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1.
Microsatellites are islands of long repeats of mono-, di- or trinucleotides evenly distributed in the eukaryotic genome with an average distance of 50–100 kb. They display a high degree of length polymorphism and heterozygosity at individual loci, making them highly useful as markers in the development of genomic maps of eukaryotes. In the present work, we examined the dinucleotide repeat motif (dG-dT)n in the Atlantic salmon, Salmo salar L., genome. The frequency of (dG-dT)n microsatellites in salmon correlates well with earlier published estimations. Cloning and sequencing of 45 salmon microsatellites revealed perfect and imperfect repeats, but no compound microsatellites. The distribution of number of repeat units in salmon microsatellites differ significantly from that of higher vertebrates. Salmon tends to have more long repeat stretches and less intermediate length repeats. 相似文献
2.
The yellow catfish Pelteobagrus fulvidraco is a freshwater fish species. Due to overfishing and pollution of freshwater ecosystems, the wild stocks of this fish reduced
substantially. We isolated and characterized 12 polymorphic microsatellites of this species. The number of alleles at the
12 microsatellite loci ranged from four to eight, with an average of 6.6/locus. The average observed heterozygosity was 0.72,
whereas the expected heterozygosity ranged from 0.60 to 0.86 (average: 0.80). All 12 microsatellites conformed to Hardy–Weinberg
Equilibrium and were in linkage equilibrium. These 12 novel microsatellites could facilitate studies of genetic diversity
and population structure of the yellow catfish to supply necessary information of conservation of the yellow catfish. 相似文献
3.
Isolation and characterization of microsatellites in trembling aspen (Populus tremuloides) 总被引:13,自引:0,他引:13
S. Dayanandan O. P. Rajora K. S. Bawa 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,96(6-7):950-956
We have identified, isolated, and characterized microsatellite/simple sequence repeat (SSR) loci in trembling aspen (Populus tremuloides) by screening partial genomic libraries. We have also examined the compatibility and use of the P. tremuloides SSR primers to resolve microsatellites in other Populus species. Fourteen microsatellites were identified from 1600 clones screened. The TC/AG microsatellites were the most abundant.
A total of 29 alleles were detected in 36 P. tremuloides individuals at the four SSR loci (two each of di- and tri-nucleotide repeats) characterized. The number of alleles at the
SSR loci ranged from 5 to 11, with an average of 7.25 alleles per locus, and the observed heterozygosity ranged from 0.19
to 0.82, with a mean of 0.46 per locus. Although the highest polymorphism was observed for a dinucleotide SSR locus, the trinucleotide
SSR loci showed substantial polymorphism. There were 34 unique multilocus genotypes among the 36 P. tremuloides individuals examined, and 89% of the individuals had unique multilocus genotypes. Two pairs of SSR primers were successful
in PCR, amplifying genomic DNA and resolving microsatellites of comparable size from Populus deltoides, P. nigra, P.×canadensis, and P. maximowiczii. The microsatellite DNA markers developed could be used for clonal fingerprinting, certification of controlled crosses, genome
mapping, marker-assisted early selection, genetic diversity assessments, and conservation and sustainable management of poplar
genetic resources.
Received: 14 November 1997 / Accepted: 17 November 1997 相似文献
4.
Development of Novel Microsatellite DNA Markers from the Pacific Oyster Crassostrea gigas 总被引:6,自引:0,他引:6
We document the potential of novel microsatellites as a genetic tool in furthering our understanding of the Crassostrea
gigas genetic structure. From the microsatellite-enriched libraries we constructed, 123 repeat regions that had sufficient sequence information to design polymerase chain reaction primer sets were isolated. From these, 9 primer pairs were screened in a C. gigas population of 67 individuals to evaluate the genetic variability. All but 1 of the 9 loci showed allelic variation (number of alleles, 2–20; observed heterozygosity, 0.119–0.925; unbiased expected heterozygosity, 0.139–0.914). Considerable discrepancy of genotypic proportions from the Hardy-Weinberg equilibrium was observed at 1 locus with an apparent heterozygote deficiency. Several loci were successfully amplified in 3 other related species with the appropriate allele size: 6 loci in C. sikamea, 4 loci in C. ariakensis, and 5 loci in C. nippona. 相似文献
5.
Guomin Huang Lan Hong Wanhui Ye Hao Shen Honglin Cao Wei Xiao 《Conservation Genetics》2009,10(4):1069-1071
Twelve novel microsatellite loci were isolated and characterized from enriched genomic libraries of Castanopsis chinensis. Four previously reported microsatellites from Castanopsis cuspidata were cross-amplified in C. chinensis. Forty-two sample trees from a wild population were tested for polymorphism using a set of the 16 polymorphic microsatellites.
The average allele number of these microsatellites was 4.6 per locus, ranging from 2 to 7. The ranges of observed and expected
heterozygosity were 0.262–1.000 and 0.238–0.818, respectively. Significant deviations from Hardy–Weinberg equilibrium were
detected at five loci and no linkage disequilibrium was observed. 相似文献
6.
We tested the cross-amplification of 26 microsatellites developed for passerines and an additional three developed for Gallinula species in eight European Coots from two populations. Sixteen microsatellite markers successfully amplified, of which nine
were polymorphic with 2–6 alleles (mean 3.7 alleles) and an expected heterozygosity (H
e) ranging from 0.375 to 0.805 (mean H
e = 0.589). On average, we found 2.22 alleles/locus and a mean H
e of 0.440 in one nest, and 2.56 alleles/locus and a mean H
e of 0.494 in the other one. These nine polymorphic markers could be of potential use in studies of genetic variability, population
structure and reproductive strategy of European Coots. 相似文献
7.
Nicolás M. Suárez Ana González Eva Betancor José J. Pestano 《Conservation Genetics》2009,10(3):581-583
The blue chaffinch, Fringilla teydea, is an endemic species of the Canary Islands. This species is formed by two subspecies: The Teneriffean blue chaffinch (F. t. teydea), and the endangered Gran Canarian blue chaffinch, (F. t. polatzeki). Here we report the isolation and characterization of nine tetranucleotide microsatellites (AAAG and AAAT) from the Gran
Canarian subspecies, using an enrichment protocol. An average of 7.8 alleles per locus and an average observed heterozygosity
of 0.773 were found (n = 28). The loci were tested for their ability to cross amplify in the Teneriffean subspecies and in the common chaffinch
(Fringilla coelebs). These microsatellites will be used to manage a captive breeding programme for the endangered Gran Canarian subspecies. 相似文献
8.
Microsatellites in Cassava (Manihot esculenta Crantz): discovery, inheritance and variability 总被引:2,自引:0,他引:2
P. P. Chavarriaga-Aguirre M. M. Maya M. W. Bonierbale S. Kresovich M. A. Fregene J. Tohme G. Kochert 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,97(3):493-501
Fourteen microsatellites containing GA-repeats were isolated and characterized in cassava (Manihot esculenta Crantz, Euphorbiaceae). Microsatellite heterozygosity (h) was estimated in 48 accessions using (32P)-end-labeled primers and in more than 500 accessions using fluorescence-based genotyping. Heterozygosity values ranged from
0.00 to 0.88 and the number of alleles detected varied from 1 to 15. The reproducibility of allele sizing was also assessed
using fluorescence-based genotyping. The average inter-gel size difference was 1.03 nucleotides. Chi-square tests (χ2) were performed to analyse segregation distortion and the linkage between alleles segregating from either or both parents
in an F1 mapping population. Most microsatellite loci segregated in the expected 1 : 1, 1 : 2 : 1 or 1 : 1 : 1 : 1 ratio. Linkage
was detected between loci segregating from either parent, and segregation distortion from the male parent was detected for
locus GA-131. Approximately 80% of the microsatellites detected one or two alleles per accession, suggesting a low degree
of microsatellite locus duplication, an unexpected finding for a putative allopolyploid, highly heterozygous species. The
high h values of most microsatellites, their amplification in other Manihot taxa and their suitability for high-throughput, fluorescence-based genotyping, make microsatellites the marker of choice
for germplasm characterization and saturation of the cassava map.
Received: 4 September 1997 / Accepted 16 March 1998 相似文献
9.
Oyster (Crassostrea plicatula) is widely distributed in coastal areas of China. We developed and evaluated simple sequence repeat (SSR) markers from expressed
sequence tags (ESTs) of Crassostrea gigas and to amplify EST-SSR in C. plicatula. Characteristics of eight EST-SSR loci were investigated using 37 wild-type C. plicatula individuals. The number of alleles per locus ranged from four to six. The observed heterozygosity (H
O) ranged from 0.1892 to 0.7027 (0.3919 on average) and the expected heterozygosity (H
E) ranged from 0.6068 to 0.7656 (0.7039 on average) (P < 0.05). The average observed heterozygosity was much lower than the average expected heterozygosity. All loci except C15
departed from Hardy-Weinberg equilibrium (P < 0.05) significantly. Contribution of the eight EST-SSR primers presented here will provide necessary and powerful molecular
tools for management and conservation studies on the species of oysters in the future. 相似文献
10.
Fourteen polymorphic microsatellite loci were isolated and characterized from an AC-enriched genomic library of Liriodendron chinense (Magnoliaceae). The average allele number of these microsatellites was 5.2 per locus, ranging from three to eight. The observed
and expected heterozygosity at population level were 0.07–1.00 and 0.10–0.83, respectively. These sets of microsatellites
will be useful for studies of population genetic structure of L. chinense and L. tulipifera as well as to estimate fine-scale gene flow rates. 相似文献
11.
Aliya El Nagar Matthew McHugh Toby Rapp David W. Sims Martin J. Genner 《Conservation Genetics》2010,11(3):1203-1206
Simple sequence repeat markers (SSRs, microsatellites) were characterised for skates (Elasmobranchii: Rajidae) from published
expressed sequence tags (ESTs) of Leucoraja erinacea. These were tested in four European species (Raja clavata, Raja montagui, Dipturus batis, and Leucoraja naevus). Thirteen of the fourteen amplified loci were polymorphic in at least one species. Polymorphic loci possessed on average
4.5–5.9 alleles per species, and expected heterozygosity ranged from 0.05 to 0.88. Possible null alleles were detected at
three loci, while one locus showed significant deviation from Hardy–Weinberg Equilibrium proportions. Three locus-pairs exhibited
significant linkage disequilibrium in one or more species. This marker set will be valuable for population genetic analyses
of the focal taxa, and may prove useful for studies of other skate species. 相似文献
12.
P. J. Fisher T. E. Richardson R. C. Gardner 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,96(6-7):969-979
Dinucleotide microsatellites were isolated from Pinus radiata using both a standard genomic library and libraries enriched for microsatellites. Locus-specific primers were designed to
amplify 43 unique microsatellites. Thirty two of these loci had interpretable PCR patterns, 11 of which were polymorphic in
a screen of 19 P. radiata individuals; all 11 polymorphic loci contained at least 17 repeats in the sequenced plasmid. Six of the eleven primer pairs
amplified multiple fragments per individual (3–8), suggesting that these loci were present in multiple copies in the genome.
Genotyping a 48-tree P. radiata production population with seven of the most polymorphic microsatellites revealed an average of 17 bands per locus (the multi-copy
microsatellites were treated as one locus). When tested on known pedigrees, both single and multi-copy microsatellites exhibited
co-dominant inheritance and Mendelian segregation. Two loci had null alleles and one locus had a high frequency of non-parental
alleles, suggesting a high mutation rate. Eight of these microsatellites, including five multi-copy loci, were placed on a
partially constructed P. radiata genetic map. Four of the five multi-copy microsatellites had two or more sets of alleles that mapped to the same locus, and
the fifth mapped to two unlinked loci. All seven tested primer pairs amplified PCR products from other species of hard pine,
three amplified products from soft-pine species, and one amplified bands in other conifers.
Received: 10 November 1997 / Accepted: 5 January 1998 相似文献
13.
Sethy NK Shokeen B Edwards KJ Bhatia S 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2006,112(8):1416-1428
Paucity of polymorphic molecular markers in chickpea (Cicer arietinum L.) has been a major limitation in the improvement of this important legume. Hence, in an attempt to develop sequence-tagged microsatellite sites (STMS) markers from chickpea, a microsatellite enriched library from the C. arietinum cv. Pusa362 nuclear genome was constructed for the identification of (CA/GT)
n
and (CT/GA)
n
microsatellite motifs. A total of 92 new microsatellites were identified, of which 74 functional STMS primer pairs were developed. These markers were validated using 9 chickpea and one C. reticulatum accession. Of the STMS markers developed, 25 polymorphic markers were used to analyze the intraspecific genetic diversity within 36 geographically diverse chickpea accessions. The 25 primer pairs amplified single loci producing a minimum of 2 and maximum of 11 alleles. A total of 159 alleles were detected with an average of 6.4 alleles per locus. The observed and expected heterozygosity values averaged 0.32 (0.08–0.91) and 0.74 (0.23–0.89) respectively. The UPGMA based dendrogram was able to distinguish all the accessions except two accessions from Afghanistan establishing that microsatellites could successfully detect intraspecific genetic diversity in chickpea. Further, cloning and sequencing of size variant alleles at two microsatellite loci revealed that the variable numbers of AG repeats in different alleles were the major source of polymorphism. Point mutations were found to occur both within and immediately upstream of the long tracts of perfect repeats, thereby bringing about a conversion of perfect motifs into imperfect or compound motifs. Such events possibly occurred in order to limit the expansion of microsatellites and also lead to the birth of new microsatellites. The microsatellite markers developed in this study will be useful for genetic diversity analysis, linkage map construction as well as for depicting intraspecific microsatellite evolution. 相似文献
14.
Mark A. Renshaw John C. Patton Caird E. RexroadIII John R. Gold 《Conservation Genetics》2007,8(4):1009-1011
Thirteen nuclear-encoded dinucleotide microsatellites were characterized from a genomic DNA library of greater amberjack,
Seriola dumerili. The microsatellites include 12 perfect-repeat motifs and one imperfect-repeat motif. The number of alleles at the 13 microsatellites
among a sample of 29 fish ranged from 3 to 25; gene diversity (expected heterozygosity) ranged from 0.296 to 0.948, while
observed heterozygosity ranged from 0.276 to 0.897. Following Bonferroni correction, genotypes at all 13 microsatellites fit
expectations of Hardy-Weinberg equilibrium. One pairwise comparison of microsatellites deviated significantly from expectations
of genotypic equilibrium, suggesting that these two microsatellites may be linked. Greater amberjack support commercial and
recreational fisheries along both the Atlantic and Gulf coasts of the U.S. and represent a species with potential for worldwide
aquaculture. The microsatellites developed will be useful for conservation and population genetic studies of ‘wild’ and domesticated
populations of greater amberjack. 相似文献
15.
C. Epplen Eduardo J. M. Santos João F. Guerreiro Paul van Helden Jörg T. Epplen 《Human genetics》1997,99(3):399-406
Although microsatellite typing is the dominant method in genome research and indirect gene diagnosis, precise relationships
of exonic and adjacent simple repeat polymorphisms are not known. We investigated exon 2 sequences of HLA-DRB1 genes and their neighbouring (GT)n(GA)m repeats including the intervening single copy spacer. DRB1 is the most polymorphic protein-coding locus in man and all vertebrates investigated. The entire DRB1 variability exists in exon 2. DRB1 genes in different haplotype groups (DR1, DR51, DR52, DR8 and DR53) are accompanied by characteristic modifications of the
(GT)n(GA)m block (3′ to group-specific single copy spacers). Among more than 520 alleles analysed, > 100 different types of microsatellites
were observed. The perfect (GT)n and (GA)m blocks vary in length and may be partly ‘degenerated’, mostly in a subgroup-specific manner. Interestingly, the extent of
microsatellite diversity varies in given DRB1 alleles. While the microsatellites of the DR7, DR9 alleles and in the DR1 group are virtually invariant, in DR4 and DR13,
in particular, simple repeats appear hypervariable with at least 15 or 17 different length alleles, respectively. Comparing
Caucasians, Bushmen and South American Indians, the microsatellite variation in identical DRB1 alleles (e.g. DRB1*0102, 03 011, 1302) is smaller than within any of the DR groups in Caucasians. Taken together, extremely polymorphic DRB1 exons evolve in concert with certain variants of an exceptionally well-preserved microsatellite.
Received: 8 October 1996 相似文献
16.
Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs) 总被引:14,自引:0,他引:14
M. R. Thomas N. S. Scott 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1993,86(8):985-990
Microsatellite repeat sequences were investigated as sequenced-tagged site (STS) DNA markers to determine the potential for genetic analysis of the grapevine genome. The PCR-generated markers detect codominant alleles at a single locus or site in the genome. The marker type is very informative detecting high heterozygosity (69%–88%) within individual grapevine cultivars and high genetic variation between cultivars, making it a useful marker type for plant genome mapping and genome typing. For five loci a screening of 26 V. vinifera cultivars found 13, 12, 8, 5, and 4 different length alleles respectively with some alleles more common than others. The genomic DNA sequences surrounding microsatellite sequences were conserved within the genus permitting STS primers to amplify STSs from other Vitis species. These Vitis species were found to have some unique alleles not present in V. vinifera. 相似文献
17.
B. D. Dow M. V. Ashley H. F. Howe 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1995,91(1):137-141
The objective of this study was to ascertain the usefulness of polymerase chain reaction (PCR)-based microsatellite analysis for studying pollination and parentage in a wind-pollinated temperate tree. A small insert genomic library of the bur oak (Quercus macrocarpa) was constructed and screened for the presence of (CA/GT)
n
and (GA/CT)
n
repeats. The proportion of positive clones yielded estimates of 3×105 such dinucleotide repeats per genome, roughly comparable to abundances reported in other eukaryotic genomes. Thirteen positive clones were sequenced. In contrast to mammalian genomes, the (GA/CT)
n
motif was more abundant than the (CA/GT)
n
motif in these clones. The (GA/CT)
n
repeats also showed longer average repeat length (mean n=16.2 versus 7.3), suggesting that they are better candidates for yielding polymorphic genetic markers in oak genomes. Indeed, a survey of adult bur oaks and offspring in a small stand in northern Illinois at 3 of these (GA/CT)
n
microsatellite loci revealed Mendelian inheritance and extremely high levels of polymorphism, with the number of alleles at each locus ranging from 11–20 and heterozygosity ranging from 0.66 to 0.75. These results, indicating that (GA/CT)
n
microsatellites are both abundant and highly polymorphic in the bur oak genome, suggest that such genetic markers have tremendous potential for applications for studies of parentage, pollination and dispersal in temperate trees. 相似文献
18.
We isolated novel dinucleotide, trinucleotide, and tetranucleotide microsatellites from the genome of Asian sea bass (Lates
calcarifer). Two genomic DNA libraries were established, one was enriched for (CA)n repeats, while the other for (GATA)n,
(GACA)n, and (AAC)n repeats. Sixty clones containing an insert between 250 and 1000 bp in size were sequenced from each library;
altogether 50 (43%) of them contained microsatellites. Forty microsatellites were characterized in 16 unrelated Asian sea
bass individuals. Twenty-eight of them (70%) showed specific amplification and polymorphism. The allele number per loci varied
between 2 and 20 with an average of 5.3, while expected heterozygosity ranged from 0.31 to 0.95 with an average of 0.64. At
some loci allele sizes spread over a wide range (>100 bp). No significant correlation (r = 0.23, df = 31, P > 0.05) was found
between the repeat number and the number of alleles. A whole broodstock containing 170 individuals was analyzed by using 8
selected polymorphic microsatellites. The average number of alleles per locus was 11.8 (range, 4–21). The expected heterozygosity
ranged from 0.57 to 0.90 with an average of 0.75, while the fixation index was 0.02. Genetic similarity between individuals
ranged from 0 to 0.72. Comparison of allele frequencies between the broodstock and the 24 nonrelated individuals revealed
some unique alleles. 相似文献
19.
T. L. Maguire K. J. Edwards P. Saenger R. Henry 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,101(1-2):279-285
An enriched microsatellite library of the mangrove species Avicennia marina was constructed, in which 85.8% of the clones contained microsatellite sequences. Of the microsatellite repeat sequences
isolated, 55.0% were di-nucleotides, 34.2% were tri-nucleotides, 50.0% were perfect, 24.2% were imperfect, and 15.0% were
compound. Four different di-nucleotide repeats were isolated with repeat lengths ranging from 5 to 33; ten different tri-nucleotide
repeats were isolated with repeat lengths ranging from 3 to 25. The most common di-nucleotide was the AC/TG repeat; the most
common tri-nucleotide was the CCG/GGC repeat. Sixteen microsatellite sequences were selected for primer design, and 6 primers
were selected to investigate the polymorphism detected among 15 individuals of A. marina from three natural populations in Australia. A total of 40 alleles were detected at 6 microsatellite loci. The number of
alleles per microsatellite locus ranged from 5 to 13. On average, 7 alleles were detected per locus. All microsatellite loci
showed high levels of gene diversity (heterozygosity), with values ranging from 0.53 to 0.88; the mean value of gene diversity
was 0.70. Microsatellite loci were also tested for conservation across Avicennia species. There was a decline in amplification success with increasing divergence between Avicennia species. The results indicate that microsatellites are abundant in the Avicennia genome and can be valuable genetic markers for assessing the effects of deforestation and forest fragmentation in mangrove
communities, which is an important issue for mangrove conservation and afforestation schemes.
Received: 8 June 1999 / Accepted: 21 September 1999 相似文献
20.
Manish Roorkiwal Atul Grover Prakash C. Sharma 《Molecular genetics and genomics : MGG》2009,282(2):205-215
Studies on microsatellite distribution and divergence in related genomes contribute towards understanding of genome evolution
in eukaryotes. Despite the availability of whole genome sequences of four rice genomes, occurrence and significance of microsatellites
in the rice genome has remained a relatively unexplored area of research. We have aligned genomes of two rice subspecies i.e.
indica and japonica to understand the trends of microsatellite conservation and divergence in the rice genome. Nearly 62% of the indica microsatellites were also found in the japonica genome. Occurrence of microsatellites showed a negative association with that of retrotransposons. Microsatellites repeat
unit length and sequence showed direct influence on the microsatellite locus length. Further, microsatellite allele length
was also influenced by the sequence characteristics of the neighbouring regions. CCG repeats were most conserved microsatellite
sequences across the different syntenic regions in the two rice genomes and often showed association with CpG islands. Our
study suggested that microsatellite distribution is not only governed by a balance between replication slippage and point
mutations as proposed earlier, but also by the microsatellite motif sequence and characteristics of microsatellite neighbouring
regions in the genome. Thus, this study is likely to prove an important reference for understanding the process of microsatellite
evolution and dynamics in the two rice subspecies. 相似文献