共查询到20条相似文献,搜索用时 15 毫秒
1.
Kurt Weising Raymond W. M. Fung D. Jeannette Keeling Ross G. Atkinson Richard C. Gardner 《Molecular breeding : new strategies in plant improvement》1996,2(2):117-131
We have identified a set of informative microsatellite markers for genome analysis in kiwifruit and related Actinidia species. A small-insert genomic library was constructed from Actinidia chinensis DNA, and screened for microsatellites. About 1.2% of the total colonies hybridised to a (GA)8 probe, 0.4% to (GT)8, and 0.1% to a mixture of three different trinucleotide repeat probes, (CAA)5, (GAA)5 and (CTA)5. From the DNA sequences of 35 hybridising clones, 18 primer pairs were designed, and used to amplify genomic DNA from 38 individual plants, representing 30 different accessions of ten Actinidia species. The banding patterns for most of the dinucleotide repeats showed a high degree of polymorphism in the diploid and tetraploid A. chinensis, and in the hexaploid A. deliciosa (kiwifruit). Heterozygosity levels of up to 100% were found among eight diploid accessions of A. chinensis examined, and the number of different-sized bands among all the species varied from 3 to 36 for each microsatellite. One simple CT microsatellite gave 21 bands with sizes suggesting that the number of repeats ranged from 9 to 37. The highest number of bands (36) and the largest size variation (>100 bp) were observed with a complex microsatellite harbouring four different repeat motifs. The majority of primer pairs amplified bands from most of the ten Actinidia species tested. The most polymorphic primer pairs were used successfully to fingerprint a range of closely related varieties of kiwifruit (A. deliciosa).Abbreviations PCR
polymerase chain reaction
- RFLP
restriction fragment length polymorphism
- VNTR
variable number of tandem repeats 相似文献
2.
Wöhrmann T Weising K 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2011,123(4):635-647
A collection of 5,659 expressed sequence tags (ESTs) from pineapple [Ananas comosus (L.) Merr.] was screened for simple sequence repeats (EST-SSRs) with motif lengths between 1 and 6 bp. Lower thresholds of
15, 7 and 5 repeat units were used to define microsatellites of the mono-, di-, and tri- to hexanucleotide repeat type, respectively.
Based on these criteria, 696 SSRs were identified among 3,389 EST unigenes, together representing 2,840 kb. This corresponds
to an average density of one SSR every 4.1 kb of non-redundant EST sequences. Dinucleotide repeats were most abundant (38.4%
of all SSRs) followed by trinucleotide repeats (38.1%). Flanking primer pairs were designed for 537 EST-SSR loci, and 49 of
these were screened for their functionality in 12 accessions of A. comosus, 14 accessions of 5 additional Ananas species and 1 species of Pseudananas. Distinct PCR products of the expected size range were obtained with 36 primer pairs. Eighteen loci analyzed in more detail
were all polymorphic in pineapple, and primer pairs flanking these loci also generated PCR products from a wide range of genera
and species from six subfamilies of the Bromeliaceae. The potential to reveal polymorphism in a heterologous target species
was demonstrated in Deuterocohnia brevifolia (subfamily Pitcairnioideae). 相似文献
3.
D. Dimitrova O. Georgiev C. Valkova B. Atanassova L. Karagyozov 《Biologia Plantarum》2008,52(1):149-152
Seven clones containing (CTG)n/(CAG)n repeats (n ≥ 4) were isolated by screening Lycopersicon esculentum genomic DNA. Four of the clones contained more than one simple sequence repeat (SSR). The SSRs were analyzed in several L. esculentum cultivars after polymerase chain reaction (PCR) amplification. No length variations were observed, suggesting considerable
locus stability. Five clones are from transcribed regions, which might explain the lack of cultivar variations. However the
conservation of CTG repeats was limited as differences in some transcribed loci were registered between L. pennellii and other Lycopersicon species. It is noted that in Lycopersicon trinucleotide repeat variation might be used for species identification. 相似文献
4.
Over the last 20 years, microsatellites have revolutionized the study of cooperation in the social insects. The Polistes paper wasps have been an important model system for investigations of cooperative behavior. Recently, an expressed sequence
tag (EST) library has been developed for P. metricus, allowing researchers to investigate the genetic basis of cooperative behavior in primitive social insect societies for the
first time. We searched these freely available EST sequences for microsatellite motifs. This represents a relatively new approach
to the development of microsatellite loci that allows for the development of a greater number of loci at less expense. We
designed 32 PCR primer pairs, of which 23 amplified PCR products and 18 were polymorphic. These loci exhibited high levels
of polymorphism, comparable to anonymous loci isolated via screens of partial genomic libraries. Thus, they are appropriate
for population genetic studies as well as the reconstruction of colony genetic structure. A screen of the entire EST database
found a total of 708 di-, tri-, tetra- and penta-nucleotide repeats with large repeat units typical of polymorphic loci and
at least 30 bp of flanking sequence for primer design. This pool of potential loci represents a new genetic tool for P. metricus, as well as Polistes more generally, as there is great promise for cross amplification in other species. 相似文献
5.
Characterization of trinucleotide SSR motifs in wheat 总被引:21,自引:0,他引:21
Song QJ Fickus EW Cregan PB 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2002,104(2-3):286-293
Length differences among trinucleotide-based microsatellite alleles can be more easily detected and frequently produce fewer
”stutter bands” as compared to dinucleotide-based microsatellite markers. Our objective was to determine which trinucleotide
motif(s) would be the most-polymorphic and abundant source of trinucleotide microsatellite markers in wheat (Triticum aestivum L.). Four genomic libraries of cultivar ’Chinese Spring’ were screened with nine trinucleotide probes. Based on the screening
of 28550 clones, the occurrences of (CTT/GAA)
n
, (GGA/CCT)
n
, (TAA/ATT)
n
, (CAA/GTT)
n
, (GGT/CCA)
n
, (CAT/GTA)
n
, (CGA/GCT)
n
, (CTA/GAT)
n
, and (CGT/GCA)
n
repeats were estimated to be 5.4×104, 3.5×104, 3.2×104, 1.2×104, 6.3×103, 4.9×103, 4.5×103, 4.5×103 and 3.6×103, i.e., once every 293 kbp, 456 kbp, 500 kbp, 1.3 Mbp, 2.6 Mbp, 3.2 Mbp, 3.6 Mbp, 3.6 Mbp and 4.5 Mbp in the wheat genome,
respectively. Of 236 clones selected for sequencing, 38 (93%) (TAA/ATT)
n
, 30 (43%) (CTT/GAA)
n
, 16 (59%) (CAA/GTT)
n
, 3 (27%) (CAT/GTA)
n
and 2 (4%) (GGA/CCT)
n
clones contained microsatellites with eight or more perfect repeats. From these data, 29, 27 and 16 PCR primer sets were
designed and tested to the (TAA/ATT)
n
, (CTT/GAA)
n
and (CAA/GTT)
n
microsatellites, respectively. A total of 12 (41.4%) primers designed to (TAA/ATT)
n
, four (14.8%) to (CTT/GAA)
n
, and two (12.5%) to (CAA/GTT)
n
resulted in polymorphic markers. The results indicated that (TAA/ATT)
n
microsatellites would provide the most-abundant and the most-polymorphic source of trinucleotide microsatellite markers in
wheat.
Received: 17 February 2001 / Accepted: 31 May 2001 相似文献
6.
Ding-Qin Tang Jiang-Jie Lu Wei Fang Shan Zhang Ming-Bing Zhou 《Molecular breeding : new strategies in plant improvement》2010,25(2):299-311
Public sequence databases provide a rapid, simple and cost-effective source of microsatellite markers. We analyzed 1,532 bamboo
(Phyllostachys pubescens) sequences available in public domain DNA databases, and found 3,241 simple sequence repeat (SSR) loci comprising repeats
of two or more nucleotides in 920 genomic survey sequences (GSSs) and 68 cDNA sequences. This corresponded to one SSR per
336 bp of GSS DNA and one SSR per 363 bp of cDNA. The SSRs consisted of 76.6 and 74.5% dinucleotide repeats, 20.0 and 22.3%
trinucleotide repeats, and 3.4 and 3.2% higher-number repeats in the GSS DNA and cDNA sequences, respectively. The repeat
motif AG/CT (or GA/TC) was the most abundant. Nineteen microsatellite markers were developed from Class I and Class II SSRs,
showing that the limited polymorphism in Ph. pubescens cultivars and provenances could be attributed to clonal propagation of the bamboo plant. The transferability of the microsatellites
reached 75.3%, and the polymorphism of loci successfully transferred was 66.7% for six additional Phyllostachys species. Microsatellite PBM014 transferred successfully to all six species, showed rich polymorphism, and could serve as species-specific
alleles for the identification of Phyllostachys interspecies hybrids. 相似文献
7.
R. Kölliker E. S. Jones M. C. Drayton M. P. Dupal J. W. Forster 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,102(2-3):416-424
Highly informative molecular markers, such as simple sequence repeats (SSRs), can greatly accelerate breeding programs. The
aim of this study was to develop and characterise a comprehensive set of SSR markers for white clover (Trifolium repens L.), which can be used to tag genes and quantitative trait loci controlling traits of agronomic interest. Sequence analysis
of 1123 clones from genomic libraries enriched for (CA)
n
repeats yielded 793 clones containing SSR loci. The majority of SSRs consisted of perfect dinucleotide repeats, only 7% being
trinucleotide repeats. After exclusion of redundant sequences and SSR loci with less than 25 bp of flanking sequence, 397
potentially useful SSRs remained. Primer pairs were designed for 117 SSR loci and PCR products in the expected size range
were amplified from 101 loci. These markers were highly polymorphic, 88% detecting polymorphism across seven white clover
genotypes with an average allele number of 4.8. Four primer pairs were tested in an F2 population revealing Mendelian segregation. Successful cross-species amplification was achieved in at least one out of eight
legume species for 46 of 54 primer pairs. The rate of successful amplification was significantly higher for Trifolium species when compared to species of other genera. The markers developed in this study not only provide valuable tools for
molecular breeding of white clover but may also have applications in related taxa.
Received: 3 April 2000 / Accepted: 12 May 2000 相似文献
8.
Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats. 总被引:9,自引:0,他引:9
Luciana Rossini Pinto Karine Miranda Oliveira Eugênio César Ulian Antonio Augusto Franco Garcia Anete Pereira de Souza 《Génome》2004,47(5):795-804
Sugarcane microsatellites or simple sequence repeats (SSR) were developed in an economical and practical way by mining EST databases. A survey in the SUCEST (sugarcane EST) database revealed a total of 2005 clusters out of 43,141 containing SSRs. Of these, 8.2% were dinucleotide, 30.5% were trinucleotide, and 61.3% were tetranucleotide repeats. Except for dinucleotides, the CG-rich motif types were the most common. Differences in abundance of trinucleotide motif types were observed between EST-SSRs and those isolated from sugarcane genomic libraries. Among the different cDNA libraries used for EST sequencing, SSRs were more frequent in the ones derived from leaf roll (LR). Twenty-three out of 30 tested SSRs produced scorable polymorphisms in 18 sugarcane commercial clones. These EST-SSRs showed a moderate level of polymorphism with some SSRs producing unique fingerprints. The number of alleles observed among the 18 clones evaluated varied from 2 to 15, with an average of 6.04 alleles/locus. The polymorphism information content (PIC) values ranged from 0.28 to 0.90 with a mean of 0.66. The EST-SSRs screened over both parents (SP 80-180; SP 80-4966) and 6 F1 individuals produced 52 segregating markers that could potentially be used for sugarcane mapping. The EST-SSRs were found in clusters that had significant homology to proteins involved in important metabolic pathways such as sugar biosynthesis, proving that EST-SSRs are a valuable tool for the construction of a functional sugarcane map. 相似文献
9.
10.
Tian Yuan Ji-Rui Gu Wen-Bo Gu Jiang Wu Shao-Rong Ge Heng Xu 《Molecular biology reports》2011,38(3):2059-2065
Adenylosuccinate lyase (ADSL) is a bifunctional enzyme acting in de novo purine synthesis and purine nucleotide recycling.
In the present study, we have constructed a grass carp (Ctenopharyngodon idella) intestinal cDNA library that has over 2.3 × 105 primary clones. An expressed sequence tag (EST) of grass carp adenylosuccinate lyase (gcADSL) gene was screened from this
library. Both 5′-RACE and 3′-RACE were carried out in order to obtain the complete cDNA sequence, which contains a 1,446 bp
open reading frame encoding 482 amino acids about 54.552 kDa. The deduced amino acid sequence shares high homology with its
vertebrate counterparts, which shares 94% similarity with zebrafish, 81% with African clawed frog as well as chicken, 77%
with human and 76% with mouse. This gcADSL genomic sequence, consisted of 13 exons and 12 introns, is 8,557 bp in size. Real-time
quantitative PCR analysis revealed that the highest expression level of gcADSL was detected in muscle and the lowest in gill.
In western blotting analysis, His6-tagged gcADSL protein expressed in Escherichia coli could be recognized not only by an anti-His6-tag monoclonal antibody but also by an anti-human ADSL polyclonal antibody, indicating immunological crossreactivity occurs
between grass carp and human ADSL protein. 1,082 bp 5′-flanking region sequence was cloned and analyzed. 相似文献
11.
Microsatellites (i.e., simple sequence repeats [SSRs]) are highly variable genetic markers that are widely used at an intraspecific
level in population genetic studies. Here we employed an enrichment strategy for microsatellite isolation by using microsatellite
oligoprobes and magnetic capture of the fragments (Fischer and Bachmann, 1998) inProsopis chilensis (Mol.) Stuntz (Fabaceae). We analyzed the obtained level of enrichment by sequencing 120 enriched genomic fragments. A total
of 521 SSR motives were detected. According to specific search criteria (SSR motifs ≥3 repeat units and ≥6 bp length), 95.8%
of the clones contained SSR motifs. Of these, 7.8% showed homology to chloroplast sequences and 92.2% to nuclear sequences.
When regarding only nuclear SSRs with 5 or more repeat units and a minimum length of 10 bp, the level of enrichment was 30.8%.
A FASTA search against the European Molecular Biology Laboratory (EMBL) database univocally revealed 4 clones in transcribed
regions, 102 clones in genomic regions with unknown function, and 9 clones in chloroplast regions. Among the loci with longer
repeat units (≥10 bp, ≥5 repeat units), 3 were in transcribed regions and 65 were in other genomic regions. We discuss the
applicability of these markers for population genetic studies. 相似文献
12.
Mammadov JA Steffenson BJ Maroof MA 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2005,111(8):1651-1660
The rapidly growing expressed sequence tag (EST) resources of species representing the Poacea family and availability of comprehensive sequence information for the rice (Oryza sativa) genome create an excellent opportunity for comparative genome analysis. Extensive synteny between rice chromosome 1 and
barley (Hordeum vulgare L.) chromosome 3 has proven extremely useful for saturation mapping of chromosomal regions containing target genes of large-genome
barley with conserved orthologous genes from the syntenic regions of the rice genome. Rph5 is a gene conferring resistance to the barley leaf rust pathogen Puccinia hordei. It was mapped to chromosome 3HS, which is syntenic with rice chromosome 1S. The objective of this study was to increase
marker density within the sub-centimorgan region around Rph5, using sequence-tagged site (STS) markers that were developed based on barley ESTs syntenic to the phage (P1)-derived artificial
chromosome (PAC) clones comprising the distal region of rice chromosome 1S. Five rice PAC clones were used as queries in a
blastn search to screen 375,187 barley ESTs. Ninety-four non-redundant EST sequences were identified from the EST database
and used as templates to design 174 pairs of primer combinations. As a result, 9 barley EST-based STS markers were incorporated
into the ‘Bowman’ × ‘Magnif 102’ high-resolution map of the Rph5 region. More importantly, six markers, including five EST-derived STS sequences, were found to co-segregate with Rph5. The results of this study demonstrate the usefulness of rice genomic resources for efficient deployment of barley ESTs for
marker saturation of targeted barley genomic regions. 相似文献
13.
We present 30 microsatellite loci isolated from expressed sequence tag (EST) and genomic libraries in Vaccinium corymbosum L. Allele number per locus in 11 tetraploid and one diploid V. corymbosum accessions ranged from two to 15 (mean = 8.16) in 24 single‐locus simple sequence repeats (SSRs). Cross‐species amplification in a panel of 12 species representing nine sections ranged from 30 to 100% (mean = 83%). 相似文献
14.
15.
X. Wang R. Trigiano M. Windham B. Scheffler T. Rinehart J. Spiers 《Tree Genetics & Genomes》2008,4(3):461-468
Abundant, codominant simple sequence repeats (SSRs) markers can be used for constructing genetic linkage maps and in marker-assisted
breeding programs. Enrichment methods for SSR motifs were optimized with the ultimate aim of developing numerous loci in flowering
dogwood (C. florida L.) genome. Small insert libraries using four motifs (GT, CT, TGG, and AAC) were constructed with C. florida ‘Cherokee Brave’ deoxyribonucleic acid (DNA). Colony polymerase chain reaction (PCR) of 2,208 selected clones with three
primers we reported previously indicated that 47% or 1,034 of the clones harbored one of the four targeted SSR motifs. Sequencing
the putative positive clones confirmed that nearly 99% (1,021 of 1,034) of them contained the desired motifs. Of the 871 unique
SSR loci, 617 were dinucleotide repeats (70.8%), and 254 were trinucleotide or longer repeats (29.2%). In total, 379 SSR loci
had perfect structure, 237 had interrupted, and 255 had compound structure. Primer pairs were designed from 351 unique sequences.
The ability of the 351 SSR primer pairs to amplify specific loci was evaluated with genomic DNA of ‘Appalachian Spring’ and
‘Cherokee Brave’. Of these primers, 311 successfully amplified product(s) with ‘Cherokee Brave’ DNA, 21 produced weak or faint
products, and 19 did not amplify any products. Additionally, 218 of the 311 primers pairs revealed polymorphisms between the
two cultivars, and 20 out of 218 primers detected an average of 13.7 alleles from 38 selected Cornus species and hybrids. These SSR loci constitute a valuable resource of ideal markers for both genetic linkage mapping and
gene tagging of flowering dogwood.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
16.
M. WOODHEAD J. RUSSELL J. SQUIRRELL P. M. HOLLINGSWORTH L. CARDLE M. GIBBY W. POWELL 《Molecular ecology resources》2007,7(4):631-634
A set of expressed sequence tag–simple sequence repeat (EST‐SSR) loci has been developed for Arabidopsis lyrata ssp. petraea. From 768 root cDNA clones, 126 microsatellites, including di‐, tri‐, tetra‐ and pentanucleotide repeat motifs were identified and primers were designed to 24 EST‐SSRs. Eleven loci were subsequently screened on 150 individuals sampled from five natural populations, which revealed three to nine alleles per locus (mean 5.36) and expected heterozygosity (HE) estimates ranging from 0.046 to 0.698. Significant deviations from random mating were observed at 10 EST‐SSR loci, likely due to inbreeding (global FIS = 0.151) and population structure (global FST = 0.246). 相似文献
17.
Zhengqiu Cai Mary Guisinger Hyi-Gyung Kim Elizabeth Ruck John C. Blazier Vanity McMurtry Jennifer V. Kuehl Jeffrey Boore Robert K. Jansen 《Journal of molecular evolution》2008,67(6):696-704
The plastid genome of Trifolium subterraneum is 144,763 bp, about 20 kb longer than those of closely related legumes, which also lost one copy of the large inverted repeat
(IR). The genome has undergone extensive genomic reconfiguration, including the loss of six genes (accD, infA, rpl22, rps16, rps18, and ycf1) and two introns (clpP and rps12) and numerous gene order changes, attributable to 14–18 inversions. All endpoints of rearranged gene clusters are flanked
by repeated sequences, tRNAs, or pseudogenes. One unusual feature of the Trifolium
subterraneum genome is the large number of dispersed repeats, which comprise 19.5% (ca. 28 kb) of the genome (versus about 4% for other
angiosperms) and account for part of the increase in genome size. Nine genes (psbT, rbcL, clpP, rps3, rpl23, atpB, psbN, trnI-cau, and ycf3) have also been duplicated either partially or completely. rpl23 is the most highly duplicated gene, with portions of this gene duplicated six times. Comparisons of the Trifolium plastid genome with the Plant Repeat Database and searches for flanking inverted repeats suggest that the high incidence
of dispersed repeats and rearrangements is not likely the result of transposition. Trifolium has 19.5 kb of unique DNA distributed among 160 fragments ranging in size from 30 to 494 bp, greatly surpassing the other
five sequenced legume plastid genomes in novel DNA content. At least some of this unique DNA may represent horizontal transfer
from bacterial genomes. These unusual features provide direction for the development of more complex models of plastid genome
evolution.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
18.
Gustavo C. S. Kuhn Trude Schwarzacher John S. Heslop-Harrison 《Molecular genetics and genomics : MGG》2010,284(4):251-262
The genome of species from the buzzatii cluster (buzzatii complex, repleta group) is hosted by a number of satellite DNAs (satDNAs) showing contrasting structural characteristics, genomic organization
and evolution, such as pBuM-alpha (~190 bp repeats), pBuM-alpha/beta (~370 bp repeats) and the DBC-150 (~150 bp repeats). In the present study, we aimed to investigate the evolution of these
three satDNAs by looking for homologous sequences in the genome of the closest outgroup species: Drosophila martensis (buzzatii complex). After PCR, we isolated and sequenced 9 alpha, 8 alpha/beta and 11 DBC-150 sequences from this species. The results were compared to all pBuM and DBC-150 sequences available in literature.
After D. martensis split from the buzzatii cluster some 6 Mya, the three satDNAs evolved differently in the genome of D. martensis by: (1) maintenance of a collection of major types of ancestral repeats in the genome (alpha); (2) fixation for a single major type of ancestral repeats (alpha/beta) or (3) fixation for new divergent species-specific repeat types (DBC-150). Curiously, D. seriema and D. martensis, although belonging to different and allopatric clusters, became independently fixed for the same major type of alpha/beta ancestral repeats, illustrating a rare case of parallelism in satDNA evolution. The contrasting pictures illustrate the diversity
of evolutionary pathways a satDNA can follow, defining a “non-regular orbit” with outcomes difficult to predict. 相似文献
19.
20.
Characterization and analysis of microsatellite loci in Elymus caninus (Triticeae: Poaceae) 总被引:4,自引:0,他引:4
G.-L. Sun B. Salomon R. V. Bothmer 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,96(5):676-682
Microsatellites are highly variable DNA sequences that can be used as markers for the genetic analysis of plants. The potential
of microsatellite markers for use in a genetic diversity study in Elymus species was evaluated. Genomic libraries of Elymus caninus were constructed. The libraries were screened with two dinucleotide, (GA)n and (GT)n, and two trinucleotide repeats, (TCT)n
and (CAC)n. A total of 19 positive clones were found for the two dinucleotide repeats; no positive clone was found for the
trinucleotide repeats. Positive clones were sequenced to confirm the presence of microsatellites and to generate polymerase
chain reaction (PCR) primers based on the sequences flanking the microsatellite. All sequenced (GA)n clones have repeats of
n>10; over half of the (GT)n microsatellites have n<10 repeats. Primer pairs were designed and evaluated for 8 selected microsatellites. PCR products were amplified from 15
Elymus caninus accessions. The number of alleles found for the eight loci varied from 1 for ECGA89 and ECGT35 to 13 for ECGA22, as determined by non-denaturing polyacrylamide electrophoresis. Six microsatellite loci were found to be polymorphic in
E. caninus. The eight primer pairs were tested on three other species; seven were successful in amplifying DNA from Elymus alaskanus and E. mutabilis, and four amplified DNA from E. caucasicus. Based on these results, microsatellites appear to be useful markers in detecting variation in E. caninus.
Received: 8 September 1997/Accepted: 6 October 1997 相似文献