scholarly journals Randomly Amplified Polymorphic DNA (RAPD) Variation among and within Cultivated and Wild American Ginseng (Panax quinquefolium L.) Populations

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 454B-454
Author(s):  
C.L. Boehm ◽  
H.C. Harrison ◽  
G. Jung ◽  
J. Nienhuis
Keyword(s):  
Rapd Markers ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Population Sample ◽  
American Ginseng ◽  
Relationship Matrix ◽  
Panax Quinquefolium ◽  
Wild Populations ◽  
Cultivated Populations ◽  
Average Gene

The magnitude of genetic differences among and the heterogeneity within cultivated and wild American ginseng populations is unknown. Variation among individual plants from 16 geographically separated, cultivated populations and 21 geographically separated, wild populations were evaluated using RAPD markers. Cultivated populations from the midwestern U.S., the southern U.S., and Canada were examined. Wild populations from the midwestern U.S., the southern U.S., and the eastern U.S. were examined. Polymorphic bands were observed for 15 RAPD primers, which resulted in 100 scored bands. Variation was found within and among populations, indicating that the selected populations are heterogeneous with respect to RAPD markers. The genetic relationships among individual genotypes were estimated using the ratio of discordant bands to total bands scored. Multidimensional scaling of the relationship matrix showed independent clusters corresponding to the geographical and cultural origins of the populations. The integrity of the clusters were confirmed using pooled chi-squares for fragment homogeneity. Average gene diversity (Hs) was calculated for each population sample, and a one-way analysis of variance showed significant differences among populations. Overall, the results demonstrate the usefulness of the RAPD procedure for evaluating genetic relationships and comparing levels of genetic diversity among populations of American ginseng genotypes.

scholarly journals Randomly Amplified Polymorphic DNA (RAPD) Variation among and within Artichoke (Cynara scolymus L.) Cultivars and Breeding Populations

1996 ◽  
Vol 121 (5) ◽  
pp. 783-788 ◽  
Author(s):  
Jan Tivang ◽  
Paul W. Skroch ◽  
James Nienhuis ◽  
Neal De Vos
Keyword(s):  
Rapd Markers ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Phenotypic Variability ◽  
Population Sample ◽  
Relationship Matrix ◽  
Globe Artichoke ◽  
Breeding Populations ◽  
Average Gene Diversity ◽  
Average Gene

The magnitude of genetic differences among and heterogeneity within globe artichoke cultivars is unknown. Variation among individual heads (capitula) from three artichoke cultivars and two breeding populations were evaluated using RAPD markers. One vegetatively propagated cultivar (`Green Globe'), two seed-propagated cultivars (`Imperial Star' and `Big Heart') and two breeding populations were examined. Two to thirteen polymorphic bands were observed for 27 RAPD primers, which resulted in 178 scored bands. Variation was found within and among all cultivars, and breeding populations indicating that all five groups represent heterogeneous populations with respect to RAPD markers. The genetic relationships among individual genotypes were estimated using the ratio of discordant bands to total bands scored. Multidimensional scaling of the relationship matrix showed five independent clusters corresponding to the three cultivars and two breeding populations. The integrity of the five clusters was confirmed using pooled chi-squares for fragment homogeneity. Average gene diversity (Hs) was calculated for each population sample, and a one-way analysis of variance showed significant differences among populations. `Big Heart' had an Hs value equivalent to the two breeding populations, while clonally propagated `Green Globe' and seed propagated `Imperial Star' had the lowest Hs values. The RAPD heterogeneity observed within clonally propagated `Green Globe' is consistent with phenotypic variability observed for this cultivar. Overall, the results demonstrate the utility of the RAPD technique for evaluating genetic relationships and contrasting levels of genetic diversity among populations of artichoke genotypes.

scholarly journals Organization of American and Asian Ginseng Germplasm Using Randomly Amplified Polymorphic DNA (RAPD) Markers

1999 ◽  
Vol 124 (3) ◽  
pp. 252-256 ◽  
Author(s):  
C.L. Boehm ◽  
H.C. Harrison ◽  
G. Jung ◽  
J. Nienhuis
Keyword(s):  
United States ◽  
Rapd Markers ◽  
The United States ◽  
Genetic Differences ◽  
Relationship Matrix ◽  
Panax Quinquefolium ◽  
Wild Type ◽  
Chi Square ◽  
South Korean ◽  
Cultivated Populations

Genetic differences among eleven cultivated and eight wild-type populations of North American ginseng (Panax quinquefolium L.) and four cultivated populations of South Korean ginseng (P. ginseng C.A. Meyer) were estimated using RAPD markers. Cultivated P. ginseng population samples were collected from four regions of S. Korea. Cultivated P. quinquefolium population samples were collected from three regions in North America: Wisconsin, the Southeastern Appalachian region of the United States, and Canada. Wild-type P. quinquefolium was collected from three states in the United States: Pennsylvania, Tennessee, and Wisconsin. Evaluation of germplasm with 10 decamer primers resulted in 100 polymorphic bands. Genetic differences among populations indicate heterogeneity. The genetic distance among individuals was estimated using the ratio of discordant bands to total bands scored. Multidimensional scaling of the relationship matrix showed independent clusters corresponding to the distinction of species, geographical region, and wild versus cultivated types. The integrity of the clusters was confirmed using pooled chi-square tests for fragment homogeneity.

scholarly journals Genetic Diversity of Salvia Species Assessed by ISSR and RAPD Markers

2016 ◽  
Vol 44 (2) ◽  
pp. 431-436 ◽  
Author(s):  
Masoumeh YOUSEFIAZARKHANIAN ◽  
Ali ASGHARI ◽  
Jafar AHMADI ◽  
Behvar ASGHARI ◽  
Ali Ashraf JAFARI
Keyword(s):  
Genetic Diversity ◽  
Genetic Polymorphisms ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Genetic Variations ◽  
Molecular Techniques ◽  
Wild Populations ◽  
Similarity Coefficients ◽  
The World

The genus Salvia includes an enormous assemblage of nearly 1,000 species dispersed around the world. Due to possible threats to this genus, there is an immediate requirement to evaluate the diversity of its wild populations. ISSR and RAPD molecular techniques were used to evaluate the genetic relationships among twenty-one ecotypes of eight Salvia species. Amplification of genomic DNA using 23 primers (15 RAPD and eight ISSR) produced 280 bands, of which 91% were polymorphic. The results of marker parameters showed no clear difference between two marker systems. It was generally observed that both ISSR and RAPD markers had similar efficiency in detecting genetic polymorphisms with remarkable ability to differentiate the closely related ecotypes of Salvia. Nei’s similarity coefficients for these techniques ranged from 0.48 to 0.98. Based on the results of clustering, PCoA and AMOVA, the genetic diversity between and within species was confirmed. So, conservation and domestication of the genus Salvia must be due to levels of genetic variations.

scholarly journals A genealogical estimate of genetic relationships

2021 ◽  
Author(s):  
Caoqi Fan ◽  
Nicholas Mancuso ◽  
Charleston W.K. Chiang
Keyword(s):  
Population Structure ◽  
Human Genetics ◽  
Genetic Relationships ◽  
Population Sample ◽  
Relationship Matrix ◽  
Current Standard ◽  
Genetic Studies ◽  
Genome Wide ◽  
Linkage Information ◽  
History Of

The application of genetic relationships among individuals, characterized by a genetic relationship matrix (GRM), has far-reaching effects in human genetics. However, the current standard to calculate the GRM generally does not take advantage of linkage information and does not reflect the underlying genealogical history of the study sample. Here, we propose a coalescent-informed framework to infer the expected relatedness between pairs of individuals given an ancestral recombination graph (ARG) of the sample. Through extensive simulations we show that the eGRM is an unbiased estimate of latent pairwise genome-wide relatedness and is robust when computed using genealogies inferred from incomplete genetic data. As a result, the eGRM better captures the structure of a population than the canonical GRM, even when using the same genetic information. More importantly, our framework allows a principled approach to estimate the eGRM at different time depths of the ARG, thereby revealing the time-varying nature of population structure in a sample. When applied to genotyping data from a population sample from Northern and Eastern Finland, we find that clustering analysis using the eGRM reveals population structure driven by subpopulations that would not be apparent using the canonical GRM, and that temporally the population model is consistent with recent divergence and expansion. Taken together, our proposed eGRM provides a robust tree-centric estimate of relatedness with wide application to genetic studies.

Genetic relationships between Sicilian wild populations of Brassica analysed with RAPD markers

2001 ◽  
Vol 120 (3) ◽  
pp. 193-196 ◽  
Author(s):  
A. Geraci ◽  
I. Divaret ◽  
F. M. Raimondo ◽  
A.-M. Chevre
Keyword(s):  
Rapd Markers ◽  
Genetic Relationships ◽  
Wild Populations

scholarly journals Use of RAPD Markers to Assess Genetic Diversity of American Ginseng (Panax quinquefolium L.) Among Wild Populations from the Catskill Mountains of New York State and Other States

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 889A-889 ◽  
Author(s):  
Wansang Lim* ◽  
Kenneth Mudge
Keyword(s):  
Genetic Diversity ◽  
New York ◽  
Nuclear Dna ◽  
Genetic Difference ◽  
New York State ◽  
American Ginseng ◽  
Panax Quinquefolium ◽  
Catskill Mountains ◽  
Wild Populations ◽  
Chi Square

The Catskill Mountains of New York are an important source of wild-collected American ginseng (Panax quinquefolium), and increasingly, of woods-cultivated ginseng. The objective of this study was to assess genetic diversity among eight different wild ginseng populations from the Catskill Mountains and to compare Catskill populations to five wild populations from other states including Kentucky, Tennessee, North Carolina, Pennsylvania, Virginia, and one cultivated population from Wisconsin. Randomly amplified polymorphic DNA markers were used to estimate the genetic difference among the 14 populations using PCR amplified nuclear DNA. Fifteen random primers were selected from a total of 64 random decamer primers by screening bulked DNA samples from the eight Catskill populations. These 15 primers were then used to compare 10 plants each from the eight Catskill populations and three to four plants each from the non-Catskill populations. The 15 primers produced 124 polymorphic bands. The genetic distance within and among populations was estimated using the ratio of discordant bands to total bands. Multidimensional scaling of the relation matrix showed separation of Catskill and non-Catskill population clusters. Significant differences between these groups was confirmed using pooled chi-square tests for fragment homogeneity. Although the eight Catskill populations differed from the non Catskill populations, there were no significant differences among the Catskill populations. This study shows that presence and absence of bands can be used as population specific markers for American ginseng. Although these results do not rule out the possibility that there may be some level of genetic differences among Catskill populations, 10 plants per population was not sufficient to establish such differences.

Restriction Fragment Length Polymorphism and Divergence in the Genomic Regions of High and Low Recombination in Self-Fertilizing and Cross-Fertilizing Aegilops Species

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 423-434
Author(s):  
Jan Dvorřák ◽  
Ming-Cheng Luo ◽  
Zu-Li Yang
Keyword(s):  
Related Species ◽  
Gene Diversity ◽  
Single Copy ◽  
Species Variation ◽  
Recombination Rates ◽  
Distal Chromosome ◽  
Phylogenetic Status ◽  
Average Gene ◽  
Genomic Regions ◽  
Chromosome Regions

Abstract RFLP was investigated at 52 single-copy gene loci among six species of Aegilops, including both cross-fertilizing and self-fertilizing species. Average gene diversity (H) was found to correlate with the level of outcrossing. No relationship was found between H and the phylogenetic status of a species. In all six species, the level of RFLP at a locus was a function of the position of the locus on the chromosome and the recombination rate in the neighborhood of the locus. Loci in the proximal chromosome regions, which show greatly reduced recombination rates relative to the distal regions, were significantly less variable than loci in the distal chromosome regions in all six species. Variation in recombination rates was also reflected in the haplotype divergence between closely related species; loci in the chromosome regions with low recombination rates were found to be diverged less than those in the chromosome regions with high recombination rates. This relationship was not found among the more distantly related species.

scholarly journals Pseudoginsenoside F11, a Novel Partial PPARγAgonist, Promotes Adiponectin Oligomerization and Secretion in 3T3-L1 Adipocytes

PPAR Research ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Guoyu Wu ◽  
Junyang Yi ◽  
Ling Liu ◽  
Pengcheng Wang ◽  
Zhijie Zhang ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Side Effects ◽  
Hormone Receptor ◽  
Adipocyte Differentiation ◽  
American Ginseng ◽  
Nuclear Hormone Receptor ◽  
Targeted Therapeutics ◽  
Panax Quinquefolium ◽  
Master Regulator

PPARγis a nuclear hormone receptor that functions as a master regulator of adipocyte differentiation and development. Full PPARγagonists, such as the thiazolidinediones (TZDs), have been widely used to treat type 2 diabetes. However, they are characterized by undesirable side effects due to their strong agonist activities. Pseudoginsenoside F11 (p-F11) is an ocotillol-type ginsenoside isolated fromPanax quinquefolium L.(American ginseng). In this study, we found that p-F11 activates PPARγwith modest adipogenic activity. In addition, p-F11 promotes adiponectin oligomerization and secretion in 3T3-L1 adipocytes. We also found that p-F11 inhibits obesity-linked phosphorylation of PPARγat Ser-273 by Cdk5. Therefore, p-F11 is a novel partial PPARγagonist, which might have the potential to be developed as a new PPARγ-targeted therapeutics for type 2 diabetes.

scholarly journals Identification of medicinal plant Schisandra chinensis using a potential DNA barcode ITS2

2013 ◽  
Vol 82 (4) ◽  
pp. 283-288 ◽  
Author(s):  
Xian-kuan Li ◽  
Bing Wang ◽  
Rong-chun Han ◽  
Yan-chao Zheng ◽  
Hai-bo Yin Yin ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Population Level ◽  
Species Level ◽  
Its2 Region ◽  
Schisandra Chinensis ◽  
Success Rates ◽  
Wild Populations ◽  
Efficient Tool ◽  
Different Populations ◽  
Cultivated Populations

To test whether the internal transcribed spacer 2 (ITS2) region is an effective marker for using in authenticating of the <em>Schisandra chinensis</em> at the species and population levels, separately. And the results showed that the wild populations had higher percentage of individuals that had substitution of C→A at site 86-bp than the cultivated populations. At sites 10-bp, 37-bp, 42-bp and 235-bp, these bases of the <em>Schisandra sphenanthera</em> samples differed from that of <em>S. chinensis</em>. Two species showed higher levels of inter-specific divergence than intra-specific divergence within ITS2 sequences. However, 24 populations did not demonstrate much difference as inter-specific and intra-specific divergences were concerned. Both <em>S. chinensis</em> and <em>S. sphenanthera</em> showed monophyly at species level, yet the samples of different populations shown polyphyly at population level. ITS2 performed well when using BLAST1 method. ITS2 obtained 100% identification success rates at the species level for <em>S. chinensis</em>, with no ambiguous identification at the genus level for ITS2 alone. The ITS2 region could be used to identify <em>S. chinensis</em> and <em>S. sphenanthera</em> in the “Chinese Pharmacopoeia”. And it could also correctly distinguish 100% of species and 100% of genera from the 193 sequences of <em>S. chinensis</em>. Hence, the ITS2 is a powerful and efficient tool for species identification of <em>S. chinensis</em>.

Sign in / Sign up

Export Citation Format

Share Document