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1.
T. Koike S. Kato Y. Shimamoto K. Kitamura S. Kawano K. Ueda T. Mikami 《Plant biology (Stuttgart, Germany)》1998,111(1):87-91
The amount and distribution of mitochondrial (mt) DNA restriction fragment length polymorphism was determined among individual tree samples of two Japanese beech species, Fagus crenata and F.japonica. Individual plants were collected from 16 F. crenata populations throughout the range of the species, and from three F. japonica populations. We detected enough variation to characterize eleven and three chondriome types in F. crenata and F.japonica, respectively. The grouping of beech chondriome types based upon the cladistic analysis of mtDNA polymorphism allowed us to recognize the apparent geographical patterns of mtDIMA diversity: the resulting three main groups occupied distinct geographic areas. This geographic differentiation is likely to reflect the history of the Japanese beech forests after the last glacial period of the Pleistocene. In addition, the mtDNA polymorphism encountered within F. crenata encompassed all the variation observed in F.japonica. Our result suggests the need for re-evaluation of their phylogenetic relationships. 相似文献
2.
María Calero-Riestra Fernando Alda Jose Antonio Dávila Jesús T. García 《European Journal of Wildlife Research》2012,58(1):379-383
New microsatellite loci for Tawny Pipit Anthus campestris were isolated from a genomic library. We were able to unambiguously score six loci: two were dinucleotide, one trinucleotide,
two tetranucleotide and one pentanucleotide that turned out to be sex-linked. Four out of six loci were polymorphic with 7–23
alleles in our population and an observed heterozygosity ranging between 0.286 and 0.936. Cross-utility of these markers was
tested in other 17 steppe-bird species of six families. In addition, 16 microsatellite loci developed for other species were
tested for cross-species amplification in A. campestris. Eight microsatellite markers were successfully amplified; seven of them were polymorphic with 2–43 alleles and an observed
heterozygosity of 0.040–0.863. Overall, 14 functional locus markers have been characterized for A. campestris that could be useful for future studies of paternity, genetic variability and population structure. 相似文献
3.
S. Siju K. Dhanya S. Syamkumar B. Sasikumar T. E. Sheeja A. I. Bhat V. A. Parthasarathy 《Molecular biotechnology》2010,44(2):140-147
Expressed sequence tags (ESTs) from turmeric (Curcuma longa L.) were used for the screening of type and frequency of Class I (hypervariable) simple sequence repeats (SSRs). A total
of 231 microsatellite repeats were detected from 12,593 EST sequences of turmeric after redundancy elimination. The average
density of Class I SSRs accounts to one SSR per 17.96 kb of EST. Mononucleotides were the most abundant class of microsatellite
repeat in turmeric ESTs followed by trinucleotides. A robust set of 17 polymorphic EST–SSRs were developed and used for evaluating
20 turmeric accessions. The number of alleles detected ranged from 3 to 8 per loci. The developed markers were also evaluated
in 13 related species of C. longa confirming high rate (100%) of cross species transferability. The polymorphic microsatellite markers generated from this
study could be used for genetic diversity analysis and resolving the taxonomic confusion prevailing in the genus. 相似文献
4.
Marta Dubreuil Federico Sebastiani Maria Mayol Santiago C. González-Martínez Miquel Riba Giovanni G. Vendramin 《Conservation Genetics》2008,9(6):1665-1668
Seven polymorphic nuclear microsatellite markers for Taxus baccata L. (English yew) were developed using an enriched-library method. An additional polymorphic SSR was obtained by testing eight
primer pairs from the congeneric species Taxus sumatrana. Mendelian inheritance for the seven Taxus baccata SSRs was proved by genotyping 17 individuals and 124 megagametophytes (conifer seed haploid tissue). A total of 96 individuals
from 5 different populations (10–26 samples per population) were used to estimate genetic diversity parameters. High levels
of genetic diversity, with values ranging from 0.533 to 0.929 (6–28 alleles per SSR) were found. No linkage disequilibrium
between pairs of loci was detected. All loci but one showed significant departures from Hardy–Weinberg equilibrium. Excess
of homozygosity was probably due to high inbreeding in English yew populations, an outcome of low effective population size
and/or fragmented distribution. Highly polymorphic SSRs will be used to conduct population genetic studies at different geographical
scales and to monitor gene flow. 相似文献
5.
The ecological significance of architectural patterns for saplings ofFagus crenata andFagus japonica co-occurring in a secondary oak forest were evaluated by comparing the size and shape of leaves, trunks and crowns.Fagus japonica saplings were different fromF. crenata saplings in some architectural properties: (i) the leaf area and specific leaf area were larger; (ii) the ratio of sapling
height to trunk length was lower, indicating greater leaning of the trunk; and (iii) the projection area of the crown was
larger and the leaf area index lower indicating less mutual shading of leaves. These architectural features indicated thatF. japonica saplings were more shade tolerant thanF. crenata andF. crenata saplings were superior toF. japonica for growth in height and could, therefore, utilize sunlight in the upper layer. An erect trunk inF. crenata and a leaning trunk inF. japonica may be important characteristics associated with the regenerations patterns of each species; regeneration from seedlings
under canopy gaps in the former and vegetative regeneration by sprouting in the latter. 相似文献
6.
Saneyoshi Ueno Yuriko Taguchi Nobuhiro Tomaru Yoshihiko Tsumura 《Conservation Genetics》2009,10(5):1477-1485
Fagus crenata Blume is widely distributed throughout Japanese cool-temperate deciduous broad-leaved forests, but there are two divergent
groups of populations in areas with contrasting winter climates separated by Japan’s Central Mountain Range. To facilitate
investigations of adaptive genetic differentiation of the species using potentially functional genes, we have collected Expressed
Sequence Tags and developed Simple Sequence Repeat markers using a cDNA library constructed from cambium and surrounding tissues.
In total, 270 primer pairs were designed, and 87 of the corresponding loci showed polymorphism in 16 individuals, with 2–21
alleles per locus and expected heterozygosities ranging from 0.06 to 0.97. EST-SSR markers developed in the present study
will be useful for genomic analyses of F. crenata populations. 相似文献
7.
A total of 12 polymorphic microsatellite loci were developed and characterized for a Chinese medicinal plant, Epimedium brevicornum (Berberidaceae). A genomic DNA enrichment protocol was used to isolate microsatellite loci and polymorphism was explored
using 38 individuals from one natural population. The observed number of alleles ranged from 2–14. The ranges of observed
and expected heterozygosity were 0.00–0.83 and 0.15–0.88, respectively. In addition, successful cross-species amplification
of this set of microsatellite markers in other four medicinal Epimedium species suggested that they would provide a useful tool for the genetic and conservation studies of Epimedium species. 相似文献
8.
Ardisia crenata, an evergreen shrub native to East Asia, has been a serious invasive plant to the southeastern USA. Here 13 polymorphic microsatellite
loci were isolated and characterized from an enrichment genomic library of A. crenata. The average allele number of these microsatellites was four per locus, ranging from two to seven. The ranges of observed
and expected heterozygosity were 0.000–1.000 and 0.239–0.789, respectively. These microsatellite markers will be useful for
investigating population genetics and reproductive ecology of A. crenata. 相似文献
9.
Cheng-Yu Hung Kuo-Hsiung Wang Chi-Chun Huang Xun Gong Xue-Jun Ge Tzen-Yuh Chiang 《Conservation Genetics》2008,9(3):779-781
We report 11 novel microsatellite primer pairs for the wild tea, Camellia sinensis (L.) O. Kuntze forma formosensis Kitamura. These simple sequence repeat markers were tested in 24 samples collected from wild tea populations, and in cultivars and
C. japonica. The number of alleles ranged from 4 to18. The expected (H
E) and observed (H
O) heterozygosity were 0.687–0.946 and 0.042–0.792, respectively. All loci were significantly deviated from Hardy-Weinberg
expectations due to the heterozygote deficiency, indicating a dramatic loss of genetic polymorphisms in the rare species.
Significant LD was discovered in most loci. These primers may provide a tool for understanding demography and population structure
in wild tea. 相似文献
10.
Microsatellite polymorphism in natural populations of wild emmer wheat,Triticum dicoccoides,in Israel 总被引:5,自引:0,他引:5
Fahima T Röder MS Wendehake K Kirzhner VM Nevo E 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2002,104(1):17-29
Diversity in 20 microsatellite loci of wild emmer wheat, Triticum dicoccoides, was examined in 15 populations (135 genotypes) representing a wide range of ecological conditions of soil, temperature, and
water availability, in Israel and Turkey. An extensive amount of diversity at microsatellite loci was observed despite the
predominantly selfing nature of this plant species. The 20 Gatersleben wheat microsatellites (GWM), representing 13 chromosomes
of genomes A and B of wheat, revealed a total of 364 alleles, with an average of 18 alleles per GWM marker (range: 5–26).
The proportion of polymorphic loci per population averaged 0.90 (range: 0.45– 1.00); genic diversity, He, averaged 0.50 (range 0.094– 0.736); and Shannon’s information index averaged 0.84 (range 0.166–1.307). The coefficients
of genetic distance between populations were high and averaged D=1.862 (range 0.876–3.320), an indication of sharp genetic divergence over short distances. Interpopulation genetic distances
showed no association with geographic distance between the population sites of origin, which ruled out a simple isolation
by distance model. Genetic dissimilarity values between genotypes were used to produce a dendrogram of the relationships among
wild wheat populations by the unweighted pair-group method with arithmetic averages (UPGMA). The results showed that all the
wild emmer wheat populations could be distinguished. Microsatellite analysis was found to be highly effective in distinguishing
genotypes of T. dicoccoides, originating from diverse ecogeographical sites in Israel and Turkey, with 88% of the 135 genotypes correctly classified into
sites of origin by discriminant analysis. Our present microsatellite results are non-random and in agreement with the previously
obtained allozyme and RAPD patterns, although the genetic-diversity values obtained with microsatellites are much higher.
Significant correlates of microsatellite markers with various climatic and soil factors suggest that, as in allozymes and
RAPDs, natural selection causes adaptive microsatellite ecogeographical differentiation, not only in coding, but most importantly
in non-coding genomic regions. Hence, the concept of ”junk DNA” needs to be replaced by at least partly regulatory DNA. The
obtained results suggest that microsatellite markers are useful for the estimation of genetic diversity in natural populations
of T. dicoccoides and for the tagging of agronomically important traits derived from wild emmer wheat.
Received: 27 February 2001 / Accepted: 22 March 2001 相似文献
11.
Udupa SM Robertson LD Weigand F Baum M Kahl G 《Molecular & general genetics : MGG》1999,261(2):354-363
A set of 12 randomly selected (TAA)n microsatellite loci of the cultivated chickpea (Cicer arietinum L.) were screened in a worldwide sample comprising 72 landraces, four improved cultivars and two wild species of the primary
gene pool (C. reticulatum and C. echinosperum) to determine the level and pattern of polymorphism in these populations. A single fragment was amplified from all the accessions
with each of 12 sequence-tagged microsatellite site markers, except for one locus where no fragment was obtained from either
of the two wild species. There was a high degree of intraspecific polymorphism at these microsatellite loci, although isozymes,
conventional RFLPs and RAPDs show very little or no polymorphism. Overall, the repeat number at a locus (excluding null alleles)
ranged from 7 to 42. The average number of alleles per locus was 14.1 and the average genetic diversity was 0.86. Based on
the estimates obtained, 11 out of the 12 frequency distributions of alleles at the loci tested can be considered to be non-normal.
A significant positive correlation between the average number of repeats (size of the locus) and the amount of variation was
observed, indicating that replication slippage may be the molecular mechanism involved in generation of variability at the
loci. A comparison between the infinite allele and stepwise mutation models revealed that for 11 out of the 12 loci the number
of alleles observed fell in between the values predicted by the two models. Phylogenetic analysis of microsatellite polymorphism
in C. arietinum showed no relationship between accession and geographic origin, which is compatible with the recent expansion of this crop
throughout the world.
Received: 18 September 1998 / Accepted: 2 December 1998 相似文献
12.
Eleven microsatellite loci have been developed from Fagus longipetiolata and the loci were characterized for 21 individuals. All eleven loci were polymorphic, with 2–8 alleles and an average of
4.8 per locus. The observed (H
O) and expected (H
E) heterozygosities were 0.053–0.714 and 0.355–0.856, respectively. There was significant deviation from Hardy–Weinberg equilibrium
at two loci. No locus pair had significant linkage disequilibrium. Cross-species amplifications of the markers were also tested
in three other congeneric species. 相似文献
13.
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
14.
Chi-Chun Huang Kuo-Hsiang Hung Tsai-Wen Hsu Kuo-Hsiung Wang Chi-Yung Lin Tzen-Yuh Chiang 《Conservation Genetics》2008,9(5):1333-1335
Fatsia polycarpa Hayata (Araliaceae) is an element of evergreen forests at middle elevations in Taiwan, also representing the southern limitation
in distribution of the genus. In this study, we described the development of 11 microsatellite loci from F. polycarpa in Taiwan for genetic studies. These new markers were tested in 20 individuals of 5 populations of the woody species. The
number of alleles ranged from 9 to 18. The expected (H
E
) and observed (H
O
) heterozygosities were 0.80–0.95 and 0.10–0.75, respectively. Six of the 11 microsatellite loci are significantly deviated
from Hardy–Weinberg expectations likely due to the population structure within samples. No linkage disequilibrium were observed
from pairwise comparisons of loci.
Chi-Chun Huang, Kuo-Hsiang Hung, and Tsai-Wen Hsu contributed equally to this article. 相似文献
15.
Sarah E. Haas Jordan V. Smith Rebecca T. Kimball A. M. Clark 《Conservation Genetics》2009,10(5):1393-1395
Populations of brown-headed nuthatches (Sitta pusilla) are declining throughout the species range. Here we characterize twelve polymorphic microsatellite loci for this species.
Analysis of 32 presumably unrelated individuals from a single population revealed an average of 14.9 alleles per locus (range
4–25), an average observed heterozygosity of 0.74 (range 0.52–0.94) and an average polymorphic information content of 0.80
(range 0.57–0.95). We anticipate that these microsatellite markers will be useful for population genetic and behavioral studies
on the brown-headed nuthatch and closely related species. 相似文献
16.
Woo-Jin Kim Young-Ok Kim Bo-Hye Nam Hee Jeong Kong Eun-Mi Park Jung-Ha Kang Jeong-Ho Lee Kyung-Kil Kim 《Conservation Genetics》2009,10(4):1105-1111
Expressed sequence tags (ESTs) can be used to identify microsatellite markers. We developed 81 polymorphic microsatellite
markers from 4,940 ESTs of the olive flounder, Paralichthys olivaceus. Out of 100 EST-derived microsatellites for which PCR primers were designed, 81 loci were polymorphic in 30 individuals from
a single natural population with 2–28 (mean 10.6) alleles per locus. The observed and expected heterozygosities of these loci
were 0.033–1.000 and 0.033–0.965, respectively. Segregation analysis within a mapping family revealed non-amplifying null
alleles at five loci. These new EST-derived microsatellite markers should be useful for population genetic analyses, pedigree
tracing and constructing a linkage map for olive flounder. 相似文献
17.
The Brown Eared-pheasant (Crossoptilon mantchuricum) is an endangered species endemic to China. Here we developed eight microsatellite loci using a modified biotin-capture method.
In the analyses of 28 individuals sampled, the number of alleles per locus ranged from four to nine. The expected (H
E) and observed (H
O) heterozygosities were 0.466–0.825 and 0.619–0.847, respectively. Results that eight microsatellite loci were highly polymorphic
indicated that these markers are sufficiently powerful to address such questions as genetic diversity and population genetic
structure of C. mantchuricum. 相似文献
18.
Soto-Cerda Braulio J. Carrasco Rodrigo A. Aravena Gabriela A. Urbina Hector A. Navarro Cristell S. 《Plant Molecular Biology Reporter》2011,29(3):753-759
One of the major concerns in genetic characterization and breeding of cultivated flax is the lack of informative microsatellite
markers (SSRs). In this regard, the development of SSRs using molecular methods might be time-consuming, laborious, and expensive.
On the other hand, using bioinformatics to mine sequences in public databases enables a cost-effective discovery of SSRs.
A total of 3,242 Linum usitatissimum genomic sequences were surveyed for the identification of SSRs. Among them, 118 non-redundant sequences containing repeats
were selected for designing primers. The most abundant motifs were tri- (72.4%) and dinudeotide (16.6%), within which AGG/CCT
and AG/CT were predominant. Primers were tested for polymorphism in 60 L. usitatissimum cultivars/accessions including 57 linseed and three fiber flax. Eighty-eight pairs gave amplifications within the expected
size range while 60 pairs were found to be polymorphic. The mean number of alleles amplified per primer was 3.0 (range, 2–8;
180 total alleles). The mean polymorphism information content (PIC) value was 0.39 (range, 0.06–0.87), and the highest average
PIC was observed in dinucleotide SSRs (0.41). The SSR data mining presented here demonstrates the usefulness of in silico
development of microsatellites. These novel genomic SSR markers could be used in genetic diversity studies, the development
of genetic linkage maps, quantitative trait loci mapping, association mapping, and marker-assisted selection. 相似文献
19.
Transferability of olive microsatellite loci across the genus <Emphasis Type="Italic">Olea</Emphasis> 总被引:3,自引:0,他引:3
Rallo P Tenzer I Gessler C Baldoni L Dorado G Martín A 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2003,107(5):940-946
The transferability of microsatellite markers developed for olive cultivars (Olea europaea L.) has been tested and confirmed in the Olea complex. Thirty two genotypes, belonging to different taxa of the genus Olea, have been analyzed with four olive SSRs. Positive amplifications at all loci were obtained in 13 taxa (at least one accession per species). Sixty seven different alleles have been detected at the four loci analyzed. Polymorphic products have been observed at the inter- and intra-species level. Some SSR loci have shown multiple amplification products in some species. The high number of unique alleles has allowed the unambiguous discrimination of most accessions. Similarity coefficients and relationships among the Olea taxa have been calculated based on SSR amplification results. The reliability of SSRs as markers for intra-species variability evaluation has been confirmed while their use to explore relationships at the inter-species level is discussed, being dependent on the locus analyzed.Communicated by H.F. Linskens 相似文献
20.
To develop a microsatellite marker set applicable to genome-wide screening of cynomolgus monkeys (Macaca fascicularis), 148 microsatellite markers were selected from the human genome database. The polymorphisms and inheritance of PCR products
were determined by screening twenty unrelated monkeys and by analysis of three families, respectively. As a result, 106 primers
(72%) gave PCR products of the size expected for humans and rhesus monkeys. Among these products, polymorphism and single-gene
inheritance in cynomolgus monkeys was observed for 66 markers (62%). The average number of alleles at the 66 polymorphic loci
was 5.86 (range 2–10), and average heterozygosity was 0.63 (range 0.10–0.88). This is the first report of microsatellite markers
for cynomolgus monkeys. Chromosomal mapping of these markers is now in progress. 相似文献