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1.
Development of microsatellite markers for white spruce (Picea glauca) and related species 总被引:9,自引:0,他引:9
R. B. Hodgetts M. A. Aleksiuk A. Brown C. Clarke E. Macdonald S. Nadeem D. Khasa E. Macdonald 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,102(8):1252-1258
We report the development of 13 primer pairs that allow the unambiguous amplification of 15 microsatellite (SSR) loci in white
spruce (Picea glauca). Fourteen of these loci were polymorphic in trees sampled at three geographically separated regions of western Canada. Segregation
analysis carried out on these loci confirmed a Mendelian inheritance pattern for all except two, which showed significant
segregation distortion. All of these primer pairs amplified SSR loci in at least one of the other Picea species tested [black spruce (P. mariana), red spruce (P. rubens), Norway spruce (P. abies), Colorado spruce (P. pungens), sitka spruce (P. sitchensis) and Engelmann spruce (P. engelmannii)]. Given the important commercial and ecological roles of these species, this set of markers will be invaluable for their
management, the improvement of commercially important traits, and the study of their ecology and genetics.
Received: 18 August 2000 / Accepted: 28 September 2000 相似文献
2.
R. Pastorelli M. J. M. Smulders W. P. C. VANT Westende B. Vosman R. Giannini C. Vettori G. G. Vendramin 《Molecular ecology resources》2003,3(1):76-78
Using an enrichment procedure, we cloned microsatellite repeats from European beech (Fagus sylvatica L.) and developed primers for the amplification of microsatellite markers. Six polymorphic loci were characterized which produced 3–21 alleles in 70 individuals from one Italian population, with an observed heterozygosity between 0.58 and 0.85. All six loci amplified fragments which were polymorphic in the closely related species, Fagus orientalis, also. Owing to their very high degree of variation, these markers should be very useful in gene flow studies of these species. 相似文献
3.
N. Fujii N. Tomaru K. Okuyama T. Koike T. Mikami K. Ueda 《Plant Systematics and Evolution》2002,232(1-2):21-33
CpDNA variation in Japanese beech, Fagus crenata (Fagaceae), was studied in 45 populations distributed throughout the species' range. Two cpDNA regions were sequenced: the
non-coding region between the trnL (UAA) 5′exon and trnF (GAA), and the trnK region (including matK). Thirteen distinct cpDNA haplotypes were recognized and each haplotype was found to be geographically structured. Two major
clades (I and II+III) were revealed in phylogenetic analyses among the haplotypes using F. sylvatica as an outgroup. The haplotypes of Clade I were distributed mainly along the Japan Sea side of the Japanese Archipelago, while
those of Clade II+III occurred chiefly along the Pacific Ocean side. Consequently, the distribution of the two major cpDNA
clades suggests that there were two migration routes in the history of F. crenata; one along the Japan Sea and the other along the Pacific Ocean side of the Japanese Islands.
Received March 19, 2001 Accepted November 22, 2001 相似文献
4.
Tsutom Hiura 《Trees - Structure and Function》1998,12(5):274-280
Relationships between leaf or shoot size, number, and arrangement in response to light were investigated to test the hypothesis
that these characteristics are linked. In order to test this hypothesis, the divergence in allometry and shoot dynamics in
saplings of Japanese beech (Fagus crenata) obtained from four populations and having different leaf sizes were examined in a nursery under both full sun and shade
conditions. Trees with different leaf sizes also showed large differences in canopy structure, particularly when shade-grown
saplings were compared. The final leaf mass distributions of the large-leaf populations were conical or “bottom - heavy”,
while those of the small-leaf populations were planar or “top - heavy”. The slope of the allometric relations between leaf
mass and shoot and branch mass in small-leaved populations were steeper than those in large-leaf populations. The four populations
were classified into two growth types: populations producing a few large leaf and shoot modules corresponded to “stem growth
type”, and those producing many small leaf and shoot modules corresponded to “leaf growth type”. These kinds of intra-specific
variation in architecture and growth of F. crenata trees may influence the structure and dynamics of forests in accordance with differences in competitive ability or sensitivity
to disturbances such as windstorm.
Received: 18 March 1997 / Accepted: 21 October 1997 相似文献
5.
Ten microsatellite loci are described in Araucaria cunninghamii, the first reported in the Araucariaceae. Eight were tested in sections Eutacta and Bunya, which diverged more than 200 MYA, and to the sister genus Agathis. Specific amplification products within the expected size range were obtained for six to eight loci in section Eutacta (depending on species), five loci in section Bunya and three loci in Agathis. Two of the loci (CRCAc1 and CRCAc2, both GA repeats) produced specific amplification products in all taxa, with orthology
confirmed by sequence analysis. The repeats were perfect in all taxa. The flanking sequences were extremely conserved, with
sequence divergence of 0% to 2.0% within Araucaria species and 2.9% to 7.5% between Araucaria and Agathis. These microsatellites represent some of the most conserved microsatellite loci reported in plants. This may be due to a
low evolutionary rate in Araucariaceae genome or the loci may be closely associated with highly conserved, unreported genes.
Received January 14, 2002; accepted June 14, 2002 Published online: February 4, 2003
Current address: The Centre for Identification and Diagnostics, School of Life Sciences, The University of Queensland, Brisbane 4072, Australia. 相似文献
6.
Microsatellite markers can yield high‐resolution genetic profiles for individual identification, and for parentage analysis, when evaluating gene dispersal in populations. Fagus crenata is an important dominant species in the cool temperate forests in Japan, and although many studies on the species have been conducted the patterns of gene dispersal via pollen and seeds are poorly understood. In order to be better informed about gene dispersal in Fagus crenata, we have developed 16 new microsatellite loci from an enriched library of genomic DNA. These 16 loci were highly variable, with 3–40 alleles per locus and an expected heterozygosity value of 0.11–0.98. 相似文献
7.
Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci 总被引:20,自引:3,他引:20
H. Akagi Y. Yokozeki A. Inagaki T. Fujimura 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,94(1):61-67
Microsatellites consisting of AT repeats are highly polymorphic in rice genomes and can be used to distinguish between even
closely related japonica cultivars in Japan. Polymorphisms of 20 microsatellite loci were determined using 59 japonica cultivars,
including both domestic and modern Japanese cultivars. Although the polymorphisms of these 20 microsatellite loci indicated
that the Japanese cultivars were genetically quite similar, microsatellites consisting of AT repeats showed high gene diversity
even among such closely related cultivars. Combinations of these hypervariable microsatellites can be employed to classify
individual cultivars, since the microsatellites were stable within each cultivar. An identification system based on these
highly polymorphic microsatellites could be used to maintain the purity of rice seeds by eliminating contamination. A parentage
diagnosis using 17 polymorphic microsatellite loci clearly demonstrated that plants which carried desired chromosome regions
had been selected in breeding programs. Thus, these hypervariable microsatellites consisting of AT repeats should promote
the selection of plants which carry desired chromosomes from genetically similar parents. Backcrossing could also help to
eliminate unnecessary chromosome regions with microsatellite polymorphisms at an early stage in breeding programs.
Received: 8 July 1996 / Accepted: 12 July 1996 相似文献
8.
We isolated 13 microsatellite loci from Euchresta japonica, an endangered shrub species that grows in warm-temperate forests in East Asia. Of these 13 loci, only one was codominant and polymorphic with five alleles. Cross-species amplification in a related species, E. formosana, detected nine of these loci, all of which were codominant and polymorphic with 2 to 9 alleles. These markers will facilitate further studies on the genetic characteristics of these two Euchresta species. 相似文献
9.
Development and characterization of microsatellite markers in Cucumis 总被引:21,自引:0,他引:21
Y. Danin-Poleg N. Reis G. Tzuri N. Katzir 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,102(1):61-72
This study provides a set of useful SSR markers and describes their development, characterization and application for diversity
studies.Sixty one Cucumis SSR markers were developed, most of them (46) from melon (Cucumis melo L.) genomic libraries. Forty of the markers (30 melon and 10 cucumber SSRs) were evaluated for length polymorphism in a sample
of 13 melon genotypes and 11 cucumber (Cucumis sativus L.) genotypes. PCR-amplification revealed up to six size alleles among the melon genotypes and up to five alleles among the
cucumber genotypes, with mean gene-diversity values of 0.52 and 0.28 for melon and cucumber, respectively. These differences
are in accordance with the known narrower genetic background of the cucumber. SSR data were applied to phylogenetic analysis
among the melon and cucumber genotypes. A clear distinction between the ’exotic’ groups and the sweet cultivated groups was
demonstrated in melon. In cucumber, separation between the two sub-species, C.sativus var. sativus and C.sativus var. hardwickii,was obtained. Conservation of SSR loci between melon and cucumber was proven by sequence comparisons.
Received: 17 April 2000 / Accepted: 16 May 2000 相似文献
10.
Development and characterization of microsatellite markers in black poplar (Populus nigra L.) 总被引:6,自引:0,他引:6
J. van der Schoot M. Pospíšková B. Vosman M. J. M. Smulders 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,101(1-2):317-322
Using an enrichment procedure, we have cloned and sequenced microsatellite loci from black poplar (Populus nigra L.) and developed primers for sequence-tagged microsatellite (STMS) analysis. Twelve primer pairs for dinucleotide repeats
produced fragments of sufficient quality which were polymorphic in P. nigra. Some of them also showed amplification in other Populus species (P. deltoides, P. tricocarpa, P. tremula, P. tremuloides, P. candicans, and/or P. lasiocarpa). The best nine and (GT) (GA) microsatellite markers were tested on a set of 23 P. nigra genotypes from all over Europe. The microsatellites were highly polymorphic, with 10–19 different alleles per microsatellite
locus among these 23 genotypes. WPMS08 sometimes amplified three fragments. Using the other eight marker loci, the level of
heterozygosity among the plants was on average 0.71 (range 0.25–1.00). The microsatellite markers developed will be useful
for screening the genetic diversity in natural populations and in gene bank collections.
Received: 21 October 1999 / Accepted: 24 November 1999 相似文献
11.
D. M. Spooner M. L. Ugarte P. W. Skroch 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,95(5-6):764-771
The more than 200 wild and cultivated species relatives of potato (Solanum sect. Petota) present a valuable germplasm base for cultivar improvement. However, species boundaries and interrelationships within sect.
Petota are controversial, inhibiting the efficient organization of the many germplasm collections of these species. One controversy
involves questions of species boundaries and interrelationships of S. astleyi and S. boliviense. Solanum boliviense is narrowly endemic to two Departments in southern Bolivia, and S. astleyi is known only from one site entirely within the range of this species, where they co-occur. Both species are diploid and
morphologically very similar. Artificial hybrids between them are fully fertile, and the species putatively hybridize naturally.
These data have been interpreted to designate them as separate species or as S. astleyi an ecotype of S. boliviense. Putative progenitors of S. astleyi are S. boliviense, S. megistacrolobum subsp. megistacrolobum, and S. megistacrolobum subsp. toralapanum. We evaluated interrelationships among these species with random amplified polymorphic DNA’s (RAPDs) generated for 2 accessions
of S. astleyi and 14 accessions of S. boliviense. These represent the entire geographic range of the former species and nearly the entire range of the latter. We also analyzed
1 accession each of S. acaule subsp. acaule, S. acaule subsp. aemulans, S. albicans, S. berthaultii, S. megistacrolobum subsp. megistacrolobum, S. megistacrolobum subsp. toralapanum, S. raphanifolium, S. sogarandinum, and S. sparsipilum. Phenetic analyses of the RAPD data show S. astleyi and S. boliviense to form two distinct groups and to be more similar to each other than to any of the other species investigated, suggesting
that S. astleyi and S. boliviense are sister taxa. The divergence of S. astleyi and S. boliviense relative to other species examined suggests that they are worthy of taxonomic recognition at the subspecies, rather than
species level, and we propose the new combination S. boliviense subsp. astleyi.
Received: 21 November 1996 / Accepted: 18 April 1997 相似文献
12.
Development, characterization and mapping of microsatellite markers in Eucalyptus grandis and E. urophylla 总被引:6,自引:0,他引:6
R. P. V. Brondani C. Brondani R. Tarchini D. Grattapaglia 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,97(5-6):816-827
We report on the development, genetic characterization and linkage mapping of a battery of SSR (simple sequence repeat) loci
in Eucalyptus grandis and E. urophylla. This study reveals the abundance of SSRs in Eucalyptus, the very high information content of these markers for mapping and individual identification, and demonstrates the feasibility
of constructing a comprehensive microsatellite-based linkage map for Eucalyptus. Primer sequence for a set of 20 highly informative EMBRA (Eucalyptus microsatellites from Brazil) loci are made available together with their map position and estimates of the expected heterozygosity
and allele size range in these two species. Using genomic library enrichment and anchored-PCR screening prior to sequencing,
the efficiency of SSR marker locus development was 63% from sequencing data to operationally useful SSR loci. Absolute transportability
between the two species and very high levels of allelic variability and expected heterozygosity (H) were seen at all SSR loci
surveyed. The number of alleles per locus ranged from 9 to 26 with an average of 16.3±4.8. The average H of 15 loci was 0.86±0.04,
0.83±0.08 and 0.89±0.04, respectively, for E. urophylla, E. grandis and the combined two-species estimate. In the mapping analysis 16 out of 20 marker loci segregated in a fully informative
configuration, allowing the determination of synteny of six homologous linkage groups between the two species. The availability
of transportable, multiallelic, PCR-based co-dominant SSR loci represents a dramatic improvement in our ability to carry out
detailed population genetic analysis and to search, understand, and manipulate allelic variation at QTLs (quantitative trait
loci) in species of Eucalyptus.
Received: 16 March 1998 / Accepted: 22 March 1998 相似文献
13.
Betula platyphylla var. japonica is a typical pioneer tree species in the secondary succession in northern Japan. We describe the cloning and characterization of 13 polymorphic, codominant microsatellite loci isolated from this species. These polymorphic loci had 2–8 alleles per locus and a range of expected heterozygosities from 0.050 to 0.808. 相似文献
14.
Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. 总被引:1,自引:0,他引:1
C. Tessier J. David P. This J. M. Boursiquot A. Charrier 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,98(1):171-177
The aim of this study was to develop a cultivar identification tool based on molecular analysis and a statistical approach.
From the PIC parameter we defined the D parameter, which evaluates the efficiency of a primer for the purpose of identification
of varieties; i.e. the probability that two randomly chosen individuals have different patterns. D can be used to compare
different types of markers even if only the allelic frequencies are known. We used this parameter to develop an algorithm
for selecting the optimal combination of primers necessary to identify a set of varieties. The optimal combination of primers
determined for a small elite group of varieties applied on a larger set induces a risk of confusion involving 1 of the elite
varieties. We estimated the risk of confusion using the D value of each primer of the combination. We applied this methodology
on a set of 224 varieties of Vitis vinifera screened with 21 RAPD primers and two microsatellite loci. The discriminating power of the primers did not only depend on
the number of patterns it generates but also on the frequencies of the different patterns. A combination of 8 primers (6 RAPD
and two microsatellite) was found to be optimum for the discrimination of these 224 varieties. A subset of 38 elite varieties
was also investigated. The determined optimal combination of 4 primers (3 RAPD and one microsatellite) applied on the 224
varieties gave 9 risks of confusion involving 1 of the elite varieties. Confusion can happen between varieties with the same
origin as well as between varieties of very diverse geographical origins.
Received: 22 April 1998 / Accepted: 9 June 1998 相似文献
15.
A new species of Erysiphe sect. Uncinula is described and illustrated from Japan. Erysiphe wadae sp. nov., found on Japanese beech (Fagus crenata, Fagaceae), is characterized by having two types of appendages, i.e., a long (true) appendage arising from the equatorial
zone of the ascomata, and a short appendage arising from the upper part of the ascomata. This characteristic is shared by
E. simulans, E. australiana, E. flexuosa, E. liquidambaris, E. prunastri, and E. togashiana. Erysiphe wadae differs from the latter five species in its brown-colored appendage. Erysiphe simulans is most similar to E. wadae, but differs in its loosely uncinate appendage and smaller number of ascospores. Identity of the nucleotide sequences of
the rDNA ITS region is 92.3% between the two species. The significance of the two types of appendage in taxonomy and phylogeny
of powdery mildews is discussed based on molecular phylogenetic analysis.
Received: November 8, 2002 / Accepted: January 29, 2003
Acknowledgments We are grateful to Drs. Yukio Harada and Hideki Naito for help in collecting powdery mildew specimens; Dr. Uwe Braun for
providing the specimen of E. flexuosa; and Mr. Tetsuya Hirata and Miss Sanae Matsuda for nucleotide sequences of E. togashiana and E. flexuosa. This work was partially supported by a Grant-in-Aid for Scientific Research (No. 13660047) from Ministry of Education, Culture,
Sports, Science and Technology, Japan. 相似文献
16.
A. Gallois J. C. Audran M. Burrus 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,97(1-2):211-219
We assessed the genetic relationships between members of the Fagaceae family by RAPDs in order to better ascertain the taxonomic status of a very particular population of Fagus sylvatica, the ‘tortuosa’ variety. Intra- and inter-population Nei and Li’s mean genetic distances were compared, and the genetic relationships
between individuals were clarified on dendrograms by the Neighbor joining method. RAPD analysis was first conducted on three
species from three genera, Quercus petraea, Castanea sativa, and Fagus sylvatica, in order to develop an efficient RAPD protocol. The variety level was then studied, and a general tendency of the individuals
to cluster by variety was observed. Individuals also clustered by geographic locations, but the genetic distances between
populations were not correlated to the distances between sites. Finally, we compared the common beech and ‘tortuosa’ varieties
from two different locations, Verzy and Süntel. Both populations from one location were closer than the same variety from
two sites. This last result is in agreement with those previously obtained with isozymes. Hypotheses concerning the origin
of the ‘tortuosa’ variety are discussed.
Received: 9 January 1998 / Accepted: 25 February 1998 相似文献
17.
Applicability of inter-simple sequence repeat polymorphisms in wheat for use as DNA markers in comparison to RFLP and RAPD markers 总被引:43,自引:0,他引:43
T. Nagaoka Y. Ogihara 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,94(5):597-602
Inter-simple sequence repeat polymorphic DNA (ISSR) was evaluated for its applicability as a genetic marker system in wheat.
PCR was carried out with primers that annealed to simple sequence repeats. The resultant products were subjected to agarose-gel
electrophoresis, and the banding patterns were compared among six wheat accessions containing diploid, tetraploid, and hexaploid
members. Out of 100 examined, 33 primers produced distinguishable as well as polymorphic bands in each of the six accessions.
Although most of the primers that gave distinct bands (30 primers out of 33) contained dinucleotide repeats, each of the primers
with tri-, tetra-, and penta-nucleotide motifs also yielded discrete bands. Primers based on (AC)n repeats gave the most polymorphic bands. In total, 224 polymorphic bands were found in the comparison between Einkorn wheats
whereas, on the average, 120 polymorphic bands were detected between common wheats. ISSR primers produced several times more
information than RAPD markers. The extent of band polymorphism was similar to that of RFLP markers, and greater than that
of RAPDs. The genetic relationships of wheat accessions estimated by the polymorphism of ISSR markers were identical with
those inferred by RFLP and RAPD markers, indicating the reliability of ISSR markers for estimation of genotypes. These polymorphic
bands are potential candidates as novel markers for use in linkage-map construction in wheat. The characteristic features
of ISSR markers, i.e. polymorphism, generation of information and ease of handling, suggest their applicability to the analysis
of genotypes as well as to the construction of PCR-based genome maps of wheats.
Received: 15 September 1996 / Accepted: 25 October 1996 相似文献
18.
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
19.
20.
The development of oat microsatellite markers and their use in identifying relationships among Avena species and oat cultivars 总被引:1,自引:0,他引:1
C. D. Li B. G. Rossnagel G. J. Scoles 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,101(8):1259-1268
Microsatellites have many desirable marker properties. There has been no report of the development and utilization of microsatellite
markers in oat. The objectives of the present study were to construct oat microsatellite-enriched libraries, to isolate microsatellite
sequences and evaluate their level of polymorphism in Avena species and oat cultivars. One hundred clones were isolated and sequenced from three oat microsatellite-libraries enriched
for either (AC/TG)
n
, (AG/TC)
n
or (AAG/TTC)
n
repeats. Seventy eight clones contained microsatellites. A database search showed that 42% of the microsatellite flanking
sequences shared significant homology with various repetitive elements. Alu and retrotransposon sequences were the two largest
groups associated with the microsatellites. Forty four primer sets were used to amplify the DNA from 12 Avena species and 20 Avena sativa cultivars. Sixty two percent of the primers revealed polymorphism among the Avena species, but only 36% among the cultivars. In the cultivars, the microsatellites associated with repetitive elements were
less polymorphic than those not associated with repetitive elements. Only 25% of the microsatellites associated with repetitive
elements were polymorphic, while 46% of the microsatellites not associated with repetitive elements showed polymorphism in
the cultivars. An average of four alleles with a polymorphism information content (PIC) of 0.57 per primer set was detected
among the Avena species, and 3.8 alleles with a PIC of 0.55 among the cultivars. In addition, 54 barley microsatellite primers were tested
in Avena species and 26% of the primers amplified microsatellites from oat. Using microsatellite polymorphisms, dendrograms were constructed
showing phylogenetic relationships among Avena species and genetic relationships among oat cultivars.
Received: 1 November 1999 / Accepted: 14 April 2000 相似文献