Chloroplast microsatellite diversity of Opisthopappus Shih (Asteraceae) endemic to China

2013 ◽  
Vol 299 (10) ◽  
pp. 1849-1858 ◽  
Author(s):  
Yiling Wang
Keyword(s):  
Chloroplast Microsatellite ◽  
Microsatellite Diversity

scholarly journals Chloroplast Microsatellite Diversity Among and Within Prunus mahaleb L. and P. avium L. Species

2012 ◽  
Vol 4 (5) ◽  
Author(s):  
Masoud Abedian ◽  
Majid Talebi ◽  
Badraldin-Ebrahim Sayed-Tabatabei ◽  
Cyrus Ghobadi
Keyword(s):  
Chloroplast Microsatellite ◽  
Prunus Mahaleb ◽  
Microsatellite Diversity

Molecular genetic variation in a widespread forest tree species Eucalyptus obliqua (Myrtaceae) on the island of Tasmania

2011 ◽  
Vol 59 (3) ◽  
pp. 226 ◽  
Author(s):  
Justin A. Bloomfield ◽  
Paul Nevill ◽  
Brad M. Potts ◽  
René E. Vaillancourt ◽  
Dorothy A. Steane
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Environmental Gradients ◽  
Molecular Genetic ◽  
Continuous Distribution ◽  
Main Mode ◽  
Chloroplast Microsatellite ◽  
Eastern Australia ◽  
Nuclear Microsatellite ◽  
Microsatellite Diversity

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.

scholarly journals Chloroplast Microsatellite Diversity in Phaseolus vulgaris

2013 ◽  
Vol 3 ◽  
Author(s):  
F. Desiderio ◽  
E. Bitocchi ◽  
E. Bellucci ◽  
D. Rau ◽  
M. Rodriguez ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Chloroplast Microsatellite ◽  
Microsatellite Diversity

Nuclear and chloroplast microsatellite diversity in Phaseolus vulgaris L. from Sardinia (Italy)

2008 ◽  
Vol 23 (3) ◽  
pp. 413-429 ◽  
Author(s):  
S. A. Angioi ◽  
D. Rau ◽  
M. Rodriguez ◽  
G. Logozzo ◽  
F. Desiderio ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Phaseolus Vulgaris L ◽  
Chloroplast Microsatellite ◽  
Microsatellite Diversity

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.

scholarly journals A PCR-based Assay for Distinguishing between A1 and A2 Mating Types of Phytophthora capsici

2017 ◽  
Vol 142 (4) ◽  
pp. 260-264
Author(s):  
Ping Li ◽  
Dong Liu ◽  
Min Guo ◽  
Yuemin Pan ◽  
Fangxin Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mating Type ◽  
Phytophthora Capsici ◽  
Mating Types ◽  
Sequence Repeat ◽  
Chain Reaction ◽  
Plant Parasite ◽  
Dna Fragment ◽  
Polymerase Chain ◽  
Microsatellite Diversity

Sexual reproduction in the plant parasite Phytophthora capsici Leonian requires the interaction of two distinct mating types, A1 and A2. Co-occurrence of these mating types can enhance the genetic diversity of P. capsici and alter its virulence or resistance characteristics. Using an intersimple sequence repeat (ISSR) screen of microsatellite diversity, we identified, cloned, and sequenced a novel 1121-base pair (bp) fragment specific to the A1 mating type of P. capsici. Primers Pcap-1 and Pcap-2 were designed from this DNA fragment to specifically detect the A1 mating type. Polymerase chain reaction (PCR) using these primers amplified an expected 997-bp fragment from known A1 mating types, but yielded a 508-bp fragment from known A2 mating types. This PCR-based assay could be adapted to accurately and rapidly detect the co-occurrence of A1 and A2 P. capsici mating types from field material.

Chloroplast DNA polymorphism reveals geographic structure and introgression in the Quercus crassifolia × Quercus crassipes hybrid complex in Mexico

Botany ◽  
2008 ◽  
Vol 86 (3) ◽  
pp. 228-239 ◽  
Author(s):  
E. Tovar-Sánchez ◽  
P. Mussali-Galante ◽  
R. Esteban-Jiménez ◽  
D. Piñero ◽  
D. M. Arias ◽  
...  
Keyword(s):  
Parental Species ◽  
Diversity Index ◽  
Hot Spot ◽  
Haplotype Diversity ◽  
Hybrid Zones ◽  
Chloroplast Microsatellite ◽  
Colonization Routes ◽  
Allopatric Populations ◽  
Genetic Structure Of Populations ◽  
Hybrid Complex

Quercus crassifolia H. & B. and Quercus crassipes H. & B. are two common temperate forest species in Mexico that form hybrids when they occur in mixed (sympatric) areas. In this study, we used chloroplast microsatellite haplotypes to infer phylogeographic patterns onto the genetic structure of populations of both parental species, thus defining probable colonization routes throughout Mexico. Haplotype diversity in seven hybrid zones and four allopatric sites with nonmixed (allopatric) populations of both putative parental species was analyzed. To determine the expansion and colonization routes for the two species, we carried out a nested clade phylogeographic analysis that would allow us to infer the haplotype correspondence to a phylogeographical approach. In spite of sharing many common populations, we determined that there is a different genetic historical colonization for Q. crassipes and for Q. crassifolia. Hybrid populations had the highest levels of genetic variation (Gv), Shannon diversity index (H), and haplotype number (nh) in comparison with nonmixed/allopatric populations of their putative parentals. Furthermore, populations of hybrid zones showed the highest values of genetic differentiation FST, RST . Moreover, both species share four distinctive cpDNA haplotypes, which were most likely acquired by introgression through hybrids located in several populations throughout the Eje Neovolcánico area. This last region was confirmed to be a “hot spot” for oak diversity, a place in which different maternal lineages merged.

scholarly journals Creation of a Chloroplast Microsatellite Reporter for Detection of Replication Slippage in Chlamydomonas reinhardtii

2008 ◽  
Vol 7 (4) ◽  
pp. 639-646 ◽  
Author(s):  
Monica GuhaMajumdar ◽  
Ethan Dawson-Baglien ◽  
Barbara B. Sears
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Forensic Analysis ◽  
Direct Repeats ◽  
Reporter Construct ◽  
Chloroplast Microsatellite ◽  
Replication Slippage ◽  
Reading Frame ◽  
Viable Cells ◽  
Short Tandem

ABSTRACT Microsatellites are composed of short tandem direct repeats; deletions or duplications of those repeats through the process of replication slippage result in microsatellite instability relative to other genomic loci. Variation in repeat number occurs so frequently that microsatellites can be used for genotyping and forensic analysis. However, an accurate assessment of the rates of change can be difficult because the presence of many repeats makes it difficult to determine whether changes have occurred through single or multiple events. The current study was undertaken to experimentally assess the rates of replication slippage that occur in vivo in the chloroplast DNA of Chlamydomonas reinhardtii. A reporter construct was created in which a stretch of AAAG repeats was inserted into a functional gene to allow changes to be observed when they occurred at the synthetic microsatellite. Restoration of the reading frame occurred through replication slippage in 15 of every million viable cells. Since only one-third of the potential insertion/deletion events would restore the reading frame, the frequency of change could be deduced to be 4.5 × 10−5. Analysis of the slippage events showed that template slippage was the primary event, resulting in deletions rather than duplications. These findings contrasted with events observed in Escherichia coli during maintenance of the plasmid, where duplications were the rule.

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