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1.
Matsuoka Y Mitchell SE Kresovich S Goodman M Doebley J 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2002,104(2-3):436-450
To evaluate the performance of microsatellites or simple sequence repeats (SSRs) for evolutionary studies in Zea, 46 microsatellite loci originally derived from maize were applied to diverse arrays of populations that represent all the
diploid species of Zea and 101 maize inbreds. Although null phenotypes and amplification of more than two alleles per plant were observed at modest
rates, no practical obstacle was encountered for applying maize microsatellites to other Zea species. Sequencing of microsatellite alleles revealed complex patterns of mutation including frequent indels in the regions
flanking microsatellite repeats. In one case, all variation at a microsatellite locus came from indels in the flanking region
rather than in the repeat motif. Maize microsatellites show great variability within populations and provide a reliable means
to measure intraspecific variation. Phylogeographic relationships of Zea populations were successfully reconstructed with good resolution using a genetic distance based on the infinite allele model,
indicating that microsatellite loci are useful in evolutionary studies in Zea. Microsatellite loci show a principal division between tropical and temperate inbred lines, and group inbreds within these
two broad germplasm groups in a manner that is largely consistent with their known pedigrees.
Received: 10 February 2001 / Accepted: 21 May 2001 相似文献
2.
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
3.
Evaluation of allelic diversity at chloroplast microsatellite loci among common wheat and its ancestral species 总被引:14,自引:0,他引:14
T. Ishii N. Mori Y. Ogihara 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,103(6-7):896-904
Twenty four chloroplast microsatellite loci having more than ten mononucleotide repeats were identified from the entire chloroplast
DNA sequence of common wheat, Triticum aestivum cv Chinese Spring. For each microsatellite, a pair of primers were designed to produce specific PCR products in the range
of 100– 200 bp. The allelic diversity at the microsatellite loci was evaluated using 43 accessions from 11 Triticum and Aegilops species involved in wheat polyploid evolution. Polymorphic banding patterns were obtained at 21 out of 24 chloroplast microsatellite
loci. The three monomorphic microsatellites were found to be located in coding regions. For the polymorphic microsatellites,
the number of alleles per microsatellite ranged from 2 to 7 with an average of 4.33, and the diversity values (H) ranged from
0.05 to 0.72 with an average of 0.47. Significant correlations (P<0.01) were observed between the number of repeats and the number of alleles, and between the number of repeats and diversity
value, respectively. The genetic diversity explained by chloroplast microsatellites and nuclear RFLP markers were compared
using 22 tetraploid accessions. Although the number of alleles for nuclear RFLP markers was found to be higher than that for
chloroplast microsatellites, similar diversity values were observed for both types of markers. Among common wheat and its
ancestral species, the percentages of common chloroplast microsatellite alleles were calculated to examine their phylogenetic
relationships. As a result, Timopheevi wheat species were clearly distinguished from other species, and Emmer and common wheat
species were divided into two main groups, each consisting of a series of wild and cultivated species from tetraploid to hexaploid.
This indicates that the two types of chloroplast genomes of common wheat might have independently originated from the corresponding
types of wild and cultivated Emmer wheat species.
Received: 6 October 2000 / Accepted: 13 March 2001 相似文献
4.
Microsatellite length variation was investigated at a highly variable microsatellite locus in four species of Apodemus. Information obtained from microsatellite allele sequences was contrasted with allele sizes, which included 18 electromorphs.
Additional analysis of a 400-bp unique sequence in the flanking region identified 26 different haplotype sequences or ``true'
alleles in the sample. Three molecular mechanisms, namely, (1) addition/deletion of repeats, (2) substitutions and indels
in the flanking region, and (3) mutations interrupting the repeat, contributed to the generation of allelic variation. Size
homoplasy can be inferred for alleles within populations, from different populations of the same species, and from different
species. We propose that microsatellite flanking sequences may be informative markers for investigating mutation processes
in microsatellite repeats as well as phylogenetic relationships among alleles, populations, and species.
Received: 3 November 1999 / Accepted: 2 May 2000 相似文献
5.
K. Loridon B. Cournoyer C. Goubely A. Depeiges G. Picard 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,97(4):591-604
The objective of this work was to assess the degree of trinucleotide microsatellite length polymorphism in the selfing species
Arabidopsis thaliana. PCR amplifications of 12 microsatellite loci among 49 natural populations revealed between one to eight length variants
(alleles) for each locus. The average number of alleles per locus was four and the average genetic diversity index was 0.43.
Divergence between length variants was investigated at the nucleotide level. Several observations emerge from the sequence
data: (1) for most loci, length polymorphism results only from variations in the number of trinucleotide repeats; (2) for
a few others, some variability was noted in the flanking sequences; (3) for compound and interrupted loci containing two arrays
of trinucleotide repeats, length variations preferentially affect the longest one. Five of the Arabidopsis thaliana accessions were clearly composed of two sublines. In 2 other accessions, some heterozygous individual plants, probably resulting
from recent outcrosses, were found. A phylogenetic tree constructed on the basis of trinucleotide microsatellite allelic diversity
shows that genetic relationships among the accessions are not correlated with their geographic origin.
Received: 4 November 1997 / Accepted: 3 March 1998 相似文献
6.
Sridhar Vaddi Venkatesan Thiruvengadam Sunil Joshi Sushil Kumar Jalali Lakshmana Reddy Dhoranalapalli Chinnappareddy Padma Nimmakayala Yan Tomason Gopinath Vajja Umesh K. Reddy 《Entomologia Experimentalis et Applicata》2016,160(2):179-187
Nearly 5 000 aphid species damage crops, either by sucking plant sap or as disease‐transmitting vectors. Microsatellites are used for understanding molecular diversity and eco‐geographical relationships among aphid species. Expressed sequence tag (EST)‐microsatellite motifs were identified through an in silico approach using inbuilt simple sequence repeat mining tools in aphid EST dataset. Microsatellite mining revealed one in every five aphid genes as containing a repeat motif, and out of 9 290 EST microsatellites mined from Aphis gossypii Glover and Acyrthosiphon pisum (Harris) (both Hemiptera: Aphididae), 80% were of A and/or T (AT, ATA, AAT, AATA, and ATTT) motifs, and the rest contained G and/or C motifs. All microsatellite sequences were annotated using BLAST. Primers for EST microsatellites were designed using the Primer 3.0 tool. 106 primer pairs of both dinucleotide repeats (DNRs) and trinucleotide repeats (TNRs), representing open reading frames (ORFs) and untranslated regions (UTRs), were synthesized to amplify 15 aphid species belonging to the subfamily Aphidinae, collected from diverse hosts. Four hundred forty‐five polymorphic alleles were amplified. Fifty TNR and 23 DNR microsatellites amplified across the species studied. Polymorphism information content values of microsatellites ranged from 0.23 to 0.91, amplifying 2–16 alleles. Genetic similarity indices were estimated using the ‘NTSYS‐pc’ software package. Unweighted pair group with arithmetic mean and principal component analysis resolved taxonomic relationships of the aphid species studied. The new aphid microsatellites developed will provide valuable information to researchers to study Indian aphid species diversity and genetic relationships. 相似文献
7.
The evolutionary dynamics of the tetra-nucleotide microsatellite locus Spl-106 were investigated at the repeat and flanking sequences in 137 individuals of 15 Acipenseriform species, giving 93 homologous
sequences, which were detected in 11 out of 15 species. Twenty-three haplotypes of flanking sequences and three distinct types
of repeats, type I, type II and type III, were found within these 93 sequences. The MS-Align phylogenetic method, newly applied
to microsatellite sequences, permitted us to understand the repeat and flanking sequence evolution of Spl-106 locus. The flanking region of locus Spl-106 was highly conserved among the species of genera Acipenser, Huso and Scaphirhynchus, which diverged about 150 million years ago (Mya). The rate of flanking sequence divergence at the microsatellite locus Spl-106 in sturgeons is between 0.011% and 0.079% with an average at 0.028% per million years. Sequence alignment and phylogenetic
trees produced by MS-Align showed that both the flanking and repeat regions can cluster the alleles of different species into
Pacific and Atlantic lineages. Our results show a synchronous evolutionary pattern between the flanking and repeat regions.
Moreover, the coexistence of different repeat types in the same species, even in the same individual, is probably due to two
duplication events encompassing the locus Spl-106 that occurred during the divergence of Pacific lineage. The first occured before the diversification of Pacific species (121–96 Mya)
and led to repeat types I and II. The second occurred more recently, just before the speciation of A. sinensis and A. dabryanus (69–10 Mya), and led to repeat type III. Sequences in the same species with different repeat types probably corresponds to
paralogous loci. This study sheds a new light on the evolutionary mechanisms that shape the complex microsatellite loci involving
different repeat types. 相似文献
8.
A. Akkak V. Scariot D. Torello Marinoni P. Boccacci C. Beltramo R. Botta 《Biologia Plantarum》2009,53(1):164-166
Forty one simple sequence repeats were isolated from two microsatellite enriched libraries of date palm (Phoenix dactylifera L.). After screening, 17 selected microsatellite loci were characterized and evaluated on a set of 31 cultivars and clones
from Algerian and Californian germplasm. All primer pairs produced an amplification product of the expected size and detected
high polymorphism among the analysed samples. These nuclear simple sequence repeat (SSR) markers are expected to be a very
effective tool for evaluating genetic diversity in date palm germplasm. Acrosstaxa amplification showed the usefulness of
most SSR markers in 14 other species across the genus Phoenix. 相似文献
9.
This brief communication reports the identification of microsatellite loci in the economically important tick species Boophilus microplus. The data are potentially useful in distinguishing different strains of B. microplus. Eight polymorphic loci were isolated in larvae, male and female adults analysed individually from 12 field isolates and laboratory strains from Australia (n = 8), Brazil, Mexico, Papua New Guinea and Zimbabwe. Nucleotide sequencing of alleles at these microsatellite loci revealed that non-repeat bases interrupted dinucleotide and tetranucleotide repeats in some loci. Loci with non-repeat bases interrupting them were shorter compared with loci that were not interrupted. Thus the presence of non-repeat bases in a repeated sequence seems to constrain the evolution of additional repeats by slip-strand misparing at these loci. 相似文献
10.
van Treuren R; Kuittinen H; Karkkainen K; Baena-Gonzalez E; Savolainen O 《Molecular biology and evolution》1997,14(3):220-229
We examined microsatellite variation in two diploid, outcrossing relatives
of Arabidopsis thaliana, Arabis petraea and Arabis lyrata. The primer
sequences were derived from A. thaliana. About 50% (14 loci) of the A.
thaliana primers could successfully amplify microsatellites in the related
species. Analysis of microsatellite structure in the related species showed
that there had been large changes in the microsatellites: there were large
differences in repeat numbers and many of the A. thaliana simple repeats
were shorter in the related species. For the loci we compared, the related
species had a much lower level of variability at the microsatellites than
Japanese wild populations of A. thaliana. This is presumably related to the
different microsatellite structures, because allozyme data showed that the
outcrossing relatives were highly polymorphic compared to other outcrossing
herbaceous species. Use of microsatellites in assessing variability or
phylogenetic relationships between different species requires caution,
because changes in microsatellite structure may alter evolutionary rates.
相似文献
11.
The possibility to perform cross-species microsatellite amplification in birds was surveyed by analysing sets of primers developed from the swallow and the pied flycatcher genomes on a panel of 48 different bird species. In total, 162 cases (species/marker combinations) of heterologous amplification were recorded. Ten amplification products were sequenced and all were found to be true homologues of the original loci. There was a significant and negative relationship between microsatellite performance and evolutionary distance between the original species and the tested species. As a rough indicator of expected cross-species microsatellite performance we estimate that 50% of markers will reveal polymorphism in a species with a DNA-DNA hybridization δTmH value of 5 separating it from the original species. This corresponds to a divergence time of = 11 million years before present for passerine birds. The established relationship between performance and evolutionary distance agrees very well with data obtained from some mammalian species. The proportion of polymorphic loci among those markers that amplified decreased with increasing genetic distance, suggesting that few long repeats are preserved during evolution. One of the swallow markers, HrU2, amplified a specific product in all species analysed and will thus allow access to nuclear sequence data over a broad range of species. The only predictor of cross-species performance was the amount of non-specific amplification seen in the original species. An analysis of 10 species from within the family Hirundinidae with the swallow primers consistently revealed extensive polymorphism with average probabilities of identical genotypes ranging from 6 times 10-4 to 6 times 10-7. There were distinct allele frequency differences between the Hirundinidae species and we envisage that microsatellite cross-species amplification will be a useful tool in phylogeny construction and in species identification. 相似文献
12.
A. Depeiges C. Goubely A. Lenoir S. Cocherel G. Picard M. Raynal F. Grellet M. Delseny 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1995,91(1):160-168
The major simple sequence repeats present in the Arabidopsis genome were identified by Southern hybridizations with 49 oligonucleotide probes matching all the possible combinations of motifs up to 4 nucleotides long. The method used allowed us to perform all the hybridizations under the same temperature conditions. A good correlation was observed with the data obtained from database analysis, indicating that the method can be useful for identifying the major classes of microsatellite loci in species for which few or no sequence data are available. AG/CT, AAG/CTT, ATG/CAT and GTG/CAC are the major motifs present in the Arabidopsis genome that can be used as convenient probes to isolate microsatellite loci by screening libraries. AAG/CTT is the more frequent of these motifs, and its relative frequency in Arabidopsis is much higher than averagely found in the plant kingdom. About 8% of the cDNA clones from an immature silique library contains AG/CT, AAG/CTT or ATG/CAT microsatellite loci. Several microsatellite loci were isolated by screening genomic and cDNA libraries. Twenty-six tri-nucleotide loci were PCR amplified from four different ecotypes, and polymorphism was observed for 12 of them; 10 loci showing two alleles and 2 loci showing three alleles. 相似文献
13.
We provide a new and valuable marker to study species relationships and population genetics in order to trace evolutionary, ecological, and conservational aspects in the genus Aristolochia. Universal primers for amplification and subsequent sequencing of a chloroplast microsatellite locus inside the trnK intron are presented. Utility of the primers has been tested in 32 species representing all clades of Aristolochia, including population studies within the A. pallida complex, A. clusii and A. rotunda. The microsatellite region is characterized as a (AnTm)k repeat of 22–438 bp containing a combination of different repeats arranged as ‘cryptically simple’. 相似文献
14.
M. B. Jamjoom R. W. Ashford P. A. Bates S. J. Kemp H.A. Noyes 《Molecular ecology resources》2002,2(2):104-106
Thirteen sets of polymerase chain reaction (PCR) primers were designed to amplify microsatellite loci identified in the genome sequence of Leishmania major. Polymorphisms were detected in L. major at all loci. In Leishmania donovani only two of these loci were informative for classification purposes with this data set. The PCR products of all loci from one L. donovani strain were sequenced and it was found that the number of repeats in the microsatellite loci were either substantially reduced with respect to L. major or absent altogether. Consequently it is unlikely to be possible to use the genome sequence of L. major to identify polymorphic microsatellite loci in other Leishmania species. 相似文献
15.
Development, inheritance and cross-species amplification of microsatellite markers from Acacia mangium 总被引:3,自引:0,他引:3
P. A. Butcher S. Decroocq Y. Gray G. F. Moran 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,101(8):1282-1290
Microsatellite markers were developed in Acacia mangium Willd. to provide highly variable co-dominant markers for linkage mapping and studies of the breeding system. After an enrichment
procedure 40% of colonies contained microsatellites in contrast with less than 1% from a non-enriched library. The majority
of microsatellite sequences were AC repeats. Co-dominant segregation of alleles in two full-sib crosses of A. mangium was demonstrated at 33 microsatellite loci. The markers were highly variable relative to restriction fragment lengths polymorphisms
(RFLPs). In the two pedigrees 53% of microsatellite loci were fully informative compared with 15% of RFLPs. Based on alleles
detected among four parental genotypes, the microsatellites consisting of dinucleotide repeats were more polymorphic than
those with tri- and tetra-nucleotide repeats. The microsatellite markers were not as transferable across species in the genus
Acacia as RFLPs. Two thirds of the primers developed in A. mangium (subgenus Phyllodineae, section Juliflorae) amplified DNA from other species within the same section but failed to amplify
in species from the subgenus Acacia. The availability of multiallelic, PCR-based, co-dominant microsatellite loci makes possible
efficient studies of gene flow and breeding systems in A. mangium, a species with low allozyme variation.
Received: 30 December 1999 / Accepted: 10 May 2000 相似文献
16.
Pepper (Capsicum annuum L.) is one of the most important crops in the family Solanaceae. However, the number of polymorphic molecular loci detected in this important crop is far behind that of other cultivated
plant species. In the present study, a total of 45 microsatellite primer pairs were developed using Capsicum expressed sequence tags databases. Microsatellite primer pairs were tested using several species of Capsicum and several genera in the family Solanaceae including tomato, potato, eggplant, and tobacco. Results indicated that microsatellite primer pairs amplified genomic targets
of C. annuum L., Capsicum baccatum L., Capsicum chacoense L., Capsicum chinense L., Capsicum frutescens L., and Capsicum pubescens Ruiz et Pavon, indicating species transferability within Capsicum. Further analyses revealed that amplicons of these primer pairs segregated 1:2:1 or 3:1 Mendelian fashions in 38 F2 individuals of pepper. It was also noted that markers derived from sequences containing dinucleotide repeats were generally
more polymorphic at the intraspecific level than sequences containing trinucleotide repeats. All the microsatellite primer
pairs developed in this study will be useful for marker-assisted selection and mapping studies in pepper. 相似文献
17.
Nishikawa T Vaughan DA Kadowaki K 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2005,110(4):696-705
Simple sequence repeats (SSR) and their flanking regions in the mitochondrial and chloroplast genomes were sequenced in order to reveal DNA sequence variation. This information was used to gain new insights into phylogenetic relationships among species in the genus Oryza. Seven mitochondrial and five chloroplast SSR loci equal to or longer than ten mononucleotide repeats were chosen from known rice mitochondrial and chloroplast genome sequences. A total of 50 accessions of Oryza that represented six different diploid genomes and three different allopolyploid genomes of Oryza species were analyzed. Many base substitutions and deletions/insertions were identified in the SSR loci as well as their flanking regions. Of mononucleotide SSR, G (or C) repeats were more variable than A (or T) repeats. Results obtained by chloroplast and mitochondrial SSR analyses showed similar phylogenetic relationships among species, although chloroplast SSR were more informative because of their higher sequence diversity. The CC genome is suggested to be the maternal parent for the two BBCC genome species (O. punctata and O. minuta) and the CCDD species O. latifolia, based on the high level of sequence conservation between the diploid CC genome species and these allotetraploid species. This is the first report of phylogenetic analysis among plant species, based on mitochondrial and chloroplast SSR and their flanking sequences. 相似文献
18.
Jun-Lin Chen Chun Li Ye Sun Fa-Guo Wang Fu-Wu Xing 《American journal of botany》2012,99(12):e474-e476
• Premise of the study: Microsatellite makers were developed in Kleinia neriifolia, an endemic Asteraceae species on the Canary Islands, for investigation of the population genetic structure and colonization history of this insular species. • Methods and Results: Seventeen polymorphic and seven monomorphic microsatellite loci were isolated and characterized from K. neriifolia using the protocol of Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO). At the population level, the number of alleles detected per locus varied from two to 16, and the observed and expected heterozygosities were 0.105–1.000 and 0.100–0.923, respectively. • Conclusions: These highly informative loci are potentially useful to obtain a deeper understanding of the evolutionary process of K. neriifolia. 相似文献
19.
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
20.
M. J. M. Smulders G. Bredemeijer W. Rus-Kortekaas P. Arens B. Vosman 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,94(2):264-272
A search of nearly 2000 sequences from Solanaceae species in the EMBL and Genbank databases yielded 220 microsatellites. Among these were 80 microsatellites from 675 Lycopersicon entries. Dinucleotide repeats, as well as (CAA)n and (TAA)n repeats, were over-represented in non-coding DNA. The other trinucleotide repeats were predominantly found in exonic DNA.
PCR analysis of 44 of the microsatellite-containing Lycopersicon loci identified 36 primer pairs that yielded well-scorable fragments, or groups of fragments, in L. esculentum cultivars and accessions of Lycopersicon species. Twenty-nine of these amplified bands that were polymorphic among the four Lycopersicon species. Ten primer pairs generated polymorphic bands among seven tomato cultivars. Upon examining the number of microsatellites
and the degree of polymorphisms in relation to the repeat type and motif, the type of DNA the microsatellite resided in, the
length of the microsatellite, and the presence of imperfections in the microsatellite, only two significant correlations were
found. (i) Imperfect repeats were less polymorphic among species than perfect repeats. (ii) The percentage of loci polymorphic
among cultivars increased from 6% for the shortest loci (with eight or less repeat units) to 60% for the group with the longest
repeats (12 repeat units or longer). Among the species, however, all length classes contained about 83% polymorphic loci.
In general, 2–4 alleles were found for each locus among the samples of the test set. In a few cases, up to eight alleles were
found. A combination of these microsatellite loci can therefore be useful in distinguishing cultivars of tomato, which are
genetically very closely related to each other.
Received: 9 August 1996 / Accepted: 23 August 1996 相似文献