sequence analysis data from 70 isolated Microsatellites, it was found that wheat Microsatellites are relatively long containing up to 40 dinucleotide repeats. Of the tested primer pairs, 36% resulted in fragments with a size corresponding to the expected length of the sequenced microsatellite clone. The variability of 15 microsatellite markers was investigated on 18 wheat accessions. Significantly, more variation was detected with the microsatellite markers than with RFLP markers with, on average, 4.6 different alleles per microsatellite. The 15 PCR-amplified Microsatellites were further localized on chromosome arms using cytogenetic stocks of Chinese Spring. Finally, the primers for the 15 wheat Microsatellites were used for PCR amplification with rye (Secale cereale) and barley accessions (Hordeum vulgare, H. spontaneum). Amplified fragments were observed for ten primer pairs with barley DNA and for nine primer pairs with rye DNA as template. A microsatellite was found by dot blot analysis in the PCR products of barley and rye DNA for only one primer pair.
