Development and characterization of chloroplast microsatellite markers in Macaranga (Euphorbiaceae)

Genome ◽  
2003 ◽  
Vol 46 (5) ◽  
pp. 845-857 ◽  
Author(s):  
Miriam Vogel ◽  
Gudrun Bänfer ◽  
Ute Moog ◽  
Kurt Weising
Keyword(s):  
Size Variation ◽  
Haplotype Network ◽  
Base Substitution ◽  
Chloroplast Microsatellites ◽  
Chloroplast Microsatellite ◽  
Interspecific Gene Flow ◽  
Size Homoplasy ◽  
Parsimony Network ◽  
Pcr Products ◽  
Small Set

As part of our study on the phylogeography of the ant-plant genus Macaranga, we have screened for polymorphic regions in the chloroplast genome. Initially, ten universal PCR primer pairs targeted at chloroplast microsatellite loci were applied to a small set of specimens, covering various taxonomic levels from intrafamilial to intraspecific. Eight primer pairs produced PCR fragments that behaved as single and discrete bands on agarose gels. The five most promising candidate pairs were further analysed with an extended set of DNA templates, and PCR products were separated on sequencing gels. The number of size variants per locus varied from two to eight, combining into 17 haplotypes among 29 Macaranga accessions from 10 species. Comparative sequencing demonstrated that microsatellites were responsible for the observed size variation at three of five loci, whereas variation at the other loci was caused by larger insertions and (or) deletions (indels). In addition to poly(A) and poly(T) repeats, which are typically found in chloroplast DNA, we also identified a variable (CT)n repeat, with n = 4 to n = 8. Sequencing revealed three examples of size homoplasy, one of which was caused by a single base substitution that raised the actual number of haplotypes to 18. Relationships between haplotypes were assessed by phenetic analyses of size variants and by constructing a parsimony network based on sequence variation. For both types of analysis, the distribution of haplotypes correlated with geographically circumscribed regions rather than with taxonomic boundaries.Key words: chloroplast microsatellites, ccmp primers, Macaranga, haplotype network, interspecific gene flow.

Cross-species microsatellite amplification in Vasconcellea and related genera and their use in germplasm classification

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 786-798 ◽  
Author(s):  
T Kyndt ◽  
B Van Droogenbroeck ◽  
A Haegeman ◽  
I Roldán-Ruiz ◽  
G Gheysen
Keyword(s):  
Population Genetics ◽  
Chloroplast Microsatellites ◽  
Microsatellite Data ◽  
Chloroplast Microsatellite ◽  
Diversity Assessment ◽  
Ssr Primers ◽  
Polymorphism Rate ◽  
Nuclear Ssr ◽  
Simple Sequence ◽  
Future Population

To generate inexpensive and efficient DNA markers for addressing a number of population genetics problems and identification of wild hybrids in Vasconcellea, we have evaluated the use of simple sequence repeat (SSR) primers previously developed for other species. A set of 103 Vasconcellea accessions and some individuals of the related genera Carica and Jacaratia were analyzed with 10 primer pairs directing amplification of chloroplast microsatellites in Nicotiana tabacum and 9 nuclear SSR primer pairs recently identified in Vasconcellea × heilbornii. Heterologous amplification of chloroplast SSRs was successful for 8 of the 10 loci, of which 6 showed polymorphism. Seven of the 9 nuclear SSR primer pairs were useful in Vasconcellea and often also in Jacaratia and Carica, all revealing polymorphism. Exclusive haplotypes for each described taxon were identified based on chloroplast microsatellite data. Clustering based on separate nuclear and chloroplast data resulted in a clear grouping per taxon, but only low resolution was obtained above species level. The codominancy of nuclear SSRs and the general high polymorphism rate of SSR markers will make them more useful in future population genetics studies and diversity assessment in conservation programs.Key words: Carica, Jacaratia, Vasconcellea, simple sequence repeats, cross-species amplification, classification, interspecific hybrids.

Causes of Size Homoplasy Among Chloroplast Microsatellites in Closely Related Clusia Species

2004 ◽  
Vol 58 (2) ◽  
pp. 182-190 ◽  
Author(s):  
Marie L. Hale ◽  
Anne M. Borland ◽  
Mats H. G. Gustafsson ◽  
Kirsten Wolff
Keyword(s):  
Chloroplast Microsatellites ◽  
Size Homoplasy

Nuclear- and chloroplast-microsatellite variation in A-genome species of rice

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 658-666 ◽  
Author(s):  
T Ishii ◽  
Y Xu ◽  
S R McCouch
Keyword(s):  
Oryza Sativa ◽  
Length Polymorphism ◽  
Allelic Diversity ◽  
Sequence Length ◽  
Chloroplast Microsatellites ◽  
Microsatellite Variation ◽  
Chloroplast Microsatellite ◽  
Genome Species ◽  
A Genome ◽  
Simple Sequence

Simple sequence length polymorphism analysis was carried out to reveal microsatellite variation and to clarify the phylogenetic relationships among A-genome species of rice. Total DNA from 29 cultivars (23 Oryza sativa and 6 O. glaberrima) and 30 accessions of wild A-genome species (12 O. rufipogon, 5 O. glumaepatula, 2 O. longistaminata, 6 O. meridionalis, and 5 O. barthii) was used as a template for PCR to detect 24 nuclear and 10 chloroplast microsatellite loci. Microsatellite allelic diversity was examined based on amplified banding patterns. Microsatellites amplified clearly in all 59 accessions, with an average of 18.4 alleles per locus. The polymorphism information content (PIC) value ranged from 0.85 to 0.94, with an average of 0.89. At the species level, high average PIC values were observed in O. sativa (0.79) and O. rufipogon (0.80). For chloroplast microsatellites, the average number of alleles per locus and the average PIC value were 2.9 and 0.38, respectively. While the magnitude of diversity was much greater for nuclear microsatellites than for chloroplast microsatellites, they showed parallel patterns of differentiation for each taxonomic group. Using the ratio of common alleles (estimated as size of amplified fragments) as a similarity index, the average percentages of common microsatellite alleles were calculated between taxa. For both nuclear and chloroplast microsatellites, O. sativa showed the highest similarity values to O. rufipogon, and O. glaberrima was most similar to O. barthii. These data support previous evidence that these cultivars originated from the corresponding wild ancestral species.Key words: simple sequence length polymorphism, SSLP, microsatellite marker, rice, Oryza sativa, allelic diversity, phylogenetics.

Diversity and genetic structure in populations of Pseudotsuga menziesii (Pinaceae) at chloroplast microsatellite loci

Genome ◽  
2001 ◽  
Vol 44 (3) ◽  
pp. 336-344 ◽  
Author(s):  
F Viard ◽  
Y A El-Kassaby ◽  
K Ritland
Keyword(s):  
Pseudotsuga Menziesii ◽  
Random Amplified Polymorphic Dna ◽  
Douglas Fir ◽  
Pinus Thunbergii ◽  
Chloroplast Microsatellites ◽  
Nuclear Markers ◽  
Chloroplast Microsatellite ◽  
High Pollen ◽  
Historical Factors ◽  
Simple Sequence

Genetic variation was compared between uniparentally-inherited (chloroplast simple sequence repeats, cpSSRs) vs. biparentally-inherited (isozyme and random amplified polymorphic DNA, RAPD) genetic markers in Douglas-fir (Pseudotsuga mensiezii) from British Columbia. Three-hundred twenty-three individuals from 11 populations were assayed. In Douglas-fir, the cpSSR primer sites were well-conserved relative to Pinus thunbergii (11 of 17 loci clearly amplified), but only 3 loci were appreciably polymorphic. At these cpSSR loci, we found an unexpectedly low level of polymorphism within populations, and no genetic differentiation among populations. By contrast, the nuclear markers showed variation typical of conifers, with significant among-population differentiation. This difference is likely the outcome of both historical factors and high pollen dispersal.Key words: chloroplast microsatellites, isozymes, RAPDs, gene flow, pollen flow.

scholarly journals Genetic analysis of European common ash (Fraxinus excelsior L.) populations affected by ash dieback

2014 ◽  
Vol 63 (1-6) ◽  
pp. 198-212 ◽  
Author(s):  
Barbara Fussi ◽  
M. Konnert
Keyword(s):  
Forest Ecosystems ◽  
Mixed Forest ◽  
Genetic Differences ◽  
Chloroplast Microsatellites ◽  
Microsatellite Variation ◽  
Chloroplast Microsatellite ◽  
Ash Dieback ◽  
Genetic Base ◽  
Genetic Potential ◽  
Adaptation Processes

AbstractEuropean common ash is an important component of mixed forest ecosystems in Bavaria and is considered a valuable tree species under climate change. The first aim of the present study was to assess the genetic diversity within and between ash populations in Bavaria in comparison with neighboring regions. Because ash stands have been heavily attacked by ash shoot disease in the last few years, the second aim of the study was to detect genetic differences between susceptible and less susceptible trees (trees with defoliation up to 30%) within populations. Altogether 41 populations were investigated using nuclear and chloroplast microsatellites. The results showed high genetic variation within and high genetic differentiation between ash populations. Higher chloroplast microsatellite variation was detected instead populations from south-eastern Bavaria compared to other regions. The comparison of susceptible and less susceptible groups of individuals within each population revealed medium to high genetic differences in some cases. For the observed heterozygosity, higher values were found for the group of less susceptible trees compared to the group of all trees or to the group of susceptible trees within populations. This could be a first indication that individuals with a higher heterozygosity might be able to withstand ash dieback in a better way compared to homozygotic individuals. Within the group of less susceptible trees a relatively wide genetic base exists whereupon a future breeding programme can be built. Thus it is of utmost importance for the species to maintain less affected trees in order to keep the genetic potential for future adaptation processes within ash populations, seed production and regeneration.

Chloroplast microsatellite analysis reveals the presence of population subdivision in Norway spruce (Picea abies K.)

Genome ◽  
2000 ◽  
Vol 43 (1) ◽  
pp. 68-78 ◽  
Author(s):  
G G Vendramin ◽  
M Anzidei ◽  
A Madaghiele ◽  
C Sperisen ◽  
G Bucci
Keyword(s):  
Picea Abies ◽  
Norway Spruce ◽  
Glacial Refugia ◽  
Population Subdivision ◽  
Chloroplast Microsatellites ◽  
Gene Pools ◽  
Chloroplast Microsatellite ◽  
Haplotypic Diversity ◽  
Main Gene ◽  
Degree Of Differentiation

Three chloroplast microsatellites (cpSSRs), previously sequence characterized and for which paternal inheritance was tested and confirmed, were used to assess their usefulness as informative markers for phylogeographic studies in Norway spruce (Picea abies K.) and to detect spatial genetic differentiation related to the possible recolonization processes in the postglacial period. Ninety-seven populations were included in the survey. Some 8, 7, and 6 different size variants for the three cpSSRs, respectively, were scored by analysing 1105 individuals. The above 21 variants combined into 41 different haplotypes. The distribution of some haplotypes showed a clear geographic structure and seems to be related to the existence of different refugia during the last glacial period. The analysis of chloroplast SSR variation detected the presence of two main gene pools (Sarmathic-Baltic and Alpine - Centre European) and a relatively low degree of differentiation (RST of about 10%), characteristic of tree species with large distribution and probably influenced by an intensive human impact on this species. Based on our data, we were not able to detect any evidence concerning the existence of additional gene pools (e.g., from Balkan and Carpathian glacial refugia), though we cannot exclude the existence of genetic discontinuity within the species' European range. A large proportion of population-specific haplotypes were scored in this species, thus indicating a possible usefulness of these markers for the identification of provenances, seed-lots, and autochthonous stands. Key words: haplotypic diversity, phylogeography, chloroplast microsatellites, recolonization.

scholarly journals Chloroplast microsatellite polymorphisms in Vitis species

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1142-1149 ◽  
Author(s):  
Rosa Arroyo-García ◽  
Francois Lefort ◽  
María Teresa de Andrés ◽  
Javier Ibáñez ◽  
Joaquín Borrego ◽  
...  
Keyword(s):  
Variable Number ◽  
Chloroplast Microsatellites ◽  
Length Variation ◽  
Consensus Primer ◽  
Chloroplast Microsatellite ◽  
Vitis Species ◽  
Vitis Riparia ◽  
Chloroplast Genomes ◽  
Growth Area ◽  
Chloroplast Haplotypes

The use of consensus chloroplast microsatellites primers for dicotyledonous chloroplast genomes revealed the existence of intra and interspecific length variation within the genus Vitis. Three chloroplast microsatellite loci were found to be polymorphic in samples of Vitis vinifera, Vitis berlandieri, Vitis riparia, and Vitis rupestris out of a total of 10 consensus primer pairs tested. These polymorphisms were always due to a variable number of mononucleotide residues within A and (or) T stretches in the amplified regions. Chloroplast microsatellite polymorphisms were used to demonstrate the maternal inheritance of chloroplast in V. vinifera and to characterise the chloroplast haplotypes present in wine grape cultivars of this species grown in Spain and Greece. The different distribution of haplotype frequencies in the two ends of the Mediterranean growth area suggests the existence of independent domestication events for grapevine.Key words: Vitis, grapevine, chloroplast microsatellites, chloroplast haplotypes, chloroplast inheritance, grapevine domestication.

Characterisation and inheritance of polymorphic plastid microsatellites in Abies

Genome ◽  
1997 ◽  
Vol 40 (6) ◽  
pp. 857-864 ◽  
Author(s):  
G. G. Vendramin ◽  
B. Ziegenhagen
Keyword(s):  
Population Genetics ◽  
Simple Sequence Repeats ◽  
Natural Populations ◽  
Abies Alba ◽  
Chloroplast Microsatellites ◽  
Length Variation ◽  
Pcr Products ◽  
Considerable Length ◽  
Polymorphic Microsatellite ◽  
Simple Sequence

Two polymorphic microsatellite loci were identified and sequenced in the genus Abies, using primer pairs derived from chloroplast simple sequence repeats (SSRs) of Pinus thunbergii. PCR products exhibited considerable length variation among six different Abies species and within Abies alba. F1 progeny of both an interspecific and an intraspecific reciprocal cross confirmed that the two SSRs were predominantly paternally inherited. The maternal size variant predominantly occurred in the megagametophytes analysed. First analysis of the two chloroplast microsatellites in seven natural populations of A. alba revealed 36 different haplotypes. The use of these highly polymorphic SSRs as potential markers in population genetics is discussed.Key words: Abies, chloroplast simple sequence repeats, sequences, inheritance, intraspecific variation, population genetics.

scholarly journals Characterization of Polymorphic Chloroplast Microsatellites in Prunus Species and Maternal Lineages in Peach Genotypes

2017 ◽  
Vol 142 (3) ◽  
pp. 217-224
Author(s):  
Chunxian Chen ◽  
William R. Okie
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Microsatellites ◽  
Nucleotide Polymorphisms ◽  
Chloroplast Microsatellite ◽  
Single Nucleotide ◽  
Chloroplast Genomes ◽  
Genome Features ◽  
Genomic Locations ◽  
Representative Material

Several available Prunus chloroplast genomes have not been exploited to develop polymorphic chloroplast microsatellites that could be useful in Prunus phylogenetic analysis and maternal lineage group (MLG) categorization. In this study, using available bioinformatics tools, 80, 75, and 78 microsatellites were identified from the chloroplast genome of P. persica (CPpe), P. kansuensis (CPka), and P. mume (CPmu), respectively. The genome features and polymorphism status of these microsatellites were characterized. The genomic locations and motif types of most chloroplast microsatellites were conserved in CPpe, CPka, and CPmu. Of the 67 microsatellites with primer sequences and names, 57 were polymorphic for their in silico motif, amplicon lengths, or both among the three genomes. Based on the genotyping data of eight most polymorphic microsatellites, eight unique MLGs were found among the 736 peach materials in a breeding program. Most peach cultivars (111 of 161 genotyped) belong to MLG-1, the Chinese Cling-derived group reflecting the heavy use of this germplasm in early peach development. Forty-one cultivars belong to MLG-2, the European-derived group of peaches. MLG-3 consists of ornamental accessions. MLG-4 and MLG-5 contain only ‘Flordaking’ and ‘Reliance’, respectively. MLG-6 to MLG-8 consists of selections derived from P. tangutica, P. davidiana, and P. mira, respectively. These amplicons from the representative material for each MLG were sequenced, revealing additional single nucleotide polymorphisms (SNPs) within the amplicons. With the polymorphism status and amplification reliability validated, these new polymorphic chloroplast microsatellite markers may be useful in Prunus phylogenetic analysis.

Chloroplast microsatellites as markers for paternity analysis in Abies alba

1998 ◽  
Vol 28 (2) ◽  
pp. 317-321 ◽  
Author(s):  
B Ziegenhagen ◽  
F Scholz ◽  
A Madaghiele ◽  
G G Vendramin
Keyword(s):  
Microsatellite Loci ◽  
Abies Alba ◽  
Paternity Analysis ◽  
Potential Usefulness ◽  
Chloroplast Microsatellites ◽  
Silver Fir ◽  
Conifer Species ◽  
Chloroplast Microsatellite ◽  
Adult Trees ◽  
Endangered Population

This study describes the application of previously characterized chloroplast microsatellites as markers for paternity analysis in a conifer species. The investigations were performed on silver fir (Abies alba Mill.) relic trees in an endangered population of the Ore Mountains (Germany). Two relatively isolated adult trees about 30 m apart, as well as 24 naturally regenerated young trees in their direct neighborhood, were analyzed at two chloroplast microsatellite loci. Results reveal the potential usefulness of the markers for paternity analysis.

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