Oenothera chloroplast DNA polymorphisms associated with plastome mutator activity

1990 ◽  
Vol 221 (1) ◽  
pp. 59-64 ◽  
Author(s):  
Wan-Ling Chiu ◽  
Ellen M. Johnson ◽  
Sara A. Kaplan ◽  
Kimberly Blasko ◽  
Mary B. Sokalski ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Dna Polymorphisms ◽  
Mutator Activity ◽  
Plastome Mutator

scholarly journals Chloroplast DNA polymorphisms in lodgepole and jack pines and their hybrids.

1987 ◽  
Vol 84 (7) ◽  
pp. 2097-2100 ◽  
Author(s):  
D. B. Wagner ◽  
G. R. Furnier ◽  
M. A. Saghai-Maroof ◽  
S. M. Williams ◽  
B. P. Dancik ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Dna Polymorphisms

Chloroplast DNA polymorphisms in eastern hemlock: range-wide genogeographic analyses and implications for gene conservation

2011 ◽  
Vol 41 (5) ◽  
pp. 1047-1059 ◽  
Author(s):  
Michée Joseph Lemieux ◽  
Jean Beaulieu ◽  
Jean Bousquet
Keyword(s):  
Chloroplast Dna ◽  
Population Differentiation ◽  
Genetic Distances ◽  
Adelges Tsugae ◽  
Eastern Hemlock ◽  
Dna Polymorphisms ◽  
Ex Situ ◽  
Glacial Refugium ◽  
Geographical Pattern ◽  
Genetic Patterns

The objective of this study was to determine if the genetic diversity of eastern hemlock ( Tsuga canadensis (L.) Carrière) is uniformly distributed or structured. Such information is relevant to help guide conservation efforts. Individuals were sampled in 60 range-wide populations of T. canadensis and genotyped at seven polymorphic chloroplast DNA loci. All 16 chlorotypes identified in T. canadensis were highly divergent from the unique chlorotype detected in Carolina hemlock ( Tsuga caroliniana Engelm.). Among-population differentiation in T. canadensis was low (GST = 0.020) and the distribution of chlorotypes did not show any strong geographical pattern, which is likely due to the homogenizing effect of pollen gene flow during the Holocene. Nevertheless, a spatial Bayesian approach revealed two distinct groups of populations. Furthermore, an analysis of relative genetic distances indicated that southeastern Appalachian populations harboured greater population differentiation while conserving relatively high allelic richness, which might represent the imprint of an ancient glacial refugium in the region. Thus, these distinctive genetic patterns and the risk of Tsuga decline following climate warming combined with the introduction of the insect Adelges tsugae (Annand) indicate that the southern part of the range should be considered of high priority for ex situ conservation.

scholarly journals Chloroplast DNA diversity among trees, populations and species in the California closed-cone pines (Pinus radiata, Pinus muricata and Pinus attenuata).

Genetics ◽  
1993 ◽  
Vol 135 (4) ◽  
pp. 1187-1196
Author(s):  
Y P Hong ◽  
V D Hipkins ◽  
S H Strauss
Keyword(s):  
Genetic Variation ◽  
Chloroplast Dna ◽  
Pinus Radiata ◽  
Nucleotide Diversity ◽  
Restriction Enzymes ◽  
Dna Polymorphisms ◽  
Pinus Muricata ◽  
Monterey Pine ◽  
Haplotypic Diversity ◽  
Closed Cone

Abstract The amount, distribution and mutational nature of chloroplast DNA polymorphisms were studied via analysis of restriction fragment length polymorphisms in three closely related species of conifers, the California closed-cone pines-knobcone pine: Pinus attenuata Lemm.; bishop pine: Pinus muricata D. Don; and Monterey pine: Pinus radiata D. Don. Genomic DNA from 384 trees representing 19 populations were digested with 9-20 restriction enzymes and probed with cloned cpDNA fragments from Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] that comprise 82% chloroplast genome. Up to 313 restriction sites were surveyed, and 25 of these were observed to be polymorphic among or within species. Differences among species accounted for the majority of genetic (haplotypic) diversity observed [Gst = 84(+/- 13)%]; nucleotide diversity among species was estimated to be 0.3(+/- 0.1)%. Knobcone pine and Monterey pine displayed almost no genetic variation within or among populations. Bishop pine also showed little variability within populations, but did display strong population differences [Gst = 87(+/- 8)%] that were a result of three distinct geographic groups. Mean nucleotide diversity within populations was 0.003(+/- 0.002)%; intrapopulation polymorphisms were found in only five populations. This pattern of genetic variation contrasts strongly with findings from study of nuclear genes (allozymes) in the group, where most genetic diversity resides within populations rather than among populations or species. Regions of the genome subject to frequent length mutations were identified; estimates of subdivision based on length variant frequencies in one region differed strikingly from those based on site mutations or allozymes. Two trees were identified with a major chloroplast DNA inversion that closely resembled one documented between Pinus and Pseudotsuga.

Identification of Curcuma plants and curcumin content level by DNA polymorphisms in the trnS-trnfM intergenic spacer in chloroplast DNA

2008 ◽  
Vol 63 (1) ◽  
pp. 75-79 ◽  
Author(s):  
Motoyasu Minami ◽  
Kaori Nishio ◽  
Yui Ajioka ◽  
Hiroaki Kyushima ◽  
Katsuki Shigeki ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Intergenic Spacer ◽  
Dna Polymorphisms

scholarly journals A Comparison of Population Differentiation Across Four Classes of Gene Marker in Limber Pine (Pinus flexilis James)

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 1153-1163 ◽  
Author(s):  
Robert G Latta ◽  
Jeffry B Mitton
Keyword(s):  
Gene Flow ◽  
Chloroplast Dna ◽  
Population Differentiation ◽  
Paternity Analysis ◽  
Allelic Frequency ◽  
Dna Polymorphisms ◽  
Gene Marker ◽  
Pinus Flexilis ◽  
Limber Pine ◽  
Allozyme Loci

We examined genetic differentiation among seven populations of limber pine using four classes of gene marker. Among-population differentiation was much higher for maternally inherited mitochondrial DNA polymorphisms than for paternally inherited chloroplast DNA, indicating that wind-dispersed pollen is the main agent of gene flow. Chloroplast DNA differentiation is consistent with gene flow estimated in a prior paternity analysis. Using the estimates of seed and pollen flow derived from mtDNA and cpDNA differentiation, we predicted the value of Fst expected at nuclear loci. Allelic frequency differentiation at seven allozyme loci was relatively homogeneous across loci and consistent with the level of differentiation predicted from the organellar haplotypes. By contrast four of the nine randomly applied polymorphic DNA (RAPD) markers we examined were more strongly differentiated than this prediction, suggesting the action of diversifying selection. However, the differentiated RAPDs and mtDNA were concordant in dividing the populations into two groups, suggesting some historical division. Simulations show that such historical division can increase the interlocus variance in Fst but neither a historical nor an equilibrium model could account for the joint distribution of Fst estimates across both allozyme and RAPD loci. Thus at least one group of loci appears to be experiencing natural selection.

Plastome Mutator–Induced Alterations Arise in Oenothera Chloroplast DNA Through Template Slippage

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 347-353 ◽  
Author(s):  
Lara L Stoike ◽  
Barbara B Sears
Keyword(s):  
Secondary Structure ◽  
Homologous Recombination ◽  
Chloroplast Dna ◽  
Inverted Repeat ◽  
Plastid Genome ◽  
Direct Repeats ◽  
Recombination Mechanism ◽  
Plastome Mutator ◽  
Target Sites ◽  
The One

Abstract The plastome mutator of Oenothera hookeri strain Johansen causes deletions and duplications at target sites defined by direct repeats in the plastid genome. Previous studies characterized the mutations long after they had occurred and could not discriminate between the possibilities that the plastome mutator acted through unequal homologous recombination or template slippage. From the known hotspots, the rRNA spacer in the large inverted repeat was chosen for this study because it contains both direct and indirect repeats. Identical deletions were recovered from independently derived plants; the altered regions were always flanked by direct repeats. The regions in which the deletions occurred have the potential to form secondary structures that would stabilize the intervening sequence. Of the two affected regions, the one with the stronger potential secondary structure was altered more frequently. Because no duplication products or inversions were recovered, it is proposed that the plastome mutator acts through template slippage rather than through a recombination mechanism.

scholarly journals Chloroplast DNA Polymorphisms in Sweet, Sour, and Ground Cherry

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 855E-855
Author(s):  
Thomas S. Brettin ◽  
Amy F. Iezzoni
Keyword(s):  
Chloroplast Dna ◽  
Sweet Cherry ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Sour Cherry ◽  
Prunus Cerasus ◽  
Dna Polymorphisms ◽  
Length Polymorphisms ◽  
Cpdna Markers

Sour cherry (Prunus cerasus) is an allotetraploid with sweet cherry (P. avium) and ground cherry (P. fruticosa) as the proposed progenitor species. Three cpDNA markers from eight sweet, four ground, and 26 sour cherry selections were analyzed to investigate the relatedness of their cp genomes. To date, two RFLP polymorphisms have been identified with both the P2 and P4 fragments of tomato cpDNA, while four length polymorphisms of an intergenic spacer have been identified by PCR amplification. Sweet and ground cherry have different cp polymorphisms, while sour cherry individuals have been identified that have the sweet and ground cherry polymorphisms plus a unique polymorphism. Additional individuals chosen to represent the diversity within each species will be screened to provide a more complete assessment of cp diversity. In addition, progeny from a sour cherry cross where the parents have different cp polymorphisms are being evaluated to determine if the chloroplasts are exclusively maternally inherited.

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