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1
Kaundun, Shiv Shankhar, et Satoru Matsumoto. « Heterologous nuclear and chloroplast microsatellite amplification and variation in tea, Camellia sinensis ». Genome 45, no 6 (1 décembre 2002) : 1041–48. http://dx.doi.org/10.1139/g02-070.
Texte intégralRésumé :
The advantage of the cross transferability of heterologous chloroplast and nuclear microsatellite primers was taken to detect polymorphism among 24 tea (Camellia sinensis (L.) O. Kuntze) genotypes, including both the assamica and the sinensis varieties. Primer information was obtained from the closely related Camellia japonica species for four nuclear microsatellites, and from Nicotiana tabaccum for seven universal chloroplast microsatellites. All of the nuclear microsatellite loci tested generated an expected DNA fragment in tea, revealing between three and five alleles per locus. Four out of the seven chloroplast microsatellites primers amplified positively, and of these only one was polymorphic with three alleles, which is in agreement with the conserved nature of chloroplast microsatellites at the intraspecific level. A factorial correspondence analysis carried out on all genotypes and nuclear microsatellite alleles separated the assamica and sinensis genotypes into two groups, thus demonstrating the value of these markers in establishing the genetic relationship between tea varieties. Genetic diversity measured with nuclear microsatellites was higher than that measured with other types of molecular markers, offering prospects for their use in fingerprinting, mapping, and population genetic studies, whereas polymorphisms detected at a cpSSR locus will allow the determination of plastid inheritance in the species. Key words: tea, Camellia sinensis, SSR, microsatellites, genetic diversity.
2
Hale, M. L., A. M. Borland et K. Wolff. « High degree of conservation of nuclear microsatellite loci in the genus Clusia ». Genome 48, no 5 (1 octobre 2005) : 946–50. http://dx.doi.org/10.1139/g05-048.
Texte intégralRésumé :
In plants, microsatellites and their flanking DNA are rarely conserved across a whole genus, let alone other genera in the same family. Therefore, the possibility of using microsatellite primers developed for a species across a large number of plant species in the same genus is often limited. Remarkably, dinucleotide nuclear microsatellites developed for Clusia minor and for Clusia nemorosa amplified homologous microsatellites in species across the whole genus Clusia. In this present study, we report on the DNA sequence variation across the genus of 3 microsatellite loci with varying levels of variation. Compared over the species, there was a correlation between the lengths of the microsatellite loci. Interrupts occurred multiple times and did not seem to lead to the death of the microsatellite. These highly conserved markers will be useful for studying the variable reproductive systems in the genus Clusia.Key words: microsatellite, Clusia, cross-species amplification, microsatellite evolution.
3
Ishii, T., Y. Xu et S. R. McCouch. « Nuclear- and chloroplast-microsatellite variation in A-genome species of rice ». Genome 44, no 4 (1 août 2001) : 658–66. http://dx.doi.org/10.1139/g01-044.
Texte intégralRésumé :
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.
4
Zhang, Dan-Dan, Pi Luo, Ying Chen, Zheng-Feng Wang, Wan-Hui Ye et Hong-Lin Cao. « Short Note : Isolation and Characterization of 12 Polymorphic Microsatellite Markers in Engelhardia roxburghiana (Juglandaceae) ». Silvae Genetica 63, no 1-6 (1 décembre 2014) : 109–12. http://dx.doi.org/10.1515/sg-2014-0014.
Texte intégralRésumé :
Abstract Engelhardia roxburghiana is a common half evergreen tree with a wide distribution in southeast Asia. Despite its ecological and pharmaceutical values, its genetic diversity is poorly studied. Our objective was to develop nuclear microsatellite markers to investigate the level of genetic diversity within and among populations in the future. Using the microsatellite-enriched library and PCR-based screening method, 12 microsatellite markers were developed and showed polymorphism in a population. The number of alleles per locus for these 12 microsatellites ranged from four to 15. The observed and expected heterozygosities ranged from 0.358 to 0.897 and from 0.369 to 0.886, respectively. The developed microsatellites will be useful for studying genetic diversity and population structure in E. roxburghiana.
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McConnell, Stewart K., Patrick O'Reilly, Lorraine Hamilton, Jonathan M. Wright et Paul Bentzen. « Polymorphic microsatellite loci from Atlantic salmon (Salmo salar) : genetic differentiation of North American and European populations ». Canadian Journal of Fisheries and Aquatic Sciences 52, no 9 (1 septembre 1995) : 1863–72. http://dx.doi.org/10.1139/f95-779.
Texte intégralRésumé :
Atlantic salmon populations show low levels of genetic differentiation relative to other salmonid species, when surveyed by allozymes, and with mitochondrial DNA and nuclear ribosomal DNA markers. Here we report the application of three novel microsatellite VNTR loci to population differentiation in Atlantic salmon. A total of 232 microsatellites, cloned from Atlantic salmon, were classified as perfect, imperfect, and compound repeats. Microsatellite length, as in other teleosts, was significantly larger than published mammalian microsatellites. Primers for PCR amplification of three salmon microsatellites were designed. Allele frequencies, degree of polymorphism, and heterozygosity were estimated for five populations from Nova Scotia, Canada, and from Europe. Nei's genetic distances of 0.02–0.9 were observed among populations. There was a clear discrimination between Canadian and European fish based on unique alleles present at two loci. These Atlantic salmon primers also amplify presumably homologous loci in nine other salmonid species. The polymorphic microsatellites loci reported here demonstrate great potential as genetic markers in population, breeding, and evolutionary studies.
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Gaffney, Patrick M., Carita M. Pascal, Jeffery Barnhart, W. Stewart Grant et James E. Seeb. « Genetic homogeneity of weathervane scallops (Patinopecten caurinus) in the northeastern Pacific ». Canadian Journal of Fisheries and Aquatic Sciences 67, no 11 (novembre 2010) : 1827–39. http://dx.doi.org/10.1139/f10-096.
Texte intégralRésumé :
We assessed genetic differentiation among populations of weathervane scallop ( Patinopecten caurinus ) in the northeastern Pacific, extending over 2500 km in the Gulf of Alaska and southeastern Bering Sea. Variability was surveyed at nuclear loci with allozyme, microsatellite, and single nucleotide polymorphism (SNP) methods, and at mitochondrial (mt)DNA loci with SNPs and nucleotide sequencing. High levels of gene diversity were detected for allozymes (H = 0.080), microsatellites (H = 0.734), and mtDNA (h = 0.781). Genotypes at nuclear loci generally fit Hardy–Weinberg proportions, except for some microsatellite loci, for which null-allele frequencies of 0.02 to 0.34 were estimated. No allele-frequency differences were detected among samples, except for the allozyme loci Gpi and Pep-4. Overall levels of differentiation ranged from FST = 0.0004 for allozymes, FST = 0.0008 for mtDNA to FST = 0.0004 for microsatellites. No isolation by distance was found for any of the markers. A unimodal mtDNA mismatch distribution and significant excesses of low-frequency variants for allozymes, microsatellites, and mtDNA may reflect a post-glacial population expansion. The lack of genetic differentiation measured by neutral markers does not preclude the existence of locally adapted, self-sustaining populations that are important in the harvest management of this species.
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Garner, Trenton WJ. « Genome size and microsatellites : the effect of nuclear size on amplification potential ». Genome 45, no 1 (1 février 2002) : 212–15. http://dx.doi.org/10.1139/g01-113.
Texte intégralRésumé :
Although the frequency of microsatellite DNA regions generally increases with increasing genome size, genome size has a negative effect on polymerase chain reaction (PCR) amplification. Thus, researchers developing sets of PCR primers, as is commonly done for microsatellite DNA regions, may encounter greater difficulty when working with species that have larger genomes. I investigated the effect of genome size on overall amplification success using data from nine different metazoan taxa. The proportion of primer sets that did not amplify PCR products was strongly and positively correlated with the haploid C value of the target species. Increasing genome size may affect amplification success negatively because of a decrease in target:nontarget DNA or by dilution of the available primer pool by nonspecific binding.Key words: microsatellites, genome size, amplification success.
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Bloomfield, Justin A., Paul Nevill, Brad M. Potts, René E. Vaillancourt et Dorothy A. Steane. « Molecular genetic variation in a widespread forest tree species Eucalyptus obliqua (Myrtaceae) on the island of Tasmania ». Australian Journal of Botany 59, no 3 (2011) : 226. http://dx.doi.org/10.1071/bt10315.
Texte intégralRésumé :
Eucalyptus obliqua L’Hér. is widespread across south-eastern Australia. On the island of Tasmania it has a more-or-less continuous distribution across its range and it dominates much of the wet sclerophyll forest managed for forestry purposes. To understand better the distribution of genetic variation in these native forests we examined nuclear microsatellite diversity in 432 mature individuals from 20 populations of E. obliqua across Tasmania, including populations from each end of three locally steep environmental gradients. In addition, chloroplast microsatellite loci were assessed in 297 individuals across 31 populations. Nuclear microsatellite diversity values in E. obliqua were high (average HE = 0.80) and inbreeding coefficients low (average F = 0.02) within these populations. The degree of differentiation between populations was very low (FST = 0.015). No significant microsatellite differentiation could be found across three locally steep environmental gradients, even though there is significant genetic differentiation in quantitative traits. This suggests that the observed quantitative variation is maintained by natural selection. Population differentiation based on chloroplast haplotypes was high (GST = 0.69) compared with that based on nuclear microsatellites, suggesting that pollen-mediated gene flow is >150 times the level of seed-mediated gene flow in this animal-pollinated species; hence, pollen is likely to be the main mode of gene flow countering selection along local environmental gradients. Implications of these results for silvicultural practices are discussed.
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LENDVAY, Bertalan, Andrzej PEDRYC et Mária Höhn. « Characterization of Nuclear Microsatellite Markers for the Narrow Endemic Syringa josikaea Jacq. fil. ex Rchb. » Notulae Botanicae Horti Agrobotanici Cluj-Napoca 41, no 1 (28 mai 2013) : 301. http://dx.doi.org/10.15835/nbha4119023.
Texte intégralRésumé :
The species of the genus Syringa L. are among the most popular ornamental plants worldwide. One particular species, Syringa josikaea, a rare endemic of the Carpathian Mountains, is of great conservation interest. Although microsatellite markers may be useful for studying the genetic variability of varieties and populations, no microsatellites have previously been characterized for any species of the Syringa genus. Our aim was therefore to test the applicability of microsatellite primers developed for neighboring genera (Olea and Ligustrum) and to complement these with markers isolated and characterized for S. josikaea. Twelve primer pairs of Olea and Ligustrum were tested by optimizing PCR conditions and checking the variability in 40 samples of two populations of S. josikaea. Two of them proved to be easy to PCR amplify and variable at the same time. To develop new primers we constructed a microsatellite enriched library and sequenced 48 clones. 18 sequences contained microsatellite motifs, and three of the designed primer pairs presented high allele variability. The five primer pairs characterized for S. josikaea proved to be highly informative and sufficient to distinguish between individuals. These microsatellite primers are valuable tools to study genetic variation of native populations, genetic lineages of hybrids and cultivars of S. josikaea.
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Hebel, I., R. Haas et Aikaterini Dounavi. « Genetic Variation of Common Ash (Fraxinus excelsior L.) Populations From Provenance Regions in Southern Germany by Using Nuclear and Chloroplast Microsatellites ». Silvae Genetica 55, no 1-6 (1 décembre 2006) : 38–44. http://dx.doi.org/10.1515/sg-2006-0006.
Texte intégralRésumé :
Abstract The genetic structure of 14 populations from three ash provenance regions (Fraxinus excelsior L.) in southern Germany (Aid Infodienst, 2003) is described by analysing the variation of four nuclear and five cpDNA microsatellites. The study of the nuclear microsatellites revealed high levels of genetic diversity but low levels of genetic differentiation, suggesting a high degree of gene flow among regions and/or human interference by introducing plant material coming from different provenances. The distributions of the allele frequencies and the genetic structures at these four microsatellite loci did not allow the identification of distinct provenance regions, although “private alleles” were encountered with moderate to low frequencies (above 5 percent). Specifically, the Rhine valley populations (provenance region 81105) and these from the Swabian Jura and Black Forest (provenance region 81107) revealed private alleles at the two microsatellite loci Femsatl4 and Femsatl12. A more distinct differentiation between provenances was found based on the cpDNA markers. Evidence on genetic delineation and characterization of ash provenances is discussed. Based on these results, provenance regions can be genetically characterised but further analysis of ash populations and of reproductive material (seeds or seedlings) would be of great importance for provenance delineation, as well as gene conservation and sustainable management of ash populations.
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Sonsthagen, Sarah A., Sandy L. Talbot et Kevin G. McCRACKEN. « Genetic Characterization of Common Eiders Breeding in the Yukon-Kuskokwim Delta, Alaska ». Condor 109, no 4 (1 novembre 2007) : 878–93. http://dx.doi.org/10.1093/condor/109.4.878.
Texte intégralRésumé :
Abstract We assessed population genetic subdivision among four colonies of Common Eiders (Somateria mollissima v-nigrum) breeding in the Yukon-Kuskokwim Delta (YKD), Alaska, using microsatellite genotypes and DNA sequences with differing modes of inheritance. Significant, albeit low, levels of genetic differentiation were observed between mainland populations and Kigigak Island for nuclear intron lamin A and mitochondrial DNA (mtDNA) control region. Intercolony variation in haplotypic frequencies also was observed at mtDNA. Positive growth signatures assayed from microsatellites, nuclear introns, and mtDNA indicate recent colonization of the YKD, and may explain the low levels of structuring observed. Gene flow estimates based on microsatellites, nuclear introns, and mtDNA suggest asymmetrical gene flow between mainland colonies and Kigigak Island, with more individuals on average dispersing from mainland populations to Kigigak Island than vice versa. The directionality of gene flow observed may be explained by the colonization of the YKD from northern glacial refugia or by YKD metapopulation dynamics.
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Weetman, David, Lorenz Hauser et Gary R. Carvalho. « Reconstruction of Microsatellite Mutation History Reveals a Strong and Consistent Deletion Bias in Invasive Clonal Snails, Potamopyrgus antipodarum ». Genetics 162, no 2 (1 octobre 2002) : 813–22. http://dx.doi.org/10.1093/genetics/162.2.813.
Texte intégralRésumé :
Abstract Direct observations of mutations and comparative analyses suggest that nuclear microsatellites show a tendency to expand, with reports of deletion biases limited to very long alleles or a few loci in multilocus studies. Here we investigate microsatellite evolution in clonal snails, Potamopyrgus antipodarum, since their introduction to Britain in the 19th century, using an analysis based on minimum spanning networks of multilocus microsatellite genotypes. British populations consist of a small number of highly distinct genotype groups with very few outlying genotypes, suggesting clonal lineages containing minor variation generated by mutation. Network patterns suggest that a single introduced genotype was the ancestor of all extant variation and also provide support for wholly apomictic reproduction within the most common clonal lineage (group A). Microsatellites within group A showed a strong tendency to delete repeats, with an overall bias exceeding 88%, irrespective of the exact method used to infer mutations. This highly unusual pattern of deletion bias is consistent across populations and loci and is unrelated to allele size. We suggest that for persistence of microsatellites in this clone, some change in the mutation mechanism must have occurred in relatively recent evolutionary time. Possible causes of such a change in mechanism are discussed.
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Schöniger, Sandra, et Josef Rüschoff. « Mismatch Repair Deficiency and Microsatellite Instability ». Encyclopedia 2, no 3 (31 août 2022) : 1559–76. http://dx.doi.org/10.3390/encyclopedia2030106.
Texte intégralRésumé :
Mismatch repair deficiency (MMRd) is caused by the biallelic inactivation of an MMR gene, which can be attributed either to an inherited or an acquired pathway. MMRd is characterized by the inability of cells to repair spontaneous mutations in microsatellites that occur during replication. Microsatellites are repetitive nucleotide sequences composed of one to six base pairs. Mutations in microsatellites lead to deletions or insertions of sequence units that are designated as microsatellite instability (MSI). MMRd is diagnosed by immunochemistry and is characterized by loss of nuclear immunostaining for at least one of the four MMR proteins that are routinely examined, i.e., MSH2, MSH6, MLH1 and PMS2. Available tests for MSI are PCR and next generation sequencing. MMRd and MSI predispose to tumor initiation and progression, increase tumor mutational burden as well as tumor immunogenicity, facilitate the activation of the programmed cell death protein 1/programmed cell death ligand 1 (PD-1/PD-L1) immune checkpoint pathway and serve as prognostic and predictive biomarkers in solid tumors.
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Verspoor, Eric, Sonia Consuegra, Olafur Fridjonsson, Sigridur Hjorleifsdottir, David Knox, Kristinn Olafsson, Scott Tompsett, Vidar Wennevik et Carlos Garcia de Leaniz. « Regional mtDNA SNP differentiation in European Atlantic salmon (Salmo salar) : an assessment of potential utility for determination of natal origin ». ICES Journal of Marine Science 69, no 9 (20 mars 2012) : 1625–36. http://dx.doi.org/10.1093/icesjms/fss029.
Texte intégralRésumé :
Abstract Verspoor, E., Consuegra, S., Fridjonsson, O., Hjorleifsdottir, S., Knox, D., Olafsson, K., Tompsett, S., Wennevik, V., and Garciá de Leániz, C. 2012. Regional mtDNA SNP differentiation in European Atlantic salmon (Salmo salar): an assessment of potential utility for determination of natal origin. – ICES Journal of Marine Science, 69: 1625–1636. The Atlantic salmon, Salmo salar, shows geographically structured differentiation at various classes of molecular genetic variation, among and within river stocks. Nuclear microsatellite locus variation at multiple loci has been exploited for more than a decade as a marker for the continental origin of fish caught at sea in distant-water fisheries. However, a simpler, more cost-effective, but still accurate, assignment can be obtained using a single microsatellite locus in combination with a mitochondrial DNA (mtDNA) single-nucleotide polymorphism (SNP) detected by restriction enzyme digestion. Following on from this, a preliminary study was made of the potential for using mtDNA SNP variation to enhance the resolving power and cost-effectiveness of within-continent assignment of European salmon as determined using microsatellites. Variation in 20 mtDNA regions, encompassing ∼43% of this genome, in 330 salmon from 29 rivers across Europe, was analysed. High levels of inter-individual and inter-river variation were found, as well as evidence of regional differentiation paralleling observed microsatellite differentiation. The observations indicate scope for using mtDNA SNPs along with microsatellites for genetically based assignment of European salmon to region and river of natal origin, but further study is needed.
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Lindner, K. R., J. E. Seeb, C. Habicht, K. L. Knudsen, E. Kretschmer, D. J. Reedy, P. Spruell et F. W. Allendorf. « Gene-centromere mapping of 312 loci in pink salmon by half-tetrad analysis ». Genome 43, no 3 (1 juin 2000) : 538–49. http://dx.doi.org/10.1139/g00-016.
Texte intégralRésumé :
We estimated recombination rates between 312 loci and their centromeres in gynogenetic diploid pink salmon (Oncorhynchus gorbuscha) that we produced by initiating development with irradiated sperm and blocking the maternal second meiotic division. Amplified fragment length polymorphisms (AFLPs) were significantly more centromeric than loci identified by three other techniques (allozymes, microsatellites, and PCR using primer sequences from interspersed nuclear elements). The near absence of AFLPs in distal regions could limit their utility in constructing linkage maps. A large proportion of loci had frequency of second division segregation (y) values approaching 1.0, indicating near complete crossover interference on many chromosome arms. As predicted from models of chromosomal evolution in salmonids based upon results with allozyme loci, all duplicated microsatellite loci that shared alleles (isoloci) had y values of nearly 1.0.Key words: meiosis, AFLP, microsatellites, isoloci, Oncorhynchus gorbuscha.
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Srinivasan, Rajini, Nataliya Nady, Neha Arora, Laura J. Hsieh, Tomek Swigut, Geeta J. Narlikar, Mark Wossidlo et Joanna Wysocka. « Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage ». Science Advances 6, no 12 (mars 2020) : eaaz9115. http://dx.doi.org/10.1126/sciadv.aaz9115.
Texte intégralRésumé :
Zinc finger protein Zscan4 is selectively expressed in mouse two-cell (2C) embryos undergoing zygotic genome activation (ZGA) and in a rare subpopulation of embryonic stem cells with 2C-like features. Here, we show that Zscan4 specifically recognizes a subset of (CA)n microsatellites, repeat sequences prone to genomic instability. Zscan4-associated microsatellite regions are characterized by low nuclease sensitivity and high histone occupancy. In vitro, Zscan4 binds nucleosomes and protects them from disassembly upon torsional strain. Furthermore, Zscan4 depletion leads to elevated DNA damage in 2C mouse embryos in a transcription-dependent manner. Together, our results identify Zscan4 as a DNA sequence–dependent microsatellite binding factor and suggest a developmentally regulated mechanism, which protects fragile genomic regions from DNA damage at a time of embryogenesis associated with high transcriptional burden and genomic stress.
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Oreshkova, N. V., t. S. Sedelnikova, S. P. Efremov et A. V. Pimenov. « Genetic polymorphism of mountain-taiga populations of siberian stone pine in Kusnetsky Alatau ». Faktori eksperimental'noi evolucii organizmiv 28 (31 août 2021) : 30–35. http://dx.doi.org/10.7124/feeo.v28.1371.
Texte intégralRésumé :
Aim. Study of DNA polymorphism of 7 coenopopulations of Siberian stone pine (Pinus sibirica) growing in theKuznetsk Alatau. Methods. Nuclear microsatellite loci developed for P. sibirica were used as genetic markers. Results. 44 allelic variants were identified from 11 nuclear microsatellite loci, which significantly differ in the composition and frequency of occurrence of the studied P. sibirica coenopopulations. The highest level of allelic diversity is found in loci Ps_80612 and Ps_1502048, where 8 and 7 alleles were identified, respectively. The calculation of the main parameters of genetic diversity showed a relatively low level of polymorphism in the studied samples (NA = 3.078; NE = 1.877; HE = 0.445; HO = 0.401). The assessment of the degree of genetic differences between populations using the Nei genetic distance (DN) showed that, despite the low genetic differentiation (DN varies from 0.019 to 0.061), the differences between them can be traced quite clearly. Conclusions. Differences in the level of genetic polymorphism of P. sibirica is defined by the presence of orographic and phytocoenotic barriers between coenopopulations, as well as a high degree of ecological and anthropogenic extremity of individual growth sites.
Keywords: Pinus sibirica, Kuznetsk Alatau, microsatellites, genetic diversity, heterozygosity.
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Esa, Yuzine, et Khairul Adha Abdul Rahim. « Genetic Structure and Preliminary Findings of Cryptic Diversity of the Malaysian Mahseer (Tor tambroidesValenciennes : Cyprinidae) Inferred from Mitochondrial DNA and Microsatellite Analyses ». BioMed Research International 2013 (2013) : 1–14. http://dx.doi.org/10.1155/2013/170980.
Texte intégralRésumé :
This study examines the population genetic structure ofTor tambroides, an important freshwater fish species in Malaysia, using fifteen polymorphic microsatellite loci and sequencing of 464 base pairs of the mitochondrial cytochrome c oxidase I (COI) gene. A total of 152 mahseer samples were collected from eight populations throughout the Malaysia river system. Microsatellites results found high levels of intrapopulation variations, but mitochondrial COI results found high levels of interpopulations differentiation. The possible reasons for their discrepancies might be the varying influence of genetic drift on each marker or the small sample sizes used in most of the populations. The Kelantan population showed very low levels of genetic variations using both mitochondrial and microsatellite analyses. Phylogenetic analysis of the COI gene found a unique haplotype (ER8*), possibly representing a cryptic lineage ofT. douronensis, from the Endau-Rompin population. Nevertheless, the inclusion of nuclear microsatellite analyses could not fully resolve the genetic identity of haplotype ER8* in the present study. Overall, the findings showed a serious need for more comprehensive and larger scale samplings, especially in remote river systems, in combination with molecular analyses using multiple markers, in order to discover more cryptic lineages or undescribed “genetic species” of mahseer.
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Patton, J. C., B. J. Gallaway, R. G. Fechhelm et M. A. Cronin. « Genetic variation of microsatellite and mitochondrial DNA markers in broad whitefish (Coregonus nasus) in the Colville and Sagavanirktok rivers in northern Alaska ». Canadian Journal of Fisheries and Aquatic Sciences 54, no 7 (1 juillet 1997) : 1548–56. http://dx.doi.org/10.1139/f97-062.
Texte intégralRésumé :
There has been concern that a causeway leading to oil production facilities in the Alaskan Beaufort Sea could affect the extent of emigration from, and immigration into, a population of broad whitefish (Coregonus nasus) in the Sagavanirktok River. To assess this, we analyzed the genetic relationships of the broad whitefish populations in the Sagavanirktok River, and the nearest adjacent population, in the Colville River. Three microsatellite loci from the nuclear genome, and the NADH-1 gene of mitochondrial DNA (mtDNA), were analyzed. Diploid genotypes were determined with PCR amplification of the microsatellite loci, and mtDNA genotypes were identified with PCR amplification followed by sequencing of 798 nucleotides. Several alleles were identified at each locus and both populations had high levels of genetic variation. There is significant differentiation of the Sagavanirktok River and Colville River broad whitefish stocks for the three microsatellite loci (FST = 0.031) but not mtDNA (FST < 0.001). Possible explanations for the lower level of differentiation of mtDNA than microsatellites include female-mediated gene flow between populations, skewed sex ratios, natural selection, or mutation. The results indicate that there is limited gene flow between the Colville and Sagavanirktok rivers, which represent semi-isolated spawning populations.
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Johansson, Helena, Perttu Seppä, Heikki Helanterä, Kalevi Trontti et Liselotte Sundström. « Weak population structure in the ant Formica fusca ». PeerJ 6 (19 juin 2018) : e5024. http://dx.doi.org/10.7717/peerj.5024.
Texte intégralRésumé :
Dispersal is a fundamental trait of a species’ biology. High dispersal results in weakly structured or even panmictic populations over large areas, whereas weak dispersal enables population differentiation and strong spatial structuring. We report on the genetic population structure in the polygyne ant Formica fusca and the relative contribution of the dispersing males and females to this. We sampled 12 localities across a ∼35 km2 study area in Finland and generated mitochondrial DNA (mtDNA) haplotype data and microsatellite data. First, we assessed queen dispersal by estimating population differentiation from mtDNA haplotype data. Second, we analysed nuclear DNA microsatellite data to determine overall population genetic substructure in the study area with principal components analysis, Bayesian clustering, hierarchical F statistics and testing for evidence of isolation-by-distance. Third, we directly compared genetic differentiation estimates from maternally inherited mtDNA and bi-parentally inherited DNA microsatellites to test for sex-bias in dispersal. Our results showed no significant spatial structure or isolation by distance in neither mtDNA nor DNA microsatellite data, suggesting high dispersal of both sexes across the study area. However, mitochondrial differentiation was weaker (Fst-mt = 0.0047) than nuclear differentiation (Fst-nuc = 0.027), which translates into a sixfold larger female migration rate compared to that of males. We conclude that the weak population substructure reflects high dispersal in both sexes, and it is consistent with F. fusca as a pioneer species exploiting unstable habitats in successional boreal forests.
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Keven, John B., Edward D. Walker et Patrick J. Venta. « A Microsatellite Multiplex Assay for Profiling Pig DNA in Mosquito Bloodmeals ». Journal of Medical Entomology 56, no 4 (13 février 2019) : 907–14. http://dx.doi.org/10.1093/jme/tjz013.
Texte intégralRésumé :
Abstract Genetic profiling has been used to link mosquito bloodmeals to the individual humans, but this analysis has not been done for other mammalian bloodmeals. In this study, we describe a microsatellite-based method for identifying individual pigs in mosquito bloodmeals based on their unique multilocus genotypes. Eleven tetranucleotide microsatellites and a sex-specific marker were selected based on Smith-Waterman DNA sequence alignment scores from the reference genome and primers were designed with features that reduce primer dimers, promote complete adenylation, and enable fluorescent labeling of amplicons. A multiplex polymerase chain reaction (PCR) assay was optimized and validated by analyzing DNA of individual pigs from several nuclear families and breeds before it was used to analyze genomic DNA of pig-derived mosquito bloodmeals from villages of Papua New Guinea. Population analysis of the nuclear families showed high expected and observed heterozygosity. The probability of observing two unrelated or sibling individuals sharing the same genotype at a single microsatellite locus or a combination of loci was vanishingly low. Samples had unique genotypes and gender was accurately predicted. Analysis of 129 pig bloodmeals identified 19 unique genotypes, which varied greatly in frequency in the mosquito bloodmeal samples. The high allelic diversity of the microsatellite loci and low probability of false attribution of identity show that this genotyping method reliably distinguishes distantly and closely related pigs and can be used to identify individual pigs from genotyped mosquito bloodmeals.
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Breidenbach, Natalie, Oliver Gailing et Konstantin V. Krutovsky. « Development of novel polymorphic nuclear and chloroplast microsatellite markers in coast redwood (Sequoia sempervirens) ». Plant Genetic Resources : Characterization and Utilization 17, no 03 (4 décembre 2018) : 293–97. http://dx.doi.org/10.1017/s147926211800045x.
Texte intégralRésumé :
AbstractThe range-wide genetic structure of the highly productive and valuable timber species Sequoia sempervirens (D. Don) Endl. is still insufficiently studied, although published data based on different genetic markers (nuclear and chloroplast microsatellites, AFLP, RFLP and isozymes) demonstrated relatively low population structure. However, more genetic markers are needed to increase the efficiency of population genetic studies in coast redwood. Therefore, we developed seven nuclear and five chloroplast microsatellite or simple sequence repeat (SSR) markers based on expressed sequence tags (ESTs) and the complete chloroplast genome sequence, respectively. All selected markers were tested in a range-wide sample representing trees from 16 locations. They are highly polymorphic microsatellite loci with the number of alleles ranging from 3 to 17, and the number of effective alleles from 1.1 to 2.48. Coast redwood is a hexaploid species, and its chloroplasts are paternally inherited. Therefore, the chloroplast SSR markers are especially useful for this species, because their genotyping is not affected by nuclear genome ploidy. Moreover, they showed high gene diversity for each locus within and across all populations and can be used to study range-wide population genetic structure, pollen-based gene flow and long-distance gene transfer. Coast redwood can propagate clonally, and nuclear polymorphic EST-SSRs can be used for clonal identification. They are linked with expressed genes and their variation can reflect variation in genes under selection, including those that could be potentially important for local adaptation of coast redwood considering the threat of climate change.
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Tóth, Zoltán, Gábor Gyulai, Zoltán Szabó, Lajos Horváth, Ferenc Gyulai et László Heszky. « Sequence heterogeneity of nSSR and cpDNA loci of Cucurbits (Citrullus sp.) ». Acta Agraria Debreceniensis, no 27 (15 novembre 2007) : 125–34. http://dx.doi.org/10.34101/actaagrar/27/3115.
Texte intégralRésumé :
The evolution of water melon (Citrullus lanatus) microsatellites from the 15th century (Debrecen); 13th (Buda); and 18th century, (Pannonhalma) were analyzed. Microsatellite (nSSR, nuclear simple sequence repeat) and cpDNA profiles of the aDNA (ancient DNA) of seed remains were compared to modern water melon cultivars and landraces. Sixteen primer pairs were applied. Sequence analysis at the (CT)26 and cpDNA trnV loci revealed a (CT)3 and Adenin deletions, respectively, form the current water melon cultivar compared to the medieval sample. Cila-1), a new LTR retrotansposon has been described. For morphological reconstruction, a dendrogram produced by SPSS11 based on the presence versus absence of 24 phenotypic characters were also analyzed.
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Ladas, Ioannis, Harvey J. Mamon, Kimmie Ng, Fangyan Yu, Ka Wai Leong, Matthew H. Kulke et G. Mike Makgrigiorgos. « Sensitive detection of microsatellite instability in tumors and liquid biopsies using nuclease-based enrichment. » Journal of Clinical Oncology 37, no 15_suppl (20 mai 2019) : e15117-e15117. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e15117.
Texte intégralRésumé :
e15117 Background: The role of MSI in colorectal cancer (CRC) is well characterized, and tumors are classified as MSI-High or MSI-Stable by screening specific microsatellites. MSI-H reflects mismatch repair deficiency, is predictive for CRC therapy outcome in chemotherapy and immunotherapy and has a higher 5-year survival. While tumor testing is the gold standard, a convenient approach to screen for MSI before and during cancer treatment is screening circulating DNA (liquid biopsy) using a blood draw. However, using electrophoresis or next generation sequencing for MSI detection presents challenges at low levels of MSI due to polymerase slippage (‘stutter’) that generate high false positive rates at positions of homo-polymers. We present a new approach for enrichment of altered micro-satellites prior to DNA-amplification thereby reducing stutter from wild-type alleles and facilitating detection of MSI. The method employs a double-strand-DNA-specific nuclease and overlapping oligonucleotide-probes interrogating multiple micro-satellite targets (‘NaMe-PrO’, nuclease-assisted minor-allele enrichment with probe-overlap). Following DNA denaturation, the probes form double-stranded regions with their targets, thereby guiding nuclease digestion to selected sites. Microsatellite indels create ‘bulges’ that inhibit digestion, thus subsequent amplification yields DNA with microsatellite alterations enhanced at multiple targets. Methods: We first validated the method by evaluating 5 MSI targets simultaneously, NR27, NR21, NR24, BAT25 and BAT26 using DNA from tumor biopsies and circulating-DNA from colorectal cancer patients. The technique detected microsatellite alterations down to 0.01% altered allele frequency, thus improving detection sensitivity by > 100-fold relative to current approaches. Next, a clinical study was performed. We screened microsatellites in circulating DNA from groups of early stage colon cancer patients with known MSI status in the tumor. Results: Combination of NAME-PRO with capillary electrophoresis demonstrated 100% sensitivity (10/10) and 90% specificity (9/10) in detecting MSI status in the blood, thereby opening the possibility of early cancer detection for MSI positive tumors, or for application in minimal residual disease detection. Conclusions: We anticipate application of this highly- multiplex-able method either with standard 5-plex reactions or with NGS-based detection of MSI on thousands of targets to enable sensitive detection in tumors and liquid biopsies.
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Georgescu, Sergiu, Oana Canareica, Andreea Dudu et Marieta Costache. « Analysis of the Microsatellite Variation in the Common Hybrid Between Russian Sturgeon (Acipenser Gueldenstaedtii Brandt and Ratzeburg, 1833) and Siberian Sturgeon (Acipenser Baerii Brandt, 1869) from Aquaculture ». Transylvanian Review of Systematical and Ecological Research 15, no 2 (1 décembre 2013) : 117–24. http://dx.doi.org/10.2478/trser-2013-0024.
Texte intégralRésumé :
ABSTRACT Sturgeons such as Acipenser baerii and Acipenser gueldenstaedtii are the most common species farm raised worldwide in aquaculture, because of the dwindling natural sources of caviar and meat. Also, these species can easily participate in the formation of an intraspecific hybrid with a great potential for growth in aquaculture. Microsatellites are nuclear markers consisting of short repetitive sequence, dispersed across the entire genome with characteristics such as relatively small size and high level of polymorphism. The aims of the present study were to optimize a protocol for microsatellite multiplexing and analysis of genetic diversity in hybrid sturgeons farmed in Romania. Genomic DNA was isolated from fins, and four pairs of primers were designed to amplify microsatellite loci: LS 19, LS 68, Aox 9, and Aox 45. Amplification of the microsatellite loci was carried out in one 3-Plex reaction for LS 19, LS 68, and Aox 9, and monoplex reaction for Aox 45. For an individual locus we obtained four alleles for Aox 45, eleven alleles for Aox 9, six alleles for LS 68, and eight alleles for LS 19. The results will be applied to test the broodstocks at Romanian hatcheries and to increase the efficiency of breeding.
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Kyndt, T., B. Van Droogenbroeck, A. Haegeman, I. Roldán-Ruiz et G. Gheysen. « Cross-species microsatellite amplification in Vasconcellea and related genera and their use in germplasm classification ». Genome 49, no 7 (1 juillet 2006) : 786–98. http://dx.doi.org/10.1139/g06-035.
Texte intégralRésumé :
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.
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Chen, Chunxian, Lorraine Rodriguez-Bonilla et Thomas G. Beckman. « Assessment of Prunus Rootstock Accessions Using Chloroplast and Nuclear Microsatellites ». Journal of the American Society for Horticultural Science 147, no 2 (mars 2022) : 95–103. http://dx.doi.org/10.21273/jashs05137-21.
Texte intégralRésumé :
Abstract A rootstock collection of Prunus species and hybrids is maintained at the U.S. Department of Agriculture stone fruit breeding program at Byron, GA. We genotyped 66 Prunus rootstock accessions and clones using chloroplast and nuclear microsatellites in this study. Chloroplast microsatellites revealed that the accessions belong to four previously defined maternal lineage groups (MLG-1 to -4) and five new ones (MLG-9 to -13). MLG-1 and -2 share the same chloroplast alleles of ‘Chinese Cling’ peach (Prunus persica) derived scions and American scions and rootstocks related to early European introductions, respectively. MLG-3 included ‘Guardian’ rootstock and its descendants. MLG-4 had a single genotype, ‘Okinawa’, that is the maternal parent of ‘Flordaking’. MLG-9 and MLG-11 to -13 included hybrids with different plums (Prunus salicina, Prunus cerasifera, Prunus tomentosa, or Prunus angustifolia) in their maternal parentage. MLG-10 included hybrids from almond (Prunus. dulcis) in the maternal parentage. The neighbor-joining phylogenetic tree based on nuclear microsatellite genotyping data showed several clusters. Cluster I included only one scion cultivar Elberta from MLG-1. Clusters II, III, and V contained peach accessions mostly in MLG-2. Clusters IV and VI included accessions mostly in MLG-3. Cluster VII included most accessions of plum-peach hybrid origin and those found within MLG-13. Cluster VIII was found to be mixed with different plum-peach hybrids and hybrids from other Prunus species, most of which were found in MLG-10, -11, and -12. Most accessions in Cluster IX were related to plums in MLG-11 and a few accessions in MLG-9.
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VOGT, GÜNTER, CHRIS LUKHAUP, BRONWYN W. WILLIAMS, MICHAEL PFEIFFER, NATHAN J. DORN, RALF SCHULZ et ANNE SCHRIMPF. « Morphological characterization and genotyping of the marbled crayfish and new evidence on its origin ». Zootaxa 4524, no 3 (22 novembre 2018) : 329. http://dx.doi.org/10.11646/zootaxa.4524.3.3.
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The obligately parthenogenetic marbled crayfish, Procambarus virginalis, is the first formally described asexual species of the Crustacea Decapoda. It is a triploid descendant of the sexually reproducing slough crayfish, Procambarus fallax. Here we describe the morphology of cultured and wild marbled crayfish of wide size ranges in detail and photodocument all taxonomically relevant characters. Some morphological traits and coloration showed considerable variation within populations despite the monoclonal nature of marbled crayfish. There were also significant differences between wild and laboratory populations with respect to body proportions, coloration and spination. Comparison with Procambarus fallax revealed no qualitative morphological characters that unambiguously identify the marbled crayfish. Analysis of the mitochondrial cytochrome c oxidase subunit I gene (COI) and nuclear microsatellites of marbled crayfish and Procambarus fallax from different sources indicated that the tri-allelic microsatellite PclG-02 is better suitable than COI to identify the marbled crayfish. A respective identification key is provided. The COI and microsatellites of Procambarus fallax from different areas of Florida and southern Georgia suggest that the parents of the first marbled crayfish may have come from northern Union County, northern Florida.
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BHATTARAI, N. R., J. C. DUJARDIN, S. RIJAL, S. DE DONCKER, M. BOELAERT et G. VAN DER AUWERA. « Development and evaluation of different PCR-based typing methods for discrimination ofLeishmania donovaniisolates from Nepal ». Parasitology 137, no 6 (29 janvier 2010) : 947–57. http://dx.doi.org/10.1017/s0031182009991752.
Texte intégralRésumé :
SUMMARYIntroduction.Leishmania donovani, the causative agent of visceral leishmaniasis in the Indian subcontinent, has been reported to be genetically homogeneous. In order to support ongoing initiatives to eliminate the disease, highly discriminative tools are required for documenting the parasite population and dynamics.Methods.Thirty-four clinical isolates ofL.donovanifrom Nepal were analysed on the basis of size and restriction endonuclease polymorphisms of PCR amplicons from kinetoplast minicircle DNA, 5 nuclear microsatellites, and nuclear loci encoding glycoprotein 63, cysteine proteinase B, and hydrophilic acylated surface protein B. We present and validate a procedure allowing standardized analysis of kDNA fingerprint patterns.Results.Our results show that parasites are best discriminated on the basis of kinetoplast minicircle DNA (14 genotypes) and 1 microsatellite defining 7 genotypes, while the remaining markers discriminated 2 groups or were monomorphic. Combination of all nuclear markers revealed 8 genotypes, while extension with kDNA data yielded 18 genotypes.Conclusion.We present tools that allow discrimination of closely relatedL.donovanistrains circulating in the Terai region of Nepal. These can be used to study the micro-epidemiology of parasite populations, determine the geographical origin of infections, distinguish relapses from re-infection, and monitor the spread of particular variants.
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Nikolic, Biljana, Dragan Kovacevic, Snezana Mladenovic-Drinic, Ana Nikolic, Zorica Mitic, Srdjan Bojovic et Petar Marin. « Relationships among some pines from subgenera Pinus and Strobus revealed by nuclear EST-microsatellites ». Genetika 50, no 1 (2018) : 69–84. http://dx.doi.org/10.2298/gensr1801069n.
Texte intégralRésumé :
Genetic relationships among 12 taxa from subgenera Pinus and Strobus were studied through fourteen microsatellite markers, previously developed for Pinus taeda. To our knowledge, this is the first comparative study of pines using nuclear EST-microsatellites (EST-SSRs). The total number of detected alleles in all investigated taxa was 72 (5.14 in average). The numbers of alleles per locus and PIC values for estimated markers ranged from 3 to 7, and from 0.43 to 0.81, respectively. Presented results are in accordance with majority of previous genetic investigations and infrageneric classification of genus Pinus up to the sectional level, while subsectional position of some species has still not dismissed, especially regarding relict ones. According to nuclear EST-SSRs, Pinus heldreichii is in early-diverging position within subsection Pinaster and shows the greatest closeness with P. halepensis, while Pinus peuce doesn't have basal position within subsection Strobus being more close to P. strobus than to P. wallichiana. Furthermore, the closest connections in subsection Pinus were found between two Pinus nigra subspecies (dalmatica and nigra) as well as between P. sylvestris and P. mugo.
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Nagamitsu, Teruyoshi, Takayuki Kawahara et Ayako Kanazashi. « Inference of allelic dosages and inheritance modes in tetraploids : a case study in Betula apoiensis with a putative hybrid origin ». Silvae Genetica 63, no 1-6 (1 décembre 2014) : 159–68. http://dx.doi.org/10.1515/sg-2014-0021.
Texte intégralRésumé :
Abstract In tetraploids, inference of allelic dosages and inheritance modes is difficult due to the ambiguous number of allele copies and the variation between disomic and tetrasomic patterns. Considering the biases of amplification and the overlaps of stutter products in polymerase chain reactions, we inferred tetraploid genotypes at three nuclear microsatellite loci in progeny arrays from six reciprocal crosses among three parents of Betula apoiensis with a putative hybrid origin. In each cross, we assigned diploid genotypes to gametes on the basis of the tetraploid genotypes of the parents and their progeny and observed the frequencies of the gamete genotypes. Segregation patterns of the observed gamete genotypes indicated few null alleles in the progeny arrays and tetrasomic inheritance with rare double reduction. This mode of inheritance was consistent between genders and between mates in the crosses. This result suggests that our method to infer tetraploid genotypes in nuclear microsatellites is successful in family samples with few null alleles when the amplification biases and the stutter-product overlaps are accessed properly.
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Healey, Amy J. E., Gavin Gouws, Sean T. Fennessy, Baraka Kuguru, Warwick H. H. Sauer, Paul W. Shaw et Niall J. McKeown. « Genetic analysis reveals harvested Lethrinus nebulosus in the Southwest Indian Ocean comprise two cryptic species ». ICES Journal of Marine Science 75, no 4 (5 janvier 2018) : 1465–72. http://dx.doi.org/10.1093/icesjms/fsx245.
Texte intégralRésumé :
Abstract This study initially aimed to investigate the genetic population/stock structuring of Lethrinus nebulosus in the Southwest Indian Ocean (SWIO) to inform management practices in light of emerging evidence of overharvesting of this species throughout its distribution. Adult samples were genotyped for 14 nuclear microsatellites and by sequencing fragments of the mtDNA control region and COI gene. A salient feature of the data was the congruent cyto-nuclear partitioning of samples into two high divergent, reciprocally monophyletic groups. This indicates that despite no a priori evidence, hitherto described L. nebulosus in the SWIO comprises two cryptic species that co-occur among southern samples. This intermingling indicates that, at least in southern samples, both species are being indiscriminately harvested, which may severely compromise sustainability. Limited microsatellite differentiation was detected within both species, though there was some evidence of isolation in the Mauritian population. In contrast, mtDNA revealed a pattern consistent with chaotic genetic patchiness, likely promoted by stochastic recruitment, which may necessitate a spatial bet-hedging approach to management to satisfy fishery management and conservation goals.
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Mattiucci, Simonetta, Eleonora Bello, Michela Paoletti, Steve C. Webb, Juan T. Timi, Arne Levsen, Paolo Cipriani et Giuseppe Nascetti. « Novel polymorphic microsatellite loci in Anisakis pegreffii and A. simplex (s. s.) (Nematoda : Anisakidae) : implications for species recognition and population genetic analysis ». Parasitology 146, no 11 (28 juin 2019) : 1387–403. http://dx.doi.org/10.1017/s003118201900074x.
Texte intégralRésumé :
AbstractThe species of Anisakis constitute one of the most widespread groups of ascaridoid nematodes in the marine ecosystem. Three closely related taxa are recognised in the A. simplex (s. l.) complex, i.e. A. pegreffii, A. simplex (s. s.) and A. berlandi. They are distributed in populations of their intermediate/paratenic (fish and squids) and definitive (cetaceans) hosts. A panel of seven microsatellite loci (Anisl 05784, Anisl 08059, Anisl 00875, Anisl 07132, Anisl 00314, Anisl 10535 and Anisl 00185), were developed and validated on a total of N = 943 specimens of A. pegreffii and A. simplex (s. s.), collected in fish and cetacean hosts from allopatric areas within the range of distribution of these parasite species. In addition, the locus Anisl 7, previously detected in those Anisakis spp., was investigated. The parasites were first identified by sequence analysis of the EF1 α-1 nDNA. The panel of the microsatellites loci here developed have allowed to: (i) detect diagnostic microsatellite loci between the two species; (ii) identify specimens of the two species A. pegreffii, A. simplex (s. s.) in a multi-marker nuclear genotyping approach; (iii) discover two sex-linked loci in both Anisakis species and (iv) estimate levels of genetic differentiation at both the inter- and intra-specific level.
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RODRIGUEZ, N., H. DE LIMA, A. RODRIGUEZ, S. BREWSTER et D. C. BARKER. « Genomic DNA repeat from Leishmania (Viannia) braziliensis (Venezuelan strain) containing simple repeats and microsatellites ». Parasitology 115, no 4 (octobre 1997) : 349–58. http://dx.doi.org/10.1017/s003118209700139x.
Texte intégralRésumé :
In this paper the Leishmania (Viannia) braziliensis complex is defined as containing all species of the actual subgenus Viannia. Organisms of the L. (V) braziliensis complex are the causative agents of localized human cutaneous and mucocutaneous leishmaniasis in South America, much of Central America and some areas of North America. In our search for better species and subspecies diagnostic probes we focused our research on repetitive DNA, since it provides a greater number of target sites for hybridization. In this work we report the isolation and sequencing of a 1·8 kb DNA region, LbJ38, which is probably tandemly repeated or dispersed at least 4 times along one chromosome and is naturally present in L. (V) braziliensis genomic DNA. This region contains microsatellites and simple repeat DNA sequences and was isolated by screening a genomic DNA cosmid library with complex- and species-specific probes. No homology was found with other Leishmania microsatellite or repetitive DNA. The utility of this repetitive sequence and primers derived from it in the identification of L. (V) braziliensis is demonstrated. As far as we are aware, this is the first report of sequence characterized repetitive microsatellite and GC rich simple repeat DNA from the nuclear genome of New World Leishmania.
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Putnová, L., R. Štohl et I. Vrtková. « Using nuclear microsatellite data to trace the gene flow and population structure in Czech horses ». Czech Journal of Animal Science 64, No. 2 (13 février 2019) : 67–77. http://dx.doi.org/10.17221/2/2018-cjas.
Texte intégralRésumé :
Based on a data set comprising 2879 animals and 17 nuclear microsatellite DNA markers, we propose the most comprehensive in-depth study mapping the genetic structure and specifying the assignment success rates in horse breeds at the Czech population scale. The STRUCTURE program was used to perform systematic Bayesian clustering via the Markov chain Monte Carlo estimation, enabling us to explain the population stratification and to identify genetic structure patterns within breeds worldwide. In total, 182 different alleles were found over all the populations and markers, with the mean number of 10.7 alleles per locus. The expected heterozygosity ranged from 0.459 (Friesian) to 0.775 (Welsh Part Bred), and the average level reached 0.721. The average observed heterozygosity corresponded to 0.709, with the highest value detected in the Czech Sport Pony (0.775). The largest number of private alleles was found in Equus przewalskii. The population inbreeding coefficient F<sub>IS</sub> ranged from –0.08 in the Merens to 0.14 in the Belgian Warmblood. The total within-population inbreeding coefficient was estimated to be moderate. As expected, very large genetic differentiation and small gene flow were established between the Friesian and Equus przewalskii (F<sub>ST </sub>= 0.37, Nm = 0.43). Zero F<sub>ST</sub> values indicated no differences between the Czech Warmblood–Slovak Warmblood and the Czech Warmblood–Bavarian Warmblood. A high level of breeding and connectivity was revealed between the Slovak Warmblood–Bavarian Warmblood, Dutch Warmblood–Oldenburg Horse, Bavarian Warmblood–Dutch Warmblood, and Bavarian Warmblood–Oldenburg Horse. The breeds’ contribution equalled about 6% of the total genetic variability. The overall proportion of individuals correctly assigned to a population corresponded to 82.4%. The posterior Bayesian approach revealed a hierarchical dynamic genetic structure in four clusters (hot-blooded, warm-blooded, cold-blooded, and pony). While most of the populations were genetically distinct from each other and well-arranged with solid breed structures, some of the entire sets showed signs of admixture and/or fragmentation.
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Schueler, Silvio, Alexandra Tusch, Mirko Schuster et Birgit Ziegenhagen. « Characterization of microsatellites in wild and sweet cherry (Prunus avium L.) markers for individual identification and reproductive processes ». Genome 46, no 1 (1 février 2003) : 95–102. http://dx.doi.org/10.1139/g02-107.
Texte intégralRésumé :
Nuclear microsatellites were characterized in Prunus avium and validated as markers for individual and cultivar identification, as well as for studies of pollen- and seed-mediated gene flow. We used 20 primer pairs from a simple sequence repeat (SSR) library of Prunus persica and identified 7 loci harboring polymorphic microsatellite sequences in P. avium. In a natural population of 75 wild cherry trees, the number of alleles per locus ranged from 4 to 9 and expected heterozygosity from 0.39 to 0.77. The variability of the SSR markers allowed an unambiguous identification of individual trees and potential root suckers. Additionally, we analyzed 13 sweet cherry cultivars and differentiated 12 of them. An exclusion probability of 0.984 was calculated, which indicates that the seven loci are suitable markers for paternity analysis. The woody endocarp was successfully used for resolution of all microsatellite loci and exhibited the same multilocus genotype as the mother tree, as shown in a single seed progeny. Hence, SSR fingerprinting of the purely maternal endocarp was also successful in this Prunus species, allowing the identification of the mother tree of the dispersed seeds. The linkage of microsatellite loci with PCR-amplified alleles of the self-incompatibility locus was tested in two full-sib families of sweet cherry cultivars. From low recombination frequencies, we inferred that two loci are linked with the S locus. The present study provides markers that will significantly facilitate studies of spatial genetic variation and gene flow in wild cherry, as well as breeding programs in sweet cherry.Key words: Prunus, SSR, S alleles, endocarp, seed dispersal, cultivar identification.
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Rathbone, Damien A., Gay E. McKinnon, Brad M. Potts, Dorothy A. Steane et René E. Vaillancourt. « Microsatellite and cpDNA variation in island and mainland populations of a regionally rare eucalypt, Eucalyptus perriniana (Myrtaceae) ». Australian Journal of Botany 55, no 5 (2007) : 513. http://dx.doi.org/10.1071/bt06203.
Texte intégralRésumé :
Eucalyptus perriniana F.Muell. ex Rodway is distributed over a wide geographic range in south-eastern Australia as a series of small and isolated populations. In Tasmania, there are only three known populations that are separated by 511 km from the closest population on mainland Australia, which is one of the largest disjunctions observed for any eucalypt species. This project utilised eight nuclear microsatellites and one chloroplast DNA marker to study the genetic diversity in E. perriniana and determine the affinities between the populations. In all, 302 individuals in nine populations across the whole range of the species were sampled. The overall nuclear microsatellite diversity in E. perriniana (Ht = 0.85), as well as the diversity in each population (He = 0.73), was comparable to that found in widespread eucalypt species that have much larger population sizes. The microsatellites revealed that the isolated Tasmanian populations were significantly differentiated from mainland populations (FST between regions = 0.08), although the mainland Baw Baw population was the most differentiated. Most populations harboured different chloroplast DNA haplotypes, but in general, there were more mutational differences among haplotypes found in Tasmania than between Tasmanian and mainland populations. The Tasmanian populations often shared chloroplast DNA haplotypes with other eucalypts from south-eastern Tasmania. In conclusion, the populations of E. perriniana are genetically variable and significantly differentiated, with geographic separation being a poor predictor of the amount of genetic divergence. The most divergent populations are those in Tasmania and on Mt Baw Baw and their conservation is important to capture the genetic diversity in the species.
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KYRKJEEIDE, MAGNI OLSEN, KRISTIAN HASSEL, BLANKA SHAW, A. JONATHAN SHAW, EVA M. TEMSCH et KJELL IVAR FLATBERG. « Sphagnum incundum a new species in Sphagnum subg. Acutifolia (Sphagnaceae) from boreal and arctic regions of North America ». Phytotaxa 333, no 1 (5 janvier 2018) : 1. http://dx.doi.org/10.11646/phytotaxa.333.1.1.
Texte intégralRésumé :
We describe Sphagnum incundum in Sphagnum subgenus Acutifolia (Sphagnaceae, Bryophyta). We used both molecular and morphological methods to describe the new species. Molecular relationships with closely related species were explored based on microsatellites and nuclear and plastid DNA sequences. The morphological description is based on qualitative examination of morphological characters and measurements of leaves and hyalocysts. Morphological characters are compared between closely related species. The results from Feulgen densitometry and microsatellite analysis show that S. incundum is gametophytically haploid. Molecular analyses show that it is a close relative to S. flavicomans, S. subfulvum and S. subnitens, but differs both genetically and in morphological key characters, justifying the description of S. incundum as a new species. The new peatmoss is found in North America along the western coast of Greenland, in Canada from Quebec and Northwest Territories, and Alaska (United States). The new species has a boreal to arctic distribution.
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Matallanas, Beatriz, Carmen Callejas et M. Dolores Ochando. « A Genetic Approach to Spanish Populations of the ThreatenedAustropotamobius italicusLocated at Three Different Scenarios ». Scientific World Journal 2012 (2012) : 1–9. http://dx.doi.org/10.1100/2012/975930.
Texte intégralRésumé :
Spanish freshwater ecosystems are suffering great modification and some macroinvertebrates likeAustropotamobius italicus, the white-clawed crayfish, are threatened. This species was once widely distributed in Spain, but its populations have shown a very strong decline over the last thirty years, due to different factors. Three Spanish populations of this crayfish—from different scenarios—were analysed with nuclear (microsatellites) and mitochondrial markers (COIand16S rDNA). Data analyses reveal the existence of four haplotypes at mitochondrial level and polymorphism for four microsatellite loci. Despite this genetic variability, bottlenecks were detected in the two natural Spanish populations tested. In addition, the distribution of the mitochondrial haplotypes and SSR alleles show a similar geographic pattern and the genetic differentiation between these samples is mainly due to genetic drift. Given the current risk status of the species across its range, this diversity offers some hope for the species from a management point of view.
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Sukhotu, Thitaporn, Osamu Kamijima et Kazuyoshi Hosaka. « Nuclear and chloroplast DNA differentiation in Andean potatoes ». Genome 47, no 1 (1 janvier 2004) : 46–56. http://dx.doi.org/10.1139/g03-105.
Texte intégralRésumé :
Over 3500 accessions of Andean landraces have been known in potato, classified into 7 cultivated species ranging from 2x to 5x (Hawkes 1990). Chloroplast DNA (ctDNA), distinguished into T, W, C, S, and A types, showed extensive overlaps in their frequencies among cultivated species and between cultivated and putative ancestral wild species. In this study, 76 accessions of cultivated and 19 accessions of wild species were evaluated for ctDNA types and examined by ctDNA high-resolution markers (ctDNA microsatellites and H3 marker) and nuclear DNA restriction fragment length polymorphisms (RFLPs). ctDNA high-resolution markers identified 25 different ctDNA haplotypes. The S- and A-type ctDNAs were discriminated as unique haplotypes from 12 haplotypes having C-type ctDNA and T-type ctDNA from 10 haplotypes having W-type ctDNA. Differences among ctDNA types were strongly correlated with those of ctDNA high-resolution markers (r = 0.822). Differentiation between W-type ctDNA and C-, S-, and A-type ctDNAs was supported by nDNA RFLPs in most species except for those of recent or immediate hybrid origin. However, differentiation among C-, S-, and A-type ctDNAs was not clearly supported by nDNA RFLPs, suggesting that frequent genetic exchange occurred among them and (or) they shared the same gene pool owing to common ancestry.Key words: potato, chloroplast DNA, microsatellite markers, nuclear DNA RFLPs.
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Poggi, Lucie, Lisa Emmenegger, Stéphane Descorps-Declère, Bruno Dumas et Guy-Franck Richard. « Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations ». Nucleic Acids Research 49, no 14 (7 juillet 2021) : 8120–34. http://dx.doi.org/10.1093/nar/gkab569.
Texte intégralRésumé :
Abstract Microsatellite expansions are the cause of >20 neurological or developmental human disorders. Shortening expanded repeats using specific DNA endonucleases may be envisioned as a gene editing approach. Here, we measured the efficacy of several CRISPR–Cas nucleases to induce recombination within disease-related microsatellites, in Saccharomyces cerevisiae. Broad variations in nuclease performances were detected on all repeat tracts. Wild-type Streptococcus pyogenes Cas9 (SpCas9) was more efficient than Staphylococcus aureus Cas9 on all repeats tested, except (CAG)33. Cas12a (Cpf1) was the most efficient on GAA trinucleotide repeats, whereas GC-rich repeats were more efficiently cut by SpCas9. The main genetic factor underlying Cas efficacy was the propensity of the recognition part of the sgRNA to form a stable secondary structure, independently of its structural part. This suggests that such structures form in vivo and interfere with sgRNA metabolism. The yeast genome contains 221 natural CAG/CTG and GAA/CTT trinucleotide repeats. Deep sequencing after nuclease induction identified three of them as carrying statistically significant low frequency mutations, corresponding to SpCas9 off-target double-strand breaks.
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Augustinos, Antonios A., Constantinos Petropoulos, Vassiliki Karasoulou, Fotios Bletsos et Vasilis Papasotiropoulos. « Assessing diversity among traditional Greek and foreign eggplant cultivars using molecular markers and morphometrical descriptors ». Spanish Journal of Agricultural Research 14, no 4 (2 décembre 2016) : e0710. http://dx.doi.org/10.5424/sjar/2016144-9020.
Texte intégralRésumé :
Eggplant is a widely cultivated vegetable crop of great economic importance. Its long lasting history of domestication, selection and breeding has led to the development of numerous cultivars with variable traits. In the present study, we assessed the diversity levels within and among eleven Greek and foreign cultivars, using 22 morphological descriptors and two different classes of molecular markers (retrotransposon microsatellite amplified polymorphism-REMAP markers and nuclear microsatellites). Our results, in accordance with other studies in the field showed: a) the limited levels of genetic polymorphism within the cultivars; b) the high morphological and genetic divergence existing among them as indicated by the genetic distance values calculated, which could be attributed to selection, inbreeding and bottleneck effects; and c) the lack of concordance among morphological descriptors and molecular markers. Despite these, our analysis showed that the utilization of combinations of markers is an effective method for the characterization of plant material providing also useful diagnostic tools for the identification and authentication of the selected Greek cultivars.
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Kurokochi, Hiroyuki, Yoko Saito et Yuji Ide. « Genetic structure of the introduced heaven tree (Ailanthus altissima) in Japan : evidence for two distinct origins with limited admixture ». Botany 93, no 3 (mars 2015) : 133–39. http://dx.doi.org/10.1139/cjb-2014-0181.
Texte intégralRésumé :
The heaven tree, Ailanthus altissima (Mill.) Swingle, was intentionally introduced from China to many temperate areas globally, where it has become successfully established. Here, we investigated the patterns of genetic differentiation between introduced Japanese A. altissima populations using both plastid and nuclear microsatellite markers. Three hundred and eighty-eight trees were sampled from six planted and 12 naturalized populations. Two distinct chloroplastic haplotypes were observed, which allowed us to separate two groups of trees, H1 and H3, containing 128 and 260 trees, respectively. Nine nuclear genetic microsatellites revealed 17.7 alleles per locus on average. These data did not indicate significant isolation-by-distance. Analysis of molecular variance showed the absence of genetic differentiation between the planted and naturalized populations. In contrast, the two groups defined according to the chloroplastic haplotypes (H1 and H3) were differentiated. STRUCTURE analysis showed that, within each haplotype group, most trees were strictly assigned to one cluster, with the exception of a few (ca. 30) trees. Our results indicate that (1) geographical genetic structure was weak, with high genetic variation among populations; (2) a congruent signal was revealed by chloroplastic and nuclear markers, indicating two distinct provenances; and (3) admixture between the two lineages has occurred, but remains limited. Several other invasive plant species have already been reported to exhibit similar trends; hence, future management of A. altissima might be required in Japan.
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Helena, Cvrčková, Máchová Pavlína, Poláková Lucie et Trčková Olga. « Evaluation of the genetic diversity of selected Fagus sylvatica L. populations in the Czech Republic using nuclear microsatellites ». Journal of Forest Science 63, No. 2 (28 février 2017) : 53–61. http://dx.doi.org/10.17221/88/2016-jfs.
Texte intégralRésumé :
Fagus sylvatica Linnaeus (European beech), the ecologically and economically most important broadleaved tree species in the Czech Republic, was strongly reduced in the past. Today there are efforts to increase the proportion of beech to ensure optimal forest tree species composition. When extensively reintroducing beech, it is important to acquire more detailed knowledge of genetic diversity. Thirteen important beech populations in different stands in the territory of the Czech Republic were genotyped using 12 polymorphic nuclear microsatellite markers. The genotypic data from adult trees imply genetic differences between the populations. The estimated genetic diversity expressed as Shannon’s information index ranged from 1.73 to 1.92. Thirteen beech populations showed excess homozygotes, as indicated by positive fixation index (F) values (F = 0.005–0.115). The pairwise F<sub>ST</sub> values indicated low genetic differentiation between the 13 Czech beech populations, because they were greater than zero, that means they confirmed the presence of population structuring in Czech European beech. Not significant linear correlations were observed between genetic and geographic distances of the 13 beech populations studied on the basis of microsatellite markers. Twelve microsatellite markers were verified as highly polymorphic and suitable for genotyping of European beech populations.
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Portnoy, David S., Christopher M. Hollenbeck, Dana M. Bethea, Bryan S. Frazier, Jim Gelsleichter et John R. Gold. « Population structure, gene flow, and historical demography of a small coastal shark (Carcharhinus isodon) in US waters of the Western Atlantic Ocean ». ICES Journal of Marine Science 73, no 9 (18 juin 2016) : 2322–32. http://dx.doi.org/10.1093/icesjms/fsw098.
Texte intégralRésumé :
AbstractPatterns of population structure, genetic demographics, and gene flow in the small coastal shark Carcharhinus isodon (finetooth shark) sampled from two discrete nurseries along the southeastern US coast (Atlantic) and three nurseries in the northern Gulf of Mexico (Gulf), were assessed using 16 nuclear-encoded microsatellites and 1077 base pairs of the mitochondrial DNA (mtDNA) control region. Significant heterogeneity in microsatellite allele distributions was detected among all localities except between the two in the Atlantic. Significant heterogeneity in mtDNA haplotypes was not detected, a result likely due to extremely low mtDNA diversity. The genetic discontinuities combined with seasonal movement patterns, a patchy distribution of appropriate nursery habitat, the apparent absence of sex-biased gene flow, and the occurrence of mating in the vicinity of nursery areas, suggest that both male and female finetooth sharks display regional philopatry to discrete nursery areas. Global and local tests of neutrality, using mtDNA haplotypes, and demographic model testing, using Approximate Bayesian Computation of microsatellite alleles, supported a range-wide expansion of finetooth sharks into US waters occurring less than ∼9000 years ago. These findings add to the growing number of studies in a variety of coastally distributed marine fishes documenting significant barriers to gene flow around peninsular Florida and in the eastern Gulf. The findings also provide further evidence that the traditional model of behavioural ecology, based on large coastal sharks, may not be appropriate for understanding and conserving small coastal sharks.
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Gömöry, D., L. Paule, D. Krajmerová, I. Romšáková et J. Piecka. « Gene exchange across a postglacial contact zone in Fraxinus excelsior L. » Silvae Genetica 61, no 1-6 (1 décembre 2012) : 18–27. http://dx.doi.org/10.1515/sg-2012-0003.
Texte intégralRésumé :
Abstract Hybridization between divergent lineages of common ash Fraxinus excelsior L. was studied in Slovakia and adjacent regions of Hungary, the Czech Republic and Poland in the contact zone between two postglacial colonization routes originating from different glacial refugia. Thirty-eight common ash populations were studied using a combination of 6 maternally inherited chloroplast microsatellite markers and 7 biparentally inherited nuclear microsatellites (nSSR). Two predominant chloroplast lineages were identified, between which the boundary was very sharp. Populations containing a mixture of different haplotypes were found only in the immediate proximity of the boundary. Bayesian analysis of population structure based on nSSR loci revealed the existence of two clusters, which largely coincided with chloroplast lineages. Both haplotype frequencies and proportions of clusters identified by the Bayesian analysis exhibited a clinal transition over the hybrid zone, with cline widths of 36 km for chloroplast haplotype frequencies (reflecting gene flow by seeds) and 275 km for Bayesian clusters based on nSSR (reflecting gene flow by pollen and seeds). Chloroplast haplotype diversity increased along the boundary between lineages not only because of admixture, but also due to the presence of rare haplotypes. In contrast, diversity at nuclear loci did not exhibit any geographical trend.
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Kokoska, Robert J., Lela Stefanovic, Hiep T. Tran, Michael A. Resnick, Dmitry A. Gordenin et Thomas D. Petes. « Destabilization of Yeast Micro- and Minisatellite DNA Sequences by Mutations Affecting a Nuclease Involved in Okazaki Fragment Processing (rad27) and DNA Polymerase δ (pol3-t) ». Molecular and Cellular Biology 18, no 5 (1 mai 1998) : 2779–88. http://dx.doi.org/10.1128/mcb.18.5.2779.
Texte intégralRésumé :
ABSTRACT We examined the effects of mutations in the Saccharomyces cerevisiae RAD27 (encoding a nuclease involved in the processing of Okazaki fragments) and POL3 (encoding DNA polymerase δ) genes on the stability of a minisatellite sequence (20-bp repeats) and microsatellites (1- to 8-bp repeat units). Both therad27 and pol3-t mutations destabilized both classes of repeats, although the types of tract alterations observed in the two mutant strains were different. The tract alterations observed in rad27 strains were primarily additions, and those observed in pol3-t strains were primarily deletions. Measurements of the rates of repetitive tract alterations in strains with both rad27 and pol3-t indicated that the stimulation of microsatellite instability by rad27 was reduced by the effects of the pol3-t mutation. We also found that rad27 and pol3-01 (an allele carrying a mutation in the “proofreading” exonuclease domain of DNA polymerase δ) mutations were synthetically lethal.
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O'Brien, David. « How did the toad get over the sea to Skye ? Tracing the colonisation of Scottish inshore islands by common toads (Bufo bufo) ». Herpetological Journal, Volume 31, Number 4 (1 octobre 2021) : 204–13. http://dx.doi.org/10.33256/31.4.204213.
Texte intégralRésumé :
Processes of island colonisation have long been of interest to biologists. Colonisation events themselves are rarely observed, but the processes involved may be inferred using genetic approaches. We investigated possible means of island colonisation by common toads (Bufo bufo) in western Scotland (the Isle of Skye and five neighbouring small islands), using evidence derived from nuclear microsatellites and mitochondrial (mt) DNA. Levels of microsatellite allelic richness for populations on Skye were high and comparable to adjacent mainland populations, but lower for populations on small islands. Pairwise measures of genetic distances between populations and a clustering algorithm were both suggestive of frequent gene flow between Skye and the mainland. For small islands the levels of genetic differentiation were higher, implying stronger isolation and no evidence for inbreeding. The distribution of mtDNA haplotypes broadly mirrored the genetic structure revealed by microsatellites. Reconciled with existing palaeoclimatological evidence, since the last glaciation, our findings rule out the possibility that the B. bufo populations stem from glacial refugia, or that recent anthropogenic transfer of toads is responsible for their current distribution. The most parsimonious explanation of our data is that the studied inshore islands have been repeatedly colonised via rafting from the mainland or neighbouring islands. This may give us insights into the processes likely to take place when ice sheets retreat poleward as a result of climate change. It also has implications for the colonisation of both native and invasive non-native species, and hence the biosecurity of island refugia.
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Borrell, Yaisel J., Jorge A. Piñera, José A. Sánchez Prado et Gloria Blanco. « Mitochondrial DNA and microsatellite genetic differentiation in the European anchovy Engraulis encrasicolus L. » ICES Journal of Marine Science 69, no 8 (1 septembre 2012) : 1357–71. http://dx.doi.org/10.1093/icesjms/fss129.
Texte intégralRésumé :
Abstract Borrell, Y. J., Piñera, J. A., Sanchez Prado, J. A., and Blanco, G. 2012. Mitochondrial DNA and microsatellite genetic differentiation in the European anchovy Engraulis encrasicolus L. – ICES Journal of Marine Science, 69: . The European anchovy Engraulisencrasicolus is currently one of the principal target species for commercial fisheries in Europe, and most stocks are overfished at present. In this work, specimens were sampled in the Bay of Biscay (Cantabrian, Basque Country, and French coasts) in 2009 and also in the Mediterranean (Adriatic Sea). Mitochondrial DNA (mtDNA; cytochrome b and 16S) was sequenced, and 14 nuclear microsatellites showing high and low levels of polymorphism were arranged in three multiplex polymerase chain reaction (PCR) systems and genotyped. Two main ancient mitochondrial clades were found. These clades are separated by 15 mutational steps and 1.7% sequence divergence, corresponding to a separation time of ∼0.5 million years ago. Our results using both mtDNA and microsatellites suggest the presence of at least three genetically differentiated groups: the west Cantabrian Sea, the rest of the populations in the Bay of Biscay, and the Mediterranean. Although it is known that western Iberian Atlantic populations of E. encrasicolus may be genetically different from those of the Bay of Biscay, the results suggest that the transition between these groups may be as close as a 100 km and that a recent genetic homogenization process in the eastward area of the Bay of Biscay has probably occurred.
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Pollegioni, P., K. Woeste, A. Major, G. Scarascia Mugnozza et Maria Emilia Malvolti. « Characterization of Juglans nigra (L.), Juglans regia (L.) and Juglans x intermedia (Carr.) by SSR markers : a case study in Italy ». Silvae Genetica 58, no 1-6 (1 décembre 2009) : 68–78. http://dx.doi.org/10.1515/sg-2009-0009.
Texte intégralRésumé :
Abstract Juglans nigra and Juglans regia are economically important species in Europe, Asia and North America. Natural hybrids between the two species, known as Juglans x intermedia (Carr), are valued for timber production. We tested ten nuclear microsatellite markers to (1) identify new J. x intermedia hybrids and characterize their parentage species J. regia and J. nigra (2) detect J. nigra genotypes with a spontaneous crossing ability with J. regia in a mixed Italian population. This study was also designed to confirm the transferability of ten black walnut SSR loci to Persian walnut All ten microsatellites amplified in both species, producing fragments of variable size; eight (7.14%) were common, 68 (60.7%) amplified in J. nigra and 36 (32.1%) in J. regia only (private alleles). Indices of genetic diversity revealed high level of variability. The Principal Coordinate Analysis on the basis of total 112 alleles divided the total sample set into three main groups: J. nigra, J. regia and J. x intermedia hybrids. Performing the microsatellite fingerprinting, a triploid hybrid plant with two genome parts of J. nigra and one part of J. regia was identified. The cytological analysis proved this triploid state showing 48 somatic chromosomes. The mother testing analysis of the 7 diploid hybrids by exclusion method indicated one putative hybridogenic mother plants. The sequence analysis of amplified fragments confirmed the cross-species amplification of SSR. Inter-specific differences between alleles were due not only to simple changes in the number of repeats but also to mutations in the flanking regions.