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1
Harr, Bettina, and Christian Schlötterer. "Long Microsatellite Alleles in Drosophila melanogaster Have a Downward Mutation Bias and Short Persistence Times, Which Cause Their Genome-Wide Underrepresentation." Genetics 155, no. 3 (July 1, 2000): 1213–20. http://dx.doi.org/10.1093/genetics/155.3.1213.
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Abstract Microsatellites are short tandemly repeated DNA sequence motifs that are highly variable in most organisms. In contrast to mammals, long microsatellites (>15 repeats) are extremely rare in the Drosophila melanogaster genome. To investigate this paucity of long microsatellites in Drosophila, we studied 19 loci with exceptionally long microsatellite alleles. Inter- and intraspecific analysis showed that long microsatellite alleles arose in D. melanogaster only very recently. This lack of old alleles with many repeats indicated that long microsatellite alleles have short persistence times. The size distribution of microsatellite mutations in mutation-accumulation lines suggests that long alleles have a mutation bias toward a reduction in the number of repeat units. This bias causes the short persistence times of long microsatellite alleles. We propose that species-specific, size-dependent mutation spectra of microsatellite alleles may provide a general mechanism to account for the observed differences in microsatellite length between species.
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Yu, Kangfu, Soon J. Park, and Vaino Poysa. "Abundance and variation of microsatellite DNA sequences in beans (Phaseolus andVigna)." Genome 42, no. 1 (February 1, 1999): 27–34. http://dx.doi.org/10.1139/g98-100.
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Microsatellites or simple sequence repeats (SSRs) have been demonstrated to be abundant and hypervariable in some eukaryotic genomes. Although the presence of microsatellites is very well documented in many plant species, no information on microsatellites in beans (Phaseolus andVigna) is available. To assess the abundance and usefulness of bean microsatellites as genetic markers, 326 DNA sequences from the GenBank databases were searched. Sixty-one simple repetitive DNA sequences with 23 different types of repetitive DNA motifs were identified as potential microsatellites. Among these were 49 microsatellites from common bean (Phaseolus vulgaris) entries and 12 microsatellites from the genus Vigna. The most abundant type of microsatellite found in this search was that with di-nucleotide repeats of AT/TA. Microsatellites with tri- and tetra-nucleotide motifs were also identified. PCR analysis of 12 of the microsatellite-containing loci revealed that 11 of the 12 primer pairs could produce easily-scorable fragments, or groups of fragments. Allelic variation of the 11 loci was surveyed in 12 common bean inbred lines representing a diversity of germplasms. Seven of the 11 microsatellite loci were polymorphic and yielded 2-10 alleles. Analyses of the polymorphic loci in a common bean F6 recombinant inbred population showed that each segregated in a Mendelian fashion.Key words: microsatellite, simple sequence repeat, molecular marker, bean.
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Zhou, Wenchun, Frederic L. Kolb, Guihua Bai, Gregory Shaner, and Leslie L. Domier. "Genetic analysis of scab resistance QTL in wheat with microsatellite and AFLP markers." Genome 45, no. 4 (August 1, 2002): 719–27. http://dx.doi.org/10.1139/g02-034.
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Three chromosomal regions associated with scab resistance were detected in a common cultivar, Ning7840, by microsatellite and AFLP analysis. Six microsatellites on chromosome 3BS, Xgwm389, Xgwm533, Xbarc147, Xgwm493, Xbarc102, and Xbarc131, were integrated into an amplified fragment length polymorphism (AFLP) linkage group containing a major quantitative trait locus (QTL) for scab resistance in a mapping population of 133 recombinant inbred lines (RILs) derived from 'Ning7840' × 'Clark'. Based on single-factor analysis of variance of scab infection data from four experiments, Xgwm533 and Xbarc147 were the two microsatellite markers most tightly associated with the major scab resistance QTL. Interval analysis based on the integrated map of AFLP and microsatellite markers showed that the major QTL was located in a chromosome region about 8 cM in length around Xgwm533 and Xbarc147. Based on mapping of six microsatellite markers on eight 3BS deletion lines, the major QTL was located distal to breakage point 3BS-8. In total, 18 microsatellites were physically located on different subarm regions on 3BS. Two microsatellites, Xgwm120 and Xgwm614, were significantly associated with QTL for scab resistance on chromosome 2BL and 2AS, respectively. The resistance alleles on 3BS, 2BL, and 2AS were all derived from 'Ning7840'. Significant interaction between the major QTL on 3BS and the QTL on 2BL was detected based on microsatellite markers linked to them. Using these microsatellite markers would facilitate marker-assisted selection to improve scab resistance in wheat.Key words: Fusarium head blight, quantitative trait locus, physical mapping, Triticum aestivum L.
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Azmir, I. A., I. S. Md-Yasin, and Y. Esa. "Microsatellite Marker Mining Using PCR-Based Isolation of Microsatellite Arrays (PIMA) Method on Blue-Spotted Mudskipper, Boleophthalmus Boddarti." IOP Conference Series: Earth and Environmental Science 995, no. 1 (April 1, 2022): 012051. http://dx.doi.org/10.1088/1755-1315/995/1/012051.
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Abstract Microsatellites are small and are codominant markers that can be amplified with polymerase chain reaction. Both prokaryotic and eukaryotic organisms possess large amounts of the microsatellites repeat. Many microsatellites have high mutation rates that generate the high levels of allelic diversity necessary for genetic studies of processes acting on ecological time scales. The high variability of microsatellites provided the foundation for their successful application in a wide range of fundamental and applied fields of biology. However, de novo isolation is needed for most species hence in this study we tried to mine the microsatellite marker using PCR-based isolation of microsatellite arrays (PIMA) on Blue spotted mudskipper, Boleophthalmus boddarti a fish uniquely restricted to coastal and estuarine habitat was also commercially important. Out of three trials, seven microsatellite repeats were detected but only three repeat types (AAG)4, (TCAG)3 and (CT)4 can be useful as microsatellite marker following PHOBOS V3.3.12 analysis. Meanwhile, the detection of octa (AATACAT)2, penta (TGACA)2 and heptanucleotides (GGAGATA)2 were unable to be continued as functional microsatellite marker as there were missense variants and interruptions detected either on forward or reverse strand of the repeat. Thus, PIMA method could be considered as tedious and detected low yields of microsatellite markers. Nevertheless, the conventional method for generating microsatellite markers from PCR based methods could be done with in silico mining of microsatellite sequences from DNA sequence databases or next generation sequencing (NGS).
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White, E., R. Sahota, and S. Edes. "Rapid microsatellite analysis using discontinuous polyacrylamide gel electrophoresis." Genome 45, no. 6 (December 1, 2002): 1107–9. http://dx.doi.org/10.1139/g02-084.
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A method for screening large numbers of samples for microsatellites using discontinuous, non-denaturing polyacrylamide gels and rapid fluorescent gel staining is described. Disc electrophoresis on slab gels provides high-resolution of PCR products. It is useful for collecting population data once microsatellite loci have been characterized.Key words: microsatellite, discontinuous polyacrylamide gel electrophoresis, non-denaturing
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Buschiazzo, E., and N. J. Gemmell. "Evolutionary and phylogenetic significance of platypus microsatellites conserved in mammalian and other vertebrate genomes." Australian Journal of Zoology 57, no. 4 (2009): 175. http://dx.doi.org/10.1071/zo09038.
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Building on the recent publication of the first monotreme genome, that of the platypus, and the discovery that many platypus microsatellites are found in the genomes of three mammals (opossum, human, mouse) and two non-mammalian vertebrates (chicken, lizard), we investigated further the evolutionary conservation of microsatellites identified in the monotreme lineage and tested whether the conservation of microsatellites we observe in vertebrates has phylogenetic signal. Most conserved platypus microsatellites (75%) were found in one species, with the platypus sharing many more microsatellites with mammals than with reptiles (83% versus 30%). Within mammals, unexpectedly, many more platypus microsatellites had orthologues in the opossum genome than in that of either human or mouse, which was at odds with the very well supported view that monotremes diverged from a lineage containing both eutherians and marsupials (Theria hypothesis). We investigated the phylogenetic significance of microsatellite conservation through Bayesian and maximum parsimony tree reconstruction using presence/absence data of microsatellite loci conserved in a total of 18 species, including the platypus. Although models of evolution implemented in current phylogenetic reconstruction algorithms are not tailor-made for microsatellite data, we were able to construct vertebrate phylogenies that correspond well to the accepted mammalian phylogeny, with two of our three reconstructions supporting the Theria hypothesis. Our analysis provides ground for new theoretical development in phylogeny-based analyses of conserved microsatellite data.
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Tanck, M. WT, A. P. Palstra, M. van de Weerd, C. P. Leffering, JJ van der Poel, H. Bovenhuis, and J. Komen. "Segregation of microsatellite alleles and residual heterozygosity at single loci in homozygous androgenetic common carp (Cyprinus carpio L.)." Genome 44, no. 5 (October 1, 2001): 743–51. http://dx.doi.org/10.1139/g01-072.
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Thirty-three androgenetic progeny groups of common carp were analysed using 11 microsatellite markers to (i) verify the homozygous status of the 566 androgenetic individuals, (ii) analyse the microsatellite allele segregation, and (iii) study the possible association of microsatellite alleles with phenotypic traits. In total, 92% of the androgenetic individuals proved to be homozygous at all 11 loci. Forty-three of the 47 heterozygous individuals were heterozygous at a single locus only. This heterozygosity was probably due to DNA fragments caused by UV irradiation of the eggs, although the maternal origin of the fragments could not be proved beyond doubt. Screening with 11 microsatellites also revealed two linkage groups, a segregation distortion at two microsatellite loci, and the possible association of some microsatellites with mass, length, stress-related plasma cortisol levels, and basal plasma glucose levels. The success of the linkage and association study could be explained by a low recombination frequency due to high chiasma interference. This would imply a relatively short genetic map for common carp.Key words: doubled haploids, residual heterozygosity, microsatellite allele segregation, linkage analysis, common carp.
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Wang, Ying, Mingjie Chen, Hong Wang, Jing-Fang Wang, and Dapeng Bao. "Microsatellites in the Genome of the Edible Mushroom,Volvariella volvacea." BioMed Research International 2014 (2014): 1–10. http://dx.doi.org/10.1155/2014/281912.
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Using bioinformatics software and database, we have characterized the microsatellite pattern in theV. volvaceagenome and compared it with microsatellite patterns found in the genomes of four other edible fungi:Coprinopsis cinerea,Schizophyllum commune,Agaricus bisporus,andPleurotus ostreatus. A total of 1346 microsatellites have been identified, with mono-nucleotides being the most frequent motif. The relative abundance of microsatellites was lower in coding regions with 21 No./Mb. However, the microsatellites in theV. volvaceagene models showed a greater tendency to be located in the CDS regions. There was also a higher preponderance of trinucleotide repeats, especially in the kinase genes, which implied a possible role in phenotypic variation. Among the five fungal genomes, microsatellite abundance appeared to be unrelated to genome size. Furthermore, the short motifs (mono- to tri-nucleotides) outnumbered other categories although these differed in proportion. Data analysis indicated a possible relationship between the most frequent microsatellite types and the genetic distance between the five fungal genomes.
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Feng, Xiaochuan, Stephen M. Rich, Donna Akiyoshi, James K. Tumwine, Addy Kekitiinwa, Nicolette Nabukeera, Saul Tzipori, and Giovanni Widmer. "Extensive Polymorphism in Cryptosporidium parvumIdentified by Multilocus Microsatellite Analysis." Applied and Environmental Microbiology 66, no. 8 (August 1, 2000): 3344–49. http://dx.doi.org/10.1128/aem.66.8.3344-3349.2000.
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ABSTRACT Restriction fragment length polymorphism and DNA sequence analysis discern two main types of Cryptosporidium parvum. We present a survey of length polymorphism at several microsatellite loci for type 1 and type 2 isolates. A total of 14 microsatellite loci were identified from C. parvum DNA sequences deposited in public databases. All repeats were mono-, di-, and trinucleotide repeats of A, AT, and AAT, reflecting the high AT content of the C. parvum genome. Several of these loci showed significant length polymorphism, with as many as seven alleles identified for a single locus. Differences between alleles ranged from 1 to 27 bp. Karyotype analysis using probes flanking three microsatellites localized each marker to an individual chromosomal band, suggesting that these markers are single copy. In a sample of 19 isolates for which at least three microsatellites were typed, a majority of isolates displayed a unique multilocus fingerprint. Microsatellite analysis of isolates passaged between different host species identified genotypic changes consistent with changes in parasite populations.
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Kaundun, Shiv Shankhar, and Satoru Matsumoto. "Heterologous nuclear and chloroplast microsatellite amplification and variation in tea, Camellia sinensis." Genome 45, no. 6 (December 1, 2002): 1041–48. http://dx.doi.org/10.1139/g02-070.
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The advantage of the cross transferability of heterologous chloroplast and nuclear microsatellite primers was taken to detect polymorphism among 24 tea (Camellia sinensis (L.) O. Kuntze) genotypes, including both the assamica and the sinensis varieties. Primer information was obtained from the closely related Camellia japonica species for four nuclear microsatellites, and from Nicotiana tabaccum for seven universal chloroplast microsatellites. All of the nuclear microsatellite loci tested generated an expected DNA fragment in tea, revealing between three and five alleles per locus. Four out of the seven chloroplast microsatellites primers amplified positively, and of these only one was polymorphic with three alleles, which is in agreement with the conserved nature of chloroplast microsatellites at the intraspecific level. A factorial correspondence analysis carried out on all genotypes and nuclear microsatellite alleles separated the assamica and sinensis genotypes into two groups, thus demonstrating the value of these markers in establishing the genetic relationship between tea varieties. Genetic diversity measured with nuclear microsatellites was higher than that measured with other types of molecular markers, offering prospects for their use in fingerprinting, mapping, and population genetic studies, whereas polymorphisms detected at a cpSSR locus will allow the determination of plastid inheritance in the species. Key words: tea, Camellia sinensis, SSR, microsatellites, genetic diversity.
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PANDEY, Saumy, Vinay SHARMA, and Afroz ALAM. "Potential of Microsatellites Markers for the Genetic Analysis of Bryophytes." Notulae Scientia Biologicae 8, no. 1 (March 16, 2016): 37–46. http://dx.doi.org/10.15835/nsb819748.
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Microsatellites have increasingly being used to study genetic diversity, phylogeny, population genetics, population ecology and genetic mapping of bryophytes. Due to co-dominant and highly reproducible features, microsatellites became markers of choice for several genetic analyses of bryophytes. However, the major limitation is de novo isolation of microsatellites from the interest species which were studied and gave genomic libraries. Initially, traditional methods of microsatellite development were tedious and time consuming, but due to the sequencing of several bryophytes available in public databases, advancement in PCR technologies and computer software, have cumulatively facilitated the development of microsatellites for bryophytes study. This review examines the features, strategies for the development of microsatellites and their utilization in many aspects of genetic and ecological studies of bryophytes.
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Ishii, T., Y. Xu, and S. R. McCouch. "Nuclear- and chloroplast-microsatellite variation in A-genome species of rice." Genome 44, no. 4 (August 1, 2001): 658–66. http://dx.doi.org/10.1139/g01-044.
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Simple sequence length polymorphism analysis was carried out to reveal microsatellite variation and to clarify the phylogenetic relationships among A-genome species of rice. Total DNA from 29 cultivars (23 Oryza sativa and 6 O. glaberrima) and 30 accessions of wild A-genome species (12 O. rufipogon, 5 O. glumaepatula, 2 O. longistaminata, 6 O. meridionalis, and 5 O. barthii) was used as a template for PCR to detect 24 nuclear and 10 chloroplast microsatellite loci. Microsatellite allelic diversity was examined based on amplified banding patterns. Microsatellites amplified clearly in all 59 accessions, with an average of 18.4 alleles per locus. The polymorphism information content (PIC) value ranged from 0.85 to 0.94, with an average of 0.89. At the species level, high average PIC values were observed in O. sativa (0.79) and O. rufipogon (0.80). For chloroplast microsatellites, the average number of alleles per locus and the average PIC value were 2.9 and 0.38, respectively. While the magnitude of diversity was much greater for nuclear microsatellites than for chloroplast microsatellites, they showed parallel patterns of differentiation for each taxonomic group. Using the ratio of common alleles (estimated as size of amplified fragments) as a similarity index, the average percentages of common microsatellite alleles were calculated between taxa. For both nuclear and chloroplast microsatellites, O. sativa showed the highest similarity values to O. rufipogon, and O. glaberrima was most similar to O. barthii. These data support previous evidence that these cultivars originated from the corresponding wild ancestral species.Key words: simple sequence length polymorphism, SSLP, microsatellite marker, rice, Oryza sativa, allelic diversity, phylogenetics.
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Smith, S., T. Joss, and A. Stow. "Successful development of microsatellite markers in a challenging species: the horizontal borer Austroplatypus incompertus (Coleoptera: Curculionidae)." Bulletin of Entomological Research 101, no. 5 (April 11, 2011): 551–55. http://dx.doi.org/10.1017/s0007485311000137.
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AbstractThe analysis of microsatellite loci has allowed significant advances in evolutionary biology and pest management. However, until very recently, the potential benefits have been compromised by the high costs of developing these neutral markers. High-throughput sequencing provides a solution to this problem. We describe the development of 13 microsatellite markers for the eusocial ambrosia beetle, Austroplatypus incompertus, a significant pest of forests in southeast Australia. The frequency of microsatellite repeats in the genome of A. incompertus was determined to be low, and previous attempts at microsatellite isolation using a traditional genomic library were problematic. Here, we utilised two protocols, microsatellite-enriched genomic library construction and high-throughput 454 sequencing and characterised 13 loci which were polymorphic among 32 individuals. Numbers of alleles per locus ranged from 2 to 17, and observed and expected heterozygosities from 0.344 to 0.767 and from 0.507 to 0.860, respectively. These microsatellites have the resolution required to analyse fine-scale colony and population genetic structure. Our work demonstrates the utility of next-generation 454 sequencing as a method for rapid and cost-effective acquisition of microsatellites where other techniques have failed, or for taxa where marker development has historically been both complicated and expensive.
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Xu, Zhenkang, Laura Gutierrez, Matthew Hitchens, Steve Scherer, Amy K. Sater, and Dan E. Wells. "Distribution of Polymorphic and Non-Polymorphic Microsatellite Repeats in Xenopus tropicalis." Bioinformatics and Biology Insights 2 (January 2008): BBI.S561. http://dx.doi.org/10.4137/bbi.s561.
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The results of our bioinformatics analysis have found over 91,000 di-, tri-, and tetranucleotide microsatellites in our survey of 25% of the X. tropicalis genome, suggesting there may be over 360,000 within the entire genome. Within the X. tropicalis genome, dinucleotide (78.7%) microsatellites vastly out numbered tri- and tetranucleotide microsatellites. Similarly, AT-rich repeats are overwhelmingly dominant. The four AT-only motifs (AT, AAT, AAAT, and AATT) account for 51,858 out of 91,304 microsatellites found. Individually, AT microsatellites were the most common repeat found, representing over half of all di-, tri-, and tetranucleotide microsatellites. This contrasts with data from other studies, which show that AC is the most frequent microsatellite in vertebrate genomes (Toth et al. 2000). In addition, we have determined the rate of polymorphism for 5,128 non-redundant microsatellites, embedded in unique sequences. Interestingly, this subgroup of microsatellites was determined to have significantly longer repeats than genomic microsatellites as a whole. In addition, microsatellite loci with tandem repeat lengths more than 30 bp exhibited a significantly higher degree of polymorphism than other loci. Pairwise comparisons show that tetranucleotide microsatellites have the highest polymorphic rates. In addition, AAT and ATC showed significant higher polymorphism than other trinucleotide microsatellites, while AGAT and AAAG were significantly more polymorphic than other tetranucleotide microsatellites.
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Reddy, K. Damodar, E. G. Abraham, and J. Nagaraju. "Microsatellites in the silkworm, Bombyx mori: Abundance, polymorphism, and strain characterization." Genome 42, no. 6 (December 1, 1999): 1057–65. http://dx.doi.org/10.1139/g99-027.
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We have isolated and characterized microsatellites (simple sequence repeat (SSR) loci) from the silkworm genome. The screening of a partial genomic library by the conventional hybridization method led to the isolation of 28 microsatellites harbouring clones. The abundance of (CA)n repeats in the silkworm genome was akin to those reported in the other organisms such as honey bee, pig, and human, but the (CT)n repeat motif is less common compared to bumble bee and honey bee genomes. Detailed analysis of 13 diverse silkworm strains with a representative of 15 microsatellite loci revealed a number of alleles ranging from 3 to 17 with heterozygosity values of 0.66-0.90. Along with strain-specific microsatellite markers, diapause and non-diapause strain-specific alleles were also identified. The repeat length did not show any relationship with the degree of polymorphism in the present study. The co-dominant inheritance of microsatellite markers was demonstrated in F1 offspring. A list of primer sequences that tag each locus is provided. The availability of microsatellite markers can be expected to enhance the power and resolution of genome analysis in silkworm.Key words: microsatellites, simple sequence repeats, polymorphisms, silkworm strains, Bombyx mori.
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Homchan, Somjit, Pradeep Bhadola, and Yash Munnalal Gupta. "Statistical Analysis of Simple Sequence Repeats in Genome Sequence: A Case of Acheta Domesticus (Orthoptera: Gryllidae)." ECS Transactions 107, no. 1 (April 24, 2022): 14799–806. http://dx.doi.org/10.1149/10701.14799ecst.
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Herein, we have described genome wide screening of microsatellites (Simple Sequence Repeats: SSRs) and their distribution in the Acheta domesticus genome using a custom python script. A total of 232,179 microsatellites were identified, in which trinucleotide repeats were found to be the most abundant repeats in the genome, representing 60 % of the total microsatellite, followed by dinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides. Among trinucleotides, dinucleotides, and tetranucleotides, the most prevalent microsatellite motifs were AAT/ATT, TG/CA, and AAAT/ATTT, respectively. Notably, statistical analysis of the SSR repetition frequency distribution showed that SSR motifs that were repeated four times were the most recurrent. Additionally, the SSR length distribution showed that SSRs with a12 bp size were the most common. As a result, the statistical analysis of the SSR dataset in A. domesticus will be a useful resource for a better understanding of microsatellite distribution in crickets for evolutionary genetics.
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Herráez, David López, Holger Schäfer, Jörn Mosner, Hans-Rudolf Fries, and Michael Wink. "Comparison of Microsatellite and Single Nucleotide Polymorphism Markers for the Genetic Analysis of a Galloway Cattle Population." Zeitschrift für Naturforschung C 60, no. 7-8 (August 1, 2005): 637–43. http://dx.doi.org/10.1515/znc-2005-7-821.
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Highly informative genetic markers are essential for efficient management of cattle populations, as well as for food safety. After a decade of domination by microsatellite markers, a new type of genetic marker, single nucleotide polymorphism (SNP), has recently appeared on the scene. In the present study, the exclusion power of both kinds of markers with regards to individual identification and parental analysis was directly compared in a Galloway cattle population. Seventeen bovine microsatellites were distributed in three incremental marker sets (10, 14 and 17 microsatellite markers) and used for cattle genotyping. A set of 43 bovine SNP was used for genotyping the same cattle population. The accuracy of both kinds of markers in individual identification was evaluated using probability of identity estimations. These were 2.4 × 10-8 for the 10 microsatellite set, 2.3 × 10-11 for the 14 microsatellite set, and 1.4 × 10-13 for the 17 microsatellite marker set. For the 43 SNP markers, the estimated probability of identity was 5.3 × 10-11. The exclusion power of both kinds of markers in parental analysis was evaluated using paternity exclusion estimations, and, in addition to this, by estimation of the parental exclusion probability in 18 Galloway family trios. Paternity exclusion was estimated to be over 99% for microsatellites, and approx. 98% for SNP. Both, microsatellite and SNP sets of markers showed similar parental exclusion probabilities.
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Anand, Khushbu, Sonu Kumar, Afroz Alam, and Asheesh Shankar. "Mining of microsatellites in mitochondrial genomes of order Hypnales (Bryopsida)." Plant Science Today 6, sp1 (December 31, 2019): 635–38. http://dx.doi.org/10.14719/pst.2019.6.sp1.697.
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Microsatellites or SSRs are the markers of selection due to their reproducibility, degree of polymorphism, distribution throughout the genome and co-dominant nature. Microsatellites are used primarily to study the genetic variability in various species and marker aided selection. Since microsatellites can be readily amplified by PCR, they have been utilized most extensively. To reduce time and cost to a great extent, the computational approach for identifying and developing microsatellite markers by mining nucleotide sequences is preferred over the conventional methods. In the present analysis, an in-silico method was used to detect microsatellites effectively in mitochondrial genomes of Anomodon rugelii (Müll. Hal.) Keissl., Anomodon attenuatus (Hedw.) Hueb., Climacium americanum (Renauld & Cardot) Kindberg, and Hypnum imponens Hedw. (Bryopsida; Hypnales). A total of 101 perfect microsatellites were mined with an average density of 1 microsatellite/4.21 kb. The hexa-nucleotide repeats were not detected in mitochondrial genomes of studied taxa. Di-nucleotides were seen to be the most frequent repeats followed by tetra-nucleotides. The identified microsatellites were also checked for variability in length between species. The mined microsatellites will be used for gene tagging, species identification and population genetic studies.
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Hariyono, Dwi. "Application of Microsatellite Markers for Genetic Diversity Analysis of Indonesian Local Cattle." Indonesian Bulletin of Animal and Veterinary Sciences 32, no. 2 (August 22, 2022): 105–18. http://dx.doi.org/10.14334/wartazoa.v32i2.3040.
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Animal genetic resources (AnGR), including cattle, have been valuable national assets that need to be preserved and developed. There are at least 16 recognized breeds of cattle that have been registered as local and new breeds by the Ministry of Agriculture of the Republic of Indonesia. Conservation and development programs of these local cattle breeds require basic information regarding their genetic diversity, relationships, and structures. There are several types of DNA markers that can be used for genetic diversity analysis, such as microsatellite markers. Microsatellites or short tandem repeats (STRs) are a group of DNA sequences consisting of tandemly repeated units (1–6 bp), which are abundant throughout the genome and can be found in both coding and non-coding regions. The primary advantages of microsatellites are that they are inherited in a Mendelian pattern (codominant markers), high polymorphism rates, and high abundances throughout the genome. The aim of this review is to discuss the application of microsatellite markers for genetic diversity analysis in Indonesian local cattle based on 3 indices: number alleles per locus, expected heterozygosity (He), and polymorphisms information content (PIC). There are at least 28 microsatellite markers that have been studied in Indonesian local cattle, with the number of alleles per locus ranging from 2 to 32, He values ranging from 0.100 to 0.985, and PIC values from 0.095 to 0.935. Based on the PIC values, several microsatellites are classified as highly informative, e.g. BM1824, ILST6, TGLA126, TGLA53, TGLA227, TGLA122, ETH225, INRA23, SPS113, SPS115, BM1818, CSSM66, ETH10, INRA005, INRA037, ETH185, HEL017, and ILSTS029. Therefore, these microsatellite markers can be potentially used for future genetic diversity analysis of other breeds of cattle.
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Sharma, P. C., Manish Roorkiwal, and Atul Grover. "Purifying Selection Bias against Microsatellites in Gene Rich Segmental Duplications in the Rice Genome." International Journal of Evolutionary Biology 2012 (September 13, 2012): 1–8. http://dx.doi.org/10.1155/2012/970920.
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Little data is available on microsatellite dynamics in the duplicated regions of the rice genome, even though efforts have been made in the past to align genome sequences of its two sub-species. Based on the coordinates of duplicated sequences in the indica genome as available in the public domain, we identified microsatellites in these regions. CCG and GAAAA repeats occurred most frequently. In all, 259 microsatellites could be identified in the duplicated sequences using the criteria of minimum 90% alignability spread over a minimum of 1 Kb sequence. More than 25% of the repeats in duplicated regions occurred in the genic sequences. Only 45 (17%) of these 259 microsatellites were found conserved in the duplicated paralogues. Among these repeats, 40% maintained both sequence and length conservation. The effect of mutability of nearby regions could also be clearly seen in microsatellite regions. The overall purpose of this study was to investigate, whether microsatellites follow an independent course of evolutionary dynamics subsequent to events like genome reshuffling that simply drives these elements to different locations in the genome. To the best of our knowledge, this is the first comprehensive analysis of microsatellite conservation in the duplicated regions of any genome.
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Colson, Isabelle, and David B. Goldstein. "Evidence for Complex Mutations at Microsatellite Loci in Drosophila." Genetics 152, no. 2 (June 1, 1999): 617–27. http://dx.doi.org/10.1093/genetics/152.2.617.
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Abstract Fifteen lines each of Drosophila melanogaster, D. simulans, and D. sechellia were scored for 19 microsatellite loci. One to four alleles of each locus in each species were sequenced, and microsatellite variability was compared with sequence structure. Only 7 loci had their size variation among species consistent with the occurrence of strictly stepwise mutations in the repeat array, the others showing extensive variability in the flanking region compared to that within the microsatellite itself. Polymorphisms apparently resulting from complex nonstepwise mutations involving the microsatellite were also observed, both within and between species. Maximum number of perfect repeats and variance of repeat count were found to be strongly correlated in microsatellites showing an apparently stepwise mutation pattern. These data indicate that many microsatellite mutation events are more complex than represented even by generalized stepwise mutation models. Care should therefore be taken in inferring population or phylogenetic relationships from microsatellite size data alone. The analysis also indicates, however, that evaluation of sequence structure may allow selection of microsatellites that more closely match the assumptions of stepwise models.
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Dobrzeniecka, S., K. K. Nkongolo, P. Michael, S. Wyss, and M. Mehes. "Identification and Characterization of Microsatellite Markers Useful for Genetic Analysis of Black Spruce (Picea mariana (Mill.) Populations." Silvae Genetica 58, no. 1-6 (December 1, 2009): 168–72. http://dx.doi.org/10.1515/sg-2009-0022.
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Summary Large - scale isolation of microsatellite and information in any conifer species is limited. Our knowledge of microsatellite in spruce (Picea spp.) is still sketchy. Genomic libraries of P. mariana were constructed and screened with (AC)15 probes. Over 200 positive clones were found for this dinucleotide and ten were analyzed in details. They were sequenced to confirm the presence of microsatellites and to generate polymerase chain reaction (PCR) primers based on sequences flanking the microsatellites. All sequenced (AC)n clones had repeats of n > 23. Primer pairs were designed from seven sequences. These primer pairs along with 15 primer pairs from white spruce (Picea glauca) were tested on individual trees. Seven primer pairs from P. mariana and three from P. glauca (white spruce) amplified DNA from P. mariana and were used for genetic analysis of black spruce populations from uplands (drylands) and lowlands (wetlands). High levels of polymorphism and heterozygosity were observed in all the populations studied. Both highlands and lowlands showed similar levels of genetic variation. The selected microsatellites sequences are being used for genome organization analysis of black spruce.
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Campomayor, Nicole Bon, Nomar Espinosa Waminal, Byung Yong Kang, Thi Hong Nguyen, Soo-Seong Lee, Jin Hoe Huh, and Hyun Hee Kim. "Subgenome Discrimination in Brassica and Raphanus Allopolyploids Using Microsatellites." Cells 10, no. 9 (September 8, 2021): 2358. http://dx.doi.org/10.3390/cells10092358.
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Intergeneric crosses between Brassica species and Raphanus sativus have produced crops with prominent shoot and root systems of Brassica and R. sativus, respectively. It is necessary to discriminate donor genomes when studying cytogenetic stability in distant crosses to identify homologous chromosome pairing, and microsatellite repeats have been used to discriminate subgenomes in allopolyploids. To identify genome-specific microsatellites, we explored the microsatellite content in three Brassica species (B. rapa, AA, B. oleracea, CC, and B. nigra, BB) and R. sativus (RR) genomes, and validated their genome specificity by fluorescence in situ hybridization. We identified three microsatellites showing A, C, and B/R genome specificity. ACBR_msat14 and ACBR_msat20 were detected in the A and C chromosomes, respectively, and ACBR_msat01 was detected in B and R genomes. However, we did not find a microsatellite that discriminated the B and R genomes. The localization of ACBR_msat20 in the 45S rDNA array in ×Brassicoraphanus 977 corroborated the association of the 45S rDNA array with genome rearrangement. Along with the rDNA and telomeric repeat probes, these microsatellites enabled the easy identification of homologous chromosomes. These data demonstrate the utility of microsatellites as probes in identifying subgenomes within closely related Brassica and Raphanus species for the analysis of genetic stability of new synthetic polyploids of these genomes.
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Rivero-Hinojosa, Samuel, Nicholas Kinney, Harold R. Garner, and Brian R. Rood. "Germline microsatellite genotypes differentiate children with medulloblastoma." Neuro-Oncology 22, no. 1 (September 28, 2019): 152–62. http://dx.doi.org/10.1093/neuonc/noz179.
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Abstract Background The germline genetic events underpinning medulloblastoma (MB) initiation, and therefore the ability to determine who is at risk, are still unknown for the majority of cases. Microsatellites are short repeated sequences that make up ~3% of the genome. Repeat lengths vary among individuals and are often nonrandomly associated with disease, including several cancers such as breast, glioma, lung, and ovarian. Due to their effects on gene function, they have been called the “tuning knobs of the genome.” Methods We have developed a novel approach for identifying a microsatellite-based signature to differentiate MB patients from controls using germline DNA. Results Analyzing germline whole exome sequencing data from a training set of 120 MB subjects and 425 controls, we identified 139 individual microsatellite loci whose genotypes differ significantly between the groups. Using a genetic algorithm, we identified a subset of 43 microsatellites that distinguish MB subjects from controls with a sensitivity and specificity of 92% and 88%, respectively. This microsatellite signature was validated in an independent dataset consisting of 102 subjects and 428 controls, with comparable sensitivity and specificity of 95% and 90%, respectively. Analysis of the allele genotypes of those 139 informative loci demonstrates that their association with MB is a consequence of individual microsatellites' genotypes rather than their hypermutability. Finally, an analysis of the genes harboring these microsatellite loci reveals cellular functions important for tumorigenesis. Conclusion This study demonstrates that MB-specific germline microsatellite variations mark those at risk for MB development and suggests mechanisms of predisposition.
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Pfeiffer, Antonella, Angelo M. Olivieri, and Michele Morgante. "Identification and characterization of microsatellites in Norway spruce (Picea abies K.)." Genome 40, no. 4 (August 1, 1997): 411–19. http://dx.doi.org/10.1139/g97-055.
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Norway spruce (Picea abies) genomic libraries were screened for presence of dinucleotide AC/GT and AG/CT microsatellites (or simple sequence repeats). On average, one (AG)n microsatellite every 194 kb and one (AC)n microsatellite every 406 kb were found. Forty-six positive clones were sequenced and primers flanking 24 AG microsatellites and 12 AC microsatellites designed. Only seven (20%) of them produced the expected single-locus polymorphic pattern when used to amplify Norway spruce DNAs. The other primer pairs gave either multiple bands or bad amplification, or a single monomorphic fragment. Such a small proportion of successful primer pairs was attributed to the high level of complexity of the Norway spruce genome. Dot blot analysis of the clones showed that many of them contained repetitive DNA and that those giving the single-locus polymorphic patterns usually corresponded to single-copy sequences. A family of repetitive DNA that contained AG repeats was identified and was present in about 40 000 copies per haploid genome. Simple Mendelian inheritance was observed for all the polymorphisms tested. The average number of alleles was 13, ranging from 6 to 22, and the expected heterozygosity was 0.79 when seven microsatellites were used to genotype a panel of 18 trees representing different populations. Compared with isozymes, microsatellites are about five times more informative and could provide an extremely valuable source of markers for genome mapping and genetic diversity studies.Key words: microsatellite, repetitive DNA, hypervariability, Picea abies, genome complexity.
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Avvaru, Akshay Kumar, Deepak Sharma, Archana Verma, Rakesh K. Mishra, and Divya Tej Sowpati. "MSDB: a comprehensive, annotated database of microsatellites." Nucleic Acids Research 48, no. D1 (October 10, 2019): D155—D159. http://dx.doi.org/10.1093/nar/gkz886.
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Abstract Microsatellites are short tandem repeats of 1–6 nucleotide motifs, studied for their utility as genome markers and in forensics. Recent evidence points to the role of microsatellites in important regulatory functions, and their length polymorphisms at coding regions are linked to various neurodegenerative disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and their evolution remains poorly understood. Though other databases of microsatellites exist, they fall short on several fronts. MSDB (MicroSatellite DataBase) is a collection of >4 billion microsatellites from 37 680 genomes presented in a user-friendly web portal for easy, interactive analysis and visualization. This is by far the most comprehensive, annotated, updated database to access and analyze microsatellite data of multiple species. The features of MSDB enable users to explore the data as tables that can be filtered and exported, and also as interactive charts to view and compare the data of multiple species simultaneously. Its modularity and architecture permit seamless updates with new data, making it a powerful tool and useful resource to researchers working on this important class of DNA elements, particularly in context of their evolution and emerging roles in genome organization and gene regulation.
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Hadonou, A. M., D. J. Sargent, F. Wilson, C. M. James, and D. W. Simpson. "Development of microsatellite markers in Fragaria, their use in genetic diversity analysis, and their potential for genetic linkage mapping." Genome 47, no. 3 (June 1, 2004): 429–38. http://dx.doi.org/10.1139/g03-142.
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We have developed 21 new microsatellites in the model diploid perennial species Fragaria vesca from an enriched genomic library developed using F. vesca 'Ruegen'. The transferability of the primer pairs to other Fragaria species was high; all 31 primer pairs produced amplicons in 3 accessions of the octoploid strawberry Fragaria × ananassa, whereas 24 (77%) amplified a product in 7 other diploid Fragaria species. We analysed the allelic variation among 15 F. vesca accessions using the 21 microsatellites reported here and 10 F. vesca microsatellites described previously. The level of polymorphism detected at these microsatellite loci was high; five loci were monomorphic. Only two microsatellites were required to unambiguously discriminate among the 15 F. vesca accessions. A preliminary survey of segregation in an F2 progeny indicates that 20 of the 26 polymorphic loci (77%) could be mapped.Key words: Fragaria, genetic fingerprinting, microsatellites.
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Moldabekov, Meirbek, Suleimen Yelubayev, Kuanysh Alipbayev, Anna Sukhenko, Timur Bopeyev, and Darya Mikhailenko. "Stability Analysis of the Microsatellite Attitude Control System." Applied Mechanics and Materials 798 (October 2015): 297–302. http://dx.doi.org/10.4028/www.scientific.net/amm.798.297.
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The problem of development of the microsatellite attitude control system on the base of reaction wheels positioned along its principal central axes of inertia is considered in this article. As difference from the classical mathematical models describing the microsatellite motion, this article includes the mathematical model of reaction wheel which is controlled by the input voltage of the electric motor. PD-controller is used as the basis for the development of the control law for microsatellite attitude. The stability analysis of the microsatellite attitude control process was carried out with the help of Lyapunov function method. This analysis allowed to prove that obtained attitude control law provides the asymptotic stability of the microsatellite rotational motion. Further, the function of control voltage for the reaction wheel’s electric motor with account of its technical specifications was obtained based on the derived mathematical model of the reaction wheel’s dynamics. The results of performed simulation showed the effectiveness of developed control. Obtained results of the study provide a base for the use of presented approach to the development of attitude control system for microsatellites with various missions.
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Sitkovskaya, A. O., E. E. Rostorguev, S. V. Timofeeva, I. V. Mezhevova, S. Yu Filippova, T. V. Shamova, N. N. Timoshkina, and D. Yu Gvaldin. "FEATURES OF EXPRESSION OF OCT4, NANOG AND ENDOGLIN IN RENAL CELL CARCINOMAS." Crimea Journal of Experimental and Clinical Medicine 10, no. 3 (2021): 39–42. http://dx.doi.org/10.37279/2224-6444-2020-10-3-39-42.
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Glial tumors, in particular those composed of astrocytes, are the most common group of primary brain tumors. The most common glial tumor is astrocytoma. The biology of glial tumors was routinely studied on immortalized cell lines. However, multiple passages result in a loss of cellular heterogeneity. Therefore, more and more scientific laboratories in their research are beginning to use primary cell lines obtained directly from the patient’s native postoperative material. The question of the timing of the genetic stability of primary cell lines remains open. A special type of genetic instability is microsatellite instability, which affects microsatellites found throughout the genome. Microsatellites have several alleles, which are determined by changes in the number of repetitions of a motif unit. Microsatellite instability is of great importance in the oncogenesis of malignant neoplasms. The aim of this work was to study the microsatellite instability of primary cell lines of poorly differentiated glial tumors at different passages in comparison with the patient’s primary tumor material. Tumor cells of primary cultures of anaplastic astrocytoma and glioblastoma at different passages were used as material for the study. Formalin-fixed paraffin wax (FFPE) slides were used as a microsatellite control. Microsatellite analysis was performed on primary cultures of anaplastic astrocytoma and glioblastoma using the following markers: D17S250, D2S123, D5S346, NR21, NR24, NR27, BAT25, BAT26 by PCR. Microsatellite analysis has shown that primary glioblastoma cell lines are genetically more stable than primary anaplastic astrocytoma cell lines.
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Abdul-Muneer, P. M. "Application of Microsatellite Markers in Conservation Genetics and Fisheries Management: Recent Advances in Population Structure Analysis and Conservation Strategies." Genetics Research International 2014 (April 7, 2014): 1–11. http://dx.doi.org/10.1155/2014/691759.
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Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management.
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Gouin, Nicolas, Scott J. Westenberger, Susan M. Mahaney, Peter Lindley, John L. VandeBerg, and Paul B. Samollow. "Development, inheritance, and linkage-group assignment of 60 novel microsatellite markers for the gray, short-tailed opossum Monodelphis domestica." Genome 48, no. 6 (December 1, 2005): 1019–27. http://dx.doi.org/10.1139/g05-059.
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Short-tandem-repeat (SSR) or microsatellite polymorphisms are some of the most extensively employed genetic markers in contemporary linkage mapping studies. To date, only a limited number of microsatellites have been isolated in the gray, short-tailed opossum Monodelphis domestica, a South American marsupial widely used for comparative biological and biomedical research. To increase the number of potentially useful mapping markers, we screened 2 microsatellite-enriched genomic libraries containing alternatively (CA)n or (GA)n repeats. A total of 184 clones were sequenced, from which 60 polymorphic microsatellite markers were successfully optimized. The efficiency of this enrichment protocol for M. domestica microsatellite isolation is discussed, and suggestions to improve the outcome are made. All 60 loci showed high allelic diversity, with allele numbers ranging from 2 to 10 in a subset of 33 unrelated animals. Normal Mendelian inheritance was confirmed for all loci by analyzing allelic segregation in 5 two-generation families. One microsatellite appeared to be X linked, and null alleles were found in 5 others. Two-point linkage analyses were implemented using the data on the 5 families, leading to the assignment of 59 of these loci to the existing linkage groups. The 60 novel microsatellites developed in this study will contribute significantly to the M. domestica linkage map, and further QTL mapping studies.Key words: Monodelphis domestica, marsupial, microsatellite, enriched libraries, genetic linkage analysis.
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Rivera, R., K. J. Edwards, JHA Barker, G. M. Arnold, G. Ayad, T. Hodgkin, and A. Karp. "Isolation and characterization of polymorphic microsatellites in Cocos nucifera L." Genome 42, no. 4 (August 1, 1999): 668–75. http://dx.doi.org/10.1139/g98-170.
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Microsatellites or simple sequence repeats (SSRs) were isolated from coconut (Cocos nucifera) and tested for polymorphism on restricted germplasm. Sequencing of 197 clones from a cv. Tagnanan Tall-enriched genomic library showed that 75% contained a microsatellite, of which 64% were dinucleotide (GA/CT, CA/GT and GC/CG), 6% were trinucleotide, and 30% were compound repeats. Of 41 primer pairs tested on Tagnanan Tall genomic DNA, 38 gave the expected size product, two amplified two loci, and another gave a multilocus pattern. On 20 coconut samples, the 38 SSRs detected 198 alleles (average: 5.2 alleles per microsatellite). Genetic diversity (D = 1 - Sigma pi2) values ranged from 0.141 to 0.809. Heterozygotes were present at high frequencies among some dwarf samples. Analysis of similarity matrices based either on shared alleles at each locus (simple matching coefficient) or on allele bands across all loci (Jaccard coefficient) showed similar results. Dwarfs grouped separately from talls and showed less genetic diversity. In a wider test on 40 samples, 8 SSRs detected 64 alleles (average: eight alleles per microsatellite). These results indicate the high potential of microsatellites to detect genetic diversity in coconut germplasm.Key words: molecular markers, microsatellite, SSR, Cocos nucifera, coconut.
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Powierska-Czarny, Jolanta, Danuta Miścicka-Sliwka, Jakub Czarny, Tomasz Grzybowski, Marcin Wozniak, Gerard Drewa, Włodzimierz Czechowicz, and Jan Sir. "Analysis of microsatellite instability and loss of heterozygosity in breast cancer with the use of a well characterized multiplex system." Acta Biochimica Polonica 50, no. 4 (December 31, 2003): 1195–203. http://dx.doi.org/10.18388/abp.2003_3643.
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Analysis of microsatellite instability (MI) and loss of heterozygosity (LOH) is recommended for screening patients with sporadic and hereditary malignancies. This study shows an application of a fluorescent hexaplex PCR system for microsatellite typing on A.L.F. DNA Sequencer (Pharmacia Biotech). This technique detects changes in microsatellites providing a time-efficient, reliable and accurate method for MI and LOH analyses. The Fragment Manager software was used for automated size calculation and quantitation of DNA fragments, enabling rapid and precise measurement of allelic ratios. We examined 70 breast cancer and 70 control DNA specimens, classified all the patterns of microsatellite alterations, and set up MI and LOH assessment criteria for the automated multiplex fluorescent method.
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Russell, Joanne, John Fuller, George Young, Bill Thomas, Malcolm Macaulay, Robbie Waugh, Wayne Powell, and Graziana Taramino. "Discriminating between barley genotypes using microsatellite markers." Genome 40, no. 4 (August 1, 1997): 442–50. http://dx.doi.org/10.1139/g97-059.
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Eleven microsatellite loci were used to survey 24 barley genotypes representing 23 cultivars and a breeding line in official trials. Three separate combinations of four microsatellites had overall probabilities of identity of less than 1 in 1000 and could distinguish between all 24 barley genotypes. It is shown that the microsatellites could distinguish genotypes with the same pedigree and also that patterns of discrimination were different from those obtained from botanical descriptors. The stability of microsatellites across different generations was demonstrated by a retrospective analysis of the pedigree of Golden Promise. One of the parents of Maythorpe, the immediate ancestor of Golden Promise, was shown to be Irish Goldthorpe rather than Goldthorpe, thereby resolving conflicting published pedigrees.Key words: barley, microsatellites, cultivar identification, stability, Golden Promise.
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Parida, Swarup K., Devendra K. Yadava, and Trilochan Mohapatra. "Microsatellites in Brassica unigenes: relative abundance, marker design, and use in comparative physical mapping and genome analysis." Genome 53, no. 1 (January 2010): 55–67. http://dx.doi.org/10.1139/g09-084.
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Microsatellites present in the transcribed regions of the genome have the potential to reveal functional diversity. Unigene sequence databases are the sources of such genic microsatellites with unique flanking sequences and genomic locations even in complex polyploids. The present study was designed to assay the unigenes of Brassica napus and B. rapa for various microsatellite repeats, and to design markers and use them in comparative genome analysis and study of evolution. The average frequency of microsatellites in Brassica unigenes was one in every 7.25 kb of sequence, as compared with one in every 8.57 kb of sequence in Arabidopsis thaliana . Trinucleotide motifs coding for serine and the dinucleotide motif GA were most abundant. We designed 2374 and 347 unigene-based microsatellite (UGMS) markers including 541 and 58 class I types in B. napus and B. rapa, respectively, and evaluated their use across diverse species and genera. Most of these markers (93.3%) gave successful amplification of target microsatellite motifs, which was confirmed by sequencing. Interspecific polymorphism between B. napus and B. rapa detected in silico for the UGMS markers was 4.16 times higher in 5′ untranslated regions than in coding sequences. Physical anchoring of Brassica UGMS markers on the A. thaliana genome indicated their significance in studying the evolutionary history of A. thaliana genomic duplications in relation to speciation. Comparative physical mapping identified 85% of Brassica unigenes as single copy and gave clues for the presence of conserved primordial gene order. Complex chromosomal rearrangements such as inversions, tandem and segmental duplications, and insertions/deletions were evident between A. thaliana and B. rapa genomes. The results obtained have encouraging implications for the use of UGMS markers in comparative genome analysis and for understanding evolutionary complexities in the family Brassicaceae.
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Chroboková, E., J. Raddová, M. Vachůn, B. Krška, and M. Pidra. "An analysis of apricot cultivars by random amplified polymorphic DNA and microsatellite primers." Horticultural Science 38, No. 4 (November 15, 2011): 125–33. http://dx.doi.org/10.17221/68/2010-hortsci.
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The random amplified polymorphic DNA (RAPD) technique and microsatellites were used to study the genetic diversity and to identify cultivars within a collection of 95 cultivars of Prunus armeniaca L. A dendrogram based on 13 RAPD primers and a dendrogram based on 9 microsatellite primers were prepared using the unweighted pair group method with average (UPGMA) group analysis. In both dendrograms, the cultivars were classified into five groups, according to their geographic origin: hybrids originated by hybridization among cultivars of European and Asian origin, European cultivars, American cultivars, Asian cultivars and interspecific hybrids. Eleven cultivars were not distinguished (9 cultivars with supposed relatedness to Velkopavlovická cv., 2 cvs Vynoslivyj and Vynoslivyj 21/1 that are assumed to be clones) using 9 microsatellite primers. The similarities and the differences revealed among incorporation of cultivars into groups were compared with the literature findings. The results of these analyses have a direct implication on the selection of new breeding progenitors at the Faculty of Horticulture, Mendel University in Brno, Lednice, Czech Republic.
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Buhard, Olivier, Nirosha Suraweera, Aude Lectard, Alex Duval, and Richard Hamelin. "Quasimonomorphic Mononucleotide Repeats for High-Level Microsatellite Instability Analysis." Disease Markers 20, no. 4-5 (2004): 251–57. http://dx.doi.org/10.1155/2004/159347.
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Microsatellite instability (MSI) analysis is becoming more and more important to detect sporadic primary tumors of the MSI phenotype as well as in helping to determine Hereditary Non-Polyposis Colorectal Cancer (HNPCC) cases. After some years of conflicting data due to the absence of consensus markers for the MSI phenotype, a meeting held in Bethesda to clarify the situation proposed a set of 5 microsatellites (2 mononucleotide repeats and 3 dinucleotide repeats) to determine MSI tumors. A second Bethesda consensus meeting was held at the end of 2002. It was discussed here that the 1998 microsatellite panel could underestimate high-level MSI tumors and overestimate low-level MSI tumors. Amongst the suggested changes was the exclusive use of mononucleotide repeats in place of dinucleotide repeats. We have already proposed a pentaplex MSI screening test comprising 5 quasimonomorphic mononucleotide repeats. This article compares the advantages of mono or dinucleotide repeats in determining microsatellite instability.
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Gonçalves-Vidigal, Maria Celeste, and Luciana Benchimol Rubiano. "Development and application of microsatellites in plant breeding." Crop Breeding and Applied Biotechnology 11, spe (June 2011): 66–72. http://dx.doi.org/10.1590/s1984-70332011000500010.
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Molecular markers are powerful tools for analyzing genome diversity within a species, and to evaluate genetic relationships between individuals and populations. Among them, microsatellites (SSRs) are one of the most important polymorphic markers that can be used effectively to distinguish germplasm accessions. These markers present high informative content due to their codominant inheritance, multiallelism, mendelian pattern and good genome coverage. The enrichment methodology for microsatellite development has a superior efficiency in plants, especially when performed using biotin-labeled microsatellite oligoprobes and streptavidin-coated magnetic beads. The development of EST-SSR markers has become a fast and relatively inexpensive way but it is limited to species for which this type of database exists. Given the high polymorphism level of microsatellites when compared to other markers, SSRs have been used to study population structure, for genetic diversity analysis, genetic mapping and marker assisted selection.
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Ming, Yao, Xueying Yu, Wei Liu, Jingzhen Wang, and Wenhua Liu. "The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation." Journal of Marine Science and Engineering 10, no. 6 (June 20, 2022): 834. http://dx.doi.org/10.3390/jmse10060834.
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Microsatellites are one of the important genome characterizations that can be a valuable resource for variety identification, genetic diversity, phylogenetic analysis, as well as comparative and conservation genomics research. Here, we developed comprehensive microsatellites through genome-wide mining for the threatened cetacean Indo-Pacific humpback dolphin (Sousa chinensis). We found 87,757 microsatellites with 2–6 bp nucleotide motifs, showing that about 32.5 microsatellites per megabase comprises microsatellites sequences. Approximately 97.8% of the markers developed in this study were consistent with the published identified markers. About 75.3% microsatellites were with dinucleotide motifs, followed by tetranucleotide motifs (17.4%), sharing the same composition pattern as other cetaceans. The microsatellites were not evenly distributed in the S. chinensis genome, mainly in non-coding regions, with only about 0.5% of the markers located in coding regions. The microsatellite-containing genes were mainly functionally enriched in the methylation process, probably demonstrating the potential impacts of microsatellites on biological functions. Polymorphic microsatellites were developed between different genders of S. chinensis, which was expected to lay the foundation for genetic diversity investigation in cetaceans. The specific markers for a male Indo-Pacific humpback dolphin will provide comprehensive and representative male candidate markers for sex identification, providing a potential biomolecular tool for further analysis of population structure and social behavior of wild populations, population trend evaluation, and species conservation management.
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Szpecht-Potocka, A., E. Obersztyn, M. Karwacki, E. Bocian, J. Bal, and T. Mazurczak. "Molecular and Clinical Studies of Polish Patients with Prader-Willi Syndrome." Acta geneticae medicae et gemellologiae: twin research 45, no. 1-2 (April 1996): 273–76. http://dx.doi.org/10.1017/s0001566000001446.
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AbstractA group of 30 patients clinically described as having the Prader-Willi Syndrome (PWS) were studied using microsatellites from 15q11-13 and methylation analysis with probe PW71B (D15S63). The patients were categorized according to clinical symptoms. 80% of all patients were informative using molecular and cytogenetic methods. Among 8 patients with an atypical PWS phenotype, 2 showed uniparental disomy, and 2 had a mosaic deletion for 15q. The last 4 atypical and 2 typical patients had neither molecular defects confirmed by microsatellite analysis nor a parent-of-origin-specific methylation pattern for PWS. Our results confirm that methylation pattern analysis provides an additional and alternative microsatellite analysis to diagnose PWS.
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Estoup, A., L. Garnery, M. Solignac, and J. M. Cornuet. "Microsatellite variation in honey bee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models." Genetics 140, no. 2 (June 1, 1995): 679–95. http://dx.doi.org/10.1093/genetics/140.2.679.
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Abstract Samples from nine populations belonging to three African (intermissa, scutellata and capensis) and four European (mellifera, ligustica, carnica and cecropia) Apis mellifera subspecies were scored for seven microsatellite loci. A large amount of genetic variation (between seven and 30 alleles per locus) was detected. Average heterozygosity and average number of alleles were significantly higher in African than in European subspecies, in agreement with larger effective population sizes in Africa. Microsatellite analyses confirmed that A. mellifera evolved in three distinct and deeply differentiated lineages previously detected by morphological and mitochondrial DNA studies. Dendrogram analysis of workers from a given population indicated that super-sisters cluster together when using a sufficient number of microsatellite data whereas half-sisters do not. An index of classification was derived to summarize the clustering of different taxonomic levels in large phylogenetic trees based on individual genotypes. Finally, individual population x loci data were used to test the adequacy of the two alternative mutation models, the infinite allele model (IAM) and the stepwise mutation models. The better fit overall of the IAM probably results from the majority of the microsatellites used including repeats of two or three different length motifs (compound microsatellites).
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Wallace, Emma C., and Lina M. Quesada-Ocampo. "Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of Pseudoperonospora populations." PeerJ 5 (May 2, 2017): e3266. http://dx.doi.org/10.7717/peerj.3266.
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Downy mildew pathogens affect several economically important crops worldwide but, due to their obligate nature, few genetic resources are available for genomic and population analyses. Draft genomes for emergent downy mildew pathogens such as the oomycete Pseudoperonospora cubensis, causal agent of cucurbit downy mildew, have been published and can be used to perform comparative genomic analysis and develop tools such as microsatellites to characterize pathogen population structure. We used bioinformatics to identify 2,738 microsatellites in the P. cubensis predicted transcriptome and evaluate them for transferability to the hop downy mildew pathogen, Pseudoperonospora humuli, since no draft genome is available for this species. We also compared the microsatellite repertoire of P. cubensis to that of the model organism Hyaloperonospora arabidopsidis, which causes downy mildew in Arabidopsis. Although trends in frequency of motif-type were similar, the percentage of SSRs identified from P. cubensis transcripts differed significantly from H. arabidopsidis. The majority of a subset of microsatellites selected for laboratory validation (92%) produced a product in P. cubensis isolates, and 83 microsatellites demonstrated transferability to P. humuli. Eleven microsatellites were found to be polymorphic and consistently amplified in P. cubensis isolates. Analysis of Pseudoperonospora isolates from diverse hosts and locations revealed higher diversity in P. cubensis compared to P. humuli isolates. These microsatellites will be useful in efforts to better understand relationships within Pseudoperonospora species and P. cubensis on a population level.
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Courchesne, Sarah, Dawn Meola, and Acacia Alcivar–Warren. "Bald Eagle (Haliaeetus leucocephalus) Feathers as an Alternative to Blood for Microsatellite DNA Analysis: Toward a Non–invasive Technique for Conservation Genetics." Wildlife Rehabilitation Bulletin 23, no. 1 (June 30, 2005): 31–39. http://dx.doi.org/10.53607/wrb.v23.213.
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The bald eagle (Haliaeetus leucocephalus) is currently classified as threatened in the lower 48 United States. In Massachusetts, only 12 active nesting sites presently exist, and the majority of breeding birds originated from a population of eaglets imported from Nova Scotia in the 1980s. Previous work using Random Amplified Polymorphic DNA (RAPD) technique demonstrated a genetic diversity among Massachusetts’s eagles of only 22 percent. RAPD, while useful for genetic analysis of blood samples, proved to be inappropriate for analysis of feather samples from the same birds. To address this, our current work aimed at determining whether microsatellites would yield identical information for blood and feather samples from the same animal. Utilizing GenBank sequences, a total of 24 microsatellite primer sets representing 18 loci were designed and tested for allele polymorphism using DNA from eight blood samples and a single annealing temperature in the polymerase chain reaction (PCR). Thirteen microsatellites (54%) representing 11 loci were polymorphic, and three of these were selected to compare allele sizes in blood and feather DNA from the same eaglet. Preliminary results using microsatellite AJ620425 showed that 18 out of 44 blood/feather pairs amplified alleles of similar sizes. Feather DNA of the other 26 blood/feather pairs tested did not amplify any alleles. Data suggest that microsatellite alleles from blood and feather of the same bird may be consistent, and the microsatellite technique could be useful for non–invasive conservation genetics studies. However, multiple repetitions of the experiment are needed in order to determine optimum DNA concentration for feather samples. Additionally, refinements to the protocol will be necessary to obtain greater amplification of feather DNA which tended to give somewhat weak signals.
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Ziegenhagen, B., F. Scholz, A. Madaghiele, and G. G. Vendramin. "Chloroplast microsatellites as markers for paternity analysis in Abies alba." Canadian Journal of Forest Research 28, no. 2 (February 1, 1998): 317–21. http://dx.doi.org/10.1139/x97-213.
Full textAbstract:
This study describes the application of previously characterized chloroplast microsatellites as markers for paternity analysis in a conifer species. The investigations were performed on silver fir (Abies alba Mill.) relic trees in an endangered population of the Ore Mountains (Germany). Two relatively isolated adult trees about 30 m apart, as well as 24 naturally regenerated young trees in their direct neighborhood, were analyzed at two chloroplast microsatellite loci. Results reveal the potential usefulness of the markers for paternity analysis.
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Ahmad, Riaz, Darush Struss, and Stephen M. Southwick. "Development and Characterization of Microsatellite Markers in Citrus." Journal of the American Society for Horticultural Science 128, no. 4 (July 2003): 584–90. http://dx.doi.org/10.21273/jashs.128.4.0584.
Full textAbstract:
We evaluated the potential of microsatellite markers for use in Citrus genome analysis. Microsatellite loci were identified by screening enriched and nonenriched libraries developed from `Washington Navel' Citrus. Microsatellite-containing clones were sequenced and 26 specific PCR primers were selected for cross-species amplification and identification of cultivars/clones in Citrus. After an enrichment procedure, on average 69.9% of clones contained dinucleotide repeats (CA)n and (CT)n, in contrast to <25% of the clones that were identified as positive in hybridization screening of a nonenriched library. A library enriched for trinucleotide (CTT)n contained <15% of the clones with (CTT)n repeats. Repeat length for most of the dinucleotide microsatellites was in the range of 10 to 30 units. We observed that enrichment procedure pulled out more of the (CA)n repeats than (CT)n repeats from the Citrus genome. All microsatellites were polymorphic except one. No correlation was observed between the number of alleles and the number of microsatellite repeats. In total, 118 putative alleles were detected using 26 primer pairs. The number of putative alleles per primer pair ranged from one to nine with an average of 4.5. Microsatellite markers discriminated sweet oranges [Citrus sinensis (L.) osb], mandarin (Citrus reticulata Blanco), grapefruit (Citrus paradisi Macf.), lemon [Citrus limon (L.) Burm.f.], and citrange (hybrids of trifoliate orange and sweet orange), at the species level, but individual cultivars/clones within sweet oranges, mandarins and grapefruit known to have evolved by somatic mutation remained undistinguishable. Since these microsatellite markers were conserved within different Citrus species, they could be used for linkage mapping, evolutionary and taxonomic study in Citrus.
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Boches, Peter, Lisa J. Rowland, Kim Hummer, and Nahla V. Bassil. "Microsatellite Markers Developed from `Bluecrop' Reveal Polymorphisms in the Genus Vaccinium and Are Suitable for Cultivar Fingerprinting." HortScience 40, no. 4 (July 2005): 1122B—1122. http://dx.doi.org/10.21273/hortsci.40.4.1122b.
Full textAbstract:
Microsatellite markers for blueberry (Vaccinium L.) were created from a preexisting blueberry expressed sequence tag (EST) library of 1305 sequences and a microsatellite-enriched genomic library of 136 clones. Microsatellite primers for 65 EST-containing simple sequence repeats (SSRs) and 29 genomic SSR were initially tested for amplification and polymorphism on agarose gels. Potential usefulness of these SSRs for estimating species relationships in the genus was assessed through cross-species transference of 45 SSR loci and cluster analysis using genetic distance values from five highly polymorphic EST-SSR loci. Cross-species amplification for 45 SSR loci ranged from 17% to 100%, and was 83% on average in nine sections. Cluster analysis of 59 Vaccinium species based on genetic distance measures obtained from 5 EST-SSR loci supported the concept of V. elliotii Chapm. as a genetically distinct diploid highbush species and indicated that V. ashei Reade is of hybrid origin. Twenty EST-SSR and 10 genomic microsatellite loci were used to determine genetic diversity in 72 tetraploid V. corymbosum L. accessions consisting mostly of common cultivars. Unique fingerprints were obtained for all accessions analyzed. Genetic relationships, based on microsatellites, corresponded well with known pedigree information. Most modern cultivars clustered closely together, but southern highbush and northern highbush cultivars were sufficiently differentiated to form distinct clusters. Future use of microsatellites in Vaccinium will help resolve species relationships in the genus, estimate genetic diversity in the National Clonal Germplasm Repository (NCGR) collection, and confirm the identity of clonal germplasm accessions.
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Järve, K., H. O. Peusha, J. Tsymbalova, S. Tamm, K. M. Devos, and T. M. Enno. "Chromosomal location of a Triticum timopheevii - derived powdery mildew resistance gene transferred to common wheat." Genome 43, no. 2 (March 15, 2000): 377–81. http://dx.doi.org/10.1139/g99-141.
Full textAbstract:
A dominant powdery mildew resistance gene introduced from Triticum timopheevii in line 146-155-T of common wheat, Triticum aestivum, was located on chromosome 6B by monosomic analysis. Restriction fragment length polymorphism (RFLP) and microsatellite analyses detected the presence of a T. timopheevii segment, translocated to chromosome 6B, with breakpoints between the loci Xpsr8/Xpsr964 on 6BS and Xpsr154/Xpsr546 on 6BL. The novel powdery mildew resistance gene, which has been designated Pm27, was shown to cosegregate with the microsatellite locus Xpsp3131, which is located on the introgressed T. timopheevii segment. The molecular data confirm the location of Pm27 on the translocated 6B chromosome. Key words: monosomic analysis, RFLP, microsatellites, Pm27.
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Weetman, David, Lorenz Hauser, and Gary R. Carvalho. "Reconstruction of Microsatellite Mutation History Reveals a Strong and Consistent Deletion Bias in Invasive Clonal Snails, Potamopyrgus antipodarum." Genetics 162, no. 2 (October 1, 2002): 813–22. http://dx.doi.org/10.1093/genetics/162.2.813.
Full textAbstract:
Abstract Direct observations of mutations and comparative analyses suggest that nuclear microsatellites show a tendency to expand, with reports of deletion biases limited to very long alleles or a few loci in multilocus studies. Here we investigate microsatellite evolution in clonal snails, Potamopyrgus antipodarum, since their introduction to Britain in the 19th century, using an analysis based on minimum spanning networks of multilocus microsatellite genotypes. British populations consist of a small number of highly distinct genotype groups with very few outlying genotypes, suggesting clonal lineages containing minor variation generated by mutation. Network patterns suggest that a single introduced genotype was the ancestor of all extant variation and also provide support for wholly apomictic reproduction within the most common clonal lineage (group A). Microsatellites within group A showed a strong tendency to delete repeats, with an overall bias exceeding 88%, irrespective of the exact method used to infer mutations. This highly unusual pattern of deletion bias is consistent across populations and loci and is unrelated to allele size. We suggest that for persistence of microsatellites in this clone, some change in the mutation mechanism must have occurred in relatively recent evolutionary time. Possible causes of such a change in mechanism are discussed.
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Santos, Carlos Antonio Fernandes, and Francisco Pinheiro Lima Neto. "Outcrossing rate between 'Haden' and 'Tommy Atkins' mangoes estimated using microsatellite and AFLP markers." Pesquisa Agropecuária Brasileira 46, no. 8 (August 2011): 899–904. http://dx.doi.org/10.1590/s0100-204x2011000800016.
Full textAbstract:
The objective of this work was to estimate outcrossing rates between Haden and Tommy Atkins mango cultivars, using AFLP and microsatellite markers. Progenies of an isolated 'Haden' plant, identified in a 'Tommy Atkins' commercial orchard, in Petrolina, PE, Brazil, were analyzed. Total DNA was isolated from the progeny leaves and used for AFLP and microsatellite reactions. Multilocus outcrossing rates (t m) were estimated by direct count of AFLP or microsatellite markers and by the mLTR software. Outcrossing rates ranged from 0.85 to 0.87 with the analysis based on seven AFLP markers, and from 0.83 to 0.91 based on three microsatellite primers. No unexpected band patterns were observed for 'Haden' and 'Tommy Atkins'. The estimates obtained with the mLTR software were close to those obtained by direct AFLP and microsatellite allele counting, which indicates that the multilocus model was appropriate for this kind of study. The microsatellites mMiCIR005, mMiCIR030, and mMiCIR036 can be used to elucidate the origin of 'Haden' and 'Tommy Atkins' seedlings.
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Busogoro, J. P., O. Duterme, and P. Lepoivre. "Development of microsatellite markers for the characterisation of Phaeoisariopsis griseola (bean angular leaf spot agent) populations in Central America." Plant Protection Science 38, SI 1 - 6th Conf EFPP 2002 (January 1, 2002): S35—S37. http://dx.doi.org/10.17221/10315-pps.
Full textAbstract:
Although several researches revealed an important diversity within Phaeoisariopsis griseola, the bean angular leaf spot (ALS) agent, no sexual recombination was already detected for this fungus. That apparent contradiction gave rise to the interest to develop codominant markers in order of a more precise analysis of the pathogen populations. Microsatellites were expected to allow characterising P. griseola populations in terms of allele frequencies. A genomic library was constructed by ligating DNA fragments, previously prepared by enzymatic restriction of total DNA of two pathogen strains, into a pZERO plasmid. After transformation of TOP 10F’ strains of E. coli with the recombinant plasmid, a total of 448 colonies were selected for zeocin resistance. The probe mixture [(GT)<sub>15</sub>, (GA)<sub>15</sub>, (GATA)<sub>8</sub>, (GTG)<sub>10</sub>], previously labelled with <sup>32</sup>P, was used to screen the genomic library for the presence of microsatellite sequences. The vector DNA was then extracted from the positive colonies and sequenced. Based on the sequences, a first group of 10 microsatellite loci was identified and the corresponding primers designed. A size analysis using an ALF express system exhibited 3 polymophic microsatellites among a total of 4 loci already considered. The identification of other polymorphic microsatellites is continuing before a large scale analysis of our pathogen collection by using this new molecular tool developed for P. griseola.