scholarly journals Genetic diversity and relatedness within and between species of the genus Oligoryzomys (Rodentia; Sigmodontinae)

2007 ◽  
Vol 67 (1) ◽  
pp. 153-160 ◽  
Author(s):  
A. Trott ◽  
SM. Callegari-Jacques ◽  
LFB. Oliveira ◽  
A. Langguth ◽  
MS. Mattevi
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Genetic Heterogeneity ◽  
Rain Forest ◽  
Rapd Analysis ◽  
Genetic Distances ◽  
Wide Area ◽  
Atlantic Rain Forest

A RAPD analysis on six species of the rodent genus Oligoryzomys trapped in a wide area (ranging from 01° N to 32° S) of Brazilian territory was performed in order to determine the levels of genetic variability within and between its populations and species. One-hundred and ninety-three animals were collected in 13 different sites (corresponding to 17 samples) located at Pampas, Atlantic Rain Forest, Cerrado, and Amazon domains. Oligoryzomys sp., O. nigripes (8 populations), O. flavescens (4 populations), O. moojeni, O. stramineus, and O. fornesi were the taxa analyzed. Of the 20 primers tested, 4 generated a total of 75 polymorphic products simultaneously amplified in 151 specimens. Various diversity estimators analyzed showed considerable differences between species and populations, indicating a great genetic variation occurring in the Oligoryzomys taxa investigated. A cluster analysis was made using Nei's standard genetic distances, however, it did not correlate the genetic heterogeneity of the species and populations with the geographical areas.

scholarly journals Analysis of intra-population variability of bald cypress (Taxodium distichum L. Rich.) in seed stand near Backa Palanka using RAPD markers

Genetika ◽  
2015 ◽  
Vol 47 (2) ◽  
pp. 571-580
Author(s):  
Vladan Popovic ◽  
Aleksandar Lucic ◽  
Danijela Ristic ◽  
Ljubinko Rakonjac ◽  
Sabahudin Hadrovic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Dna Markers ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Genetic Distances ◽  
Similarity Coefficients ◽  
Bald Cypress ◽  
Seed Stand

The analysis of Bald cypress genetic variability at the level of test trees was performed using RAPD (Random Amlified Polymorphic DNA) markers. RAPD analysis was performed on 20 test trees with 13 primers. A total of ten primers gave a clear picture while three primers amplified weakly. 60 is a total number of detected bands obtained by RAPD analysis with 10 selected primers, and the average number of bands is 6. Based on presence/absence of RAPD fragments among all 20 Bald cypress test trees were calculated similarity coefficients by Dice and they range from 0.73 to 1. Based on similarity coefficients was performed the cluster analysis and results were presented as a dendrogram. All 20 test trees were grouped into two sub-clusters. Test trees 1, 4 and 11 were grouped in the first sub-cluster while other test trees were grouped in the second sub-cluster. By analysis of relations within every sub-cluster and sub-sub-cluster the existence of genetic distances between observed test trees can be noticed. The greatest similarity is between test trees 2, 12, 15 and 18. The results of genetic similarity and distance between observed test trees indicate the overwhelming presence of genetic diversity.

scholarly journals Genetic variation among Iranian alfalfa (Medicago sativa L.) populations based on RAPD markers

2011 ◽  
Vol 18 (2) ◽  
pp. 93-104 ◽  
Author(s):  
Fatemeh Mohammadzadeh ◽  
Hassan Monirifar ◽  
Jalal Saba ◽  
Mostafa Valizadeh ◽  
Ahmad Razban Haghighi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Breeding Population ◽  
Genetic Distances ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Geographical Patterns ◽  
Plant Taxon ◽  
High Level

Genetic diversity among and within 10 populations of Iranian alfalfa, from different areas of Azarbaijan, Iran was analyzed by screening DNA from seeds of individual plants and bulk samples. In individual study, 10 randomly amplified polymorphic DNA (RAPD) primers produced 156 polymorphic bands and a high level of genetic diversity was observed within populations. The averages of total and within population genetic diversity were 0.2349 and 0.1892, respectively. Results of analysis of molecular variance (AMOVA) showed the great genetic variation existed within populations (81.37%). These Results were in agreement with allogamous and polyploid nature of alfalfa. Cluster analysis was performed based on Nei’s genetic distances resulting in grouping into 3 clusters which could separate breeding population from other populations. Results of cluster analysis were in consistent with morphological and geographical patterns of populations. The results of bulk method were different from individual analysis. Our results showed that RAPD analysis is a suitable method to study genetic diversity and relationships among alfalfa populations.Keywords: Alfalfa; RAPD; Genetic diversity; Analysis of Molecular Variance; Cluster analysis.DOI: http://dx.doi.org/10.3329/bjpt.v18i2.9296Bangladesh J. Plant Taxon. 18: (2): 93-104, 2011 (December)

scholarly journals Genetic variation in the emblematic Puya raimondii (Bromeliaceae) from Huascarán National Park, Peru

2013 ◽  
Vol 13 (1) ◽  
pp. 67-74 ◽  
Author(s):  
Claudia Teresa Hornung-Leoni ◽  
Victoria Sosa ◽  
June Simpson ◽  
Katia Gil
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Variability ◽  
National Park ◽  
Conservation Strategies ◽  
Long Distance Dispersal ◽  
Long Distance ◽  
Mountain Systems

Puya raimondii, the giant Peruvian and Bolivian terrestrial bromeliad, is an emblematic endemic Andean species well represented in Huascarán National Park in Peru. This park is the largest reserve of puna (high altitude plateau) vegetation. The objective of this study is to report on genetic variation in populations of P. raimondii from Huascarán and neighboring areas. AFLP profiles with four selective primer combinations were retrieved for 60 individuals from different zones. Genetic variability was estimated and a total of 172 bands were detected, of which 79.1% were polymorphic loci. The results showed genetic differentiation among populations, and gene flow. A cluster analysis showed that individuals of P. raimondii populations located in different mountain systems could be grouped together, suggesting long distance dispersal. Thus, conservation strategies for P. raimondii have to take into account exchange between populations located far apart in distance in order to preserve the genetic diversity of this showy species.

RAPD analysis off genetic variation in the Australian fan flower, Scaevola

Genome ◽  
1997 ◽  
Vol 40 (5) ◽  
pp. 600-606 ◽  
Author(s):  
Ines Swoboda ◽  
Prem L. Bhalla
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Genetic Distance ◽  
Rapd Analysis ◽  
Genetic Distances ◽  
Randomly Amplified Polymorphic Dna ◽  
Similarity Coefficients ◽  
Arbitrary Primers ◽  
Australian Species ◽  
Commercial Cultivars

The use of randomly amplified polymorphic DNA (RAPD) to study genetic variability in Scaevola (family Goodeniaceae), a native Australian species used in ornamental horticulture, is demonstrated. Plants of the genus Scaevola are commonly known as "fan flowers," due to the fan-like shape of the flowers. Nineteen accessions of Scaevola (12 cultivated and 7 wild) were studied using 20 random decamer arbitrary primers. Eight primers gave a distinct reproducible amplification profile of 90 scorable polymorphic fragments, enabling the differentiation of the Scaevola accessions. RAPD amplification of genomic DNA revealed a high genetic variability among the different species of Scaevola studied. Molecular markers were used to calculate the similarity coefficients, which were then used for determining genetic distances between each of the accessions. Based on genetic distances, a dendrogram was constructed. Though the dendrogram is in general agreement with the taxonomy, it also highlights discrepancies in the classification. The RAPD data showed that Scaevola aemula (series Pogogynae) is closer to Scaevola glandulifera of series Globuliferae than to the rest of members of series Pogogynae. In addition, the RAPD banding pattern of white flower S. aemula, one of the commercial cultivars, was identical to that of Scaevola albida, indicating their genetic similarity. Our study showed that there is a large genetic distance between commercial cultivars of Scaevola (Purple Fanfare, Pink Perfection, and Mauve Cluster), indicating considerable genetic variation among them. The use of RAPDs in intra- and inter-specific breeding of Scaevola is also explored.Key words: Scaevola, Australian native, RAPD, genetic distance, genetic variability.

scholarly journals Molecular Genetic Variability of Spigelia marilandica and S. gentianoides

2015 ◽  
Vol 140 (2) ◽  
pp. 120-128
Author(s):  
Amanda J. Hershberger ◽  
Tracie M. Jenkins ◽  
Carol Robacker
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Gene Diversity ◽  
Molecular Genetic ◽  
Genetic Distances ◽  
Population Variation ◽  
Group Method ◽  
Polymorphism Analysis ◽  
Two Samples

Despite the ecologic and ornamental potential of southeastern U.S. native Spigelia, little is known about the intraspecific or the interpopulation genetic variation. The southeastern U.S. native Spigelia habitat is becoming more and more fragmented as a result of human activity, making it imperative to gain an understanding of natural genetic variation among and within species and populations for the purpose of obtaining variability for plant breeding and preserve the genetic variability in Spigelia. Therefore, the objective of this study was to use amplified fragment length polymorphism analysis to determine interspecific and intraspecific genetic variation and to evaluate gene flow. Thirteen populations of two species of native Spigelia, S. marilandica (SM), S. gentianoides var. gentianoides (SGG), and S. gentianoides var. alabamensis (SGA), were analyzed using four primer pairs that amplified a total of 269 bands. Based on analysis of molecular variance and estimates of Nei’s coefficients of gene diversity (percentage of polymorphic loci, average genetic diversity within populations, average genetic diversity within species, and proportion of species genetic diversity attributed to among population variation), the majority of variation found in Spigelia occurs within populations. Both among-species and among-population variation was low, likely the effect of common ancestry as well as relatively frequent introgression among individuals (and populations) of Spigelia. When all individuals were evaluated using Nei’s unbiased genetic distances and viewed as a unweighted pair group method with arithmetic mean phenogram, three main groups were shown, one with two samples of SGG from one population, one with 13 individuals from both SGG populations used in this study, and one with all of the SM, SGA, and remaining SGG individuals. Further evaluation using STRUCTURE software showed introgression between populations and species, although all allele clusters have not entirely introgressed into all populations. The significance of these results is discussed in relation to breeding in Spigelia.

scholarly journals 090 Identification and Genetic Relatedness among Pecan Cultivars Detected by Randomly Amplified Polymorphic DNA (RAPD) Analysis

HortScience ◽  
2000 ◽  
Vol 35 (3) ◽  
pp. 404B-404
Author(s):  
Patrick J. Conner ◽  
Bruce W. Wood
Keyword(s):  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Genetic Relatedness ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
Carya Illinoinensis ◽  
Randomly Amplified Polymorphic Dna

Genetic variation among pecan [Carya illinoinensis (Wangenh.) K. Koch] cultivars was studied using randomly amplified polymorphic DNA (RAPD) markers. Using a combination of primers, a unique fingerprint was produced for each of the pecan genotypes studied. The genetic relatedness between 44 cultivars was estimated using more than 100 RAPD markers. Genetic distances based on the simple matching coefficient varied from 0.91 to 0.59. The phenetic dendogram developed from cluster analysis showed relatively weak grouping association. However, cultivars with known pedigrees usually grouped with at least one of the parents and genetic similarity estimates appear to agree with known genetic relationships. Using RAPD information in determining genetic relationships among pecan cultivars with unknown or questionable pedigrees and the integration of that knowledge into the breeding program is discussed.

Detection of genetic diversity in tea (Camellia sinensis) using RAPD markers

Genome ◽  
1995 ◽  
Vol 38 (2) ◽  
pp. 201-210 ◽  
Author(s):  
F. N. Wachira ◽  
R. Waugh ◽  
W. Powell ◽  
C. A. Hackett
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Southeast Asia ◽  
Camellia Sinensis ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Systematic Assessment ◽  
Tree Crop ◽  
Taxonomic Relationships

Camellia sinensis is a beverage tree crop native to Southeast Asia and introductions have been made into several nonindigenous countries. No systematic assessment of genetic variability in tea has been done anywhere. In this study, random amplified polymorphic DNA (RAPD) analysis was used to estimate genetic diversity and taxonomic relationships in 38 clones belonging to the three tea varieties, assamica, sinensis, and assamica ssp. lasiocalyx. Extensive genetic variability was detected between species, which was partitioned into between and within population components. Seventy percent of the variation was detected within populations. Analyses based on band sharing separated the three populations in a manner consistent with both the present taxonomy of tea and with the known pedigrees of some clones. RAPD analysis also discriminated all of the 38 commercial clones, even those which cannot be distinguished on the basis of morphological and phenotypic traits.Key words: genetic diversity, RAPDs, Camellia sinensis.

scholarly journals Genetic variability and relationship among different accessions of Froriepia subpinata Bail (Gijavash) an endangered medicinal plant from Iran revealed by ISSR and IRAP markers

2021 ◽  
Vol 35 (1) ◽  
Author(s):  
Abbas Jorkesh ◽  
Yousef Hamidoghli ◽  
Jamalali Olfati ◽  
Habibollah Samizadeh ◽  
Davood Bakhshi
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variability ◽  
Medicinal Plant ◽  
Genetic Information ◽  
Conservation Strategies ◽  
Polymorphic Band ◽  
Mean Values ◽  
Endangered Medicinal Plant ◽  
Irap Markers

The genetic variability of Froriepia subpinata Ledeb. Bail., an endangered Iranian endemic species, has been estimated with a total of 52 accessions using 20 markers including ISSR and IRAP. The results showed the polymorphic band produced by primers was 82.3%. The best mean values of genetic diversity parameters observed in ISSRs markers, being UBC873, UBC811, and UBC873 the best primers tested. The similarity range among accessions was 34.45% to 93.3%. The cluster analysis classified the accessions into five main groups that in totally, accessions with similarity in region generally were clustered in the same group. Overall, present study could provide elementary information for formulation of conservation strategies and invaluable elementary genetic information for next breeding or designing conservation programs.

scholarly journals Genetic analysis of silver-fir populations in the Beskids

2011 ◽  
Vol 72 (2) ◽  
pp. 115-119 ◽  
Author(s):  
Leon Mejnartowicz
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Analysis ◽  
Abies Alba ◽  
Genetic Distances ◽  
Silver Fir ◽  
Geographical Distance ◽  
Polymorphic Loci ◽  
Expected Heterozygosity ◽  
Rare Alleles

Twenty-eight isozymic loci were studied in the Beskid Mts., in four populations of common silver-fir (<em>Abies alba</em>): one in Beskid Makowski (BM) and three populations in Beskid Sądecki (BS). Their genetic variation and diversity were analyzed, and Nei's genetic distances between the populations were calculated. The results show that the geographical distance between the BM population and the three BS populations is reflected in genetic distances. The BM population is clearly distinct from the others. It has the lowest genetic diversity (<em>I</em> = <em>0.42</em>), percentage of polymorphic loci <em>(%PoL </em>= <em>64.29</em>) and number of rare alleles (<em>NoRa </em>= <em>5</em>). Besides, the BM population has the highest observed heterozygosity (<em>Ho </em>= <em>0.291</em>), which exceeds the expected heterozygosity (<em>He </em>= <em>0.254</em>), estimated on the basis of the Hardy-Weinberg Principle. On the contrary, BS populations are in the state of equilibrium, which is manifested, in similar values of <em>He </em>= <em>0.262 </em>and <em>Ho </em>= <em>0.264</em>.

scholarly journals Measurement of Genetic Diversity of Chinese Seashore Paspalum Resources through Morphological and Sequence-related Amplified Polymorphism Analysis

2019 ◽  
Vol 144 (6) ◽  
pp. 379-386
Author(s):  
Yan Liu ◽  
Hailin Guo ◽  
Yi Wang ◽  
Jingang Shi ◽  
Dandan Li ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Distance ◽  
Morphological Characteristics ◽  
The United States ◽  
Germplasm Resources ◽  
Seashore Paspalum ◽  
Chinese Germplasm

Seashore paspalum (Paspalum vaginatum) is a notable warm-season turfgrass. Certain germplasm resources are distributed in the southern regions of China. The objectives of this study were to investigate the genetic diversity and genetic variation of Chinese seashore paspalum resources. Morphological characteristics and sequence-related amplified polymorphism (SRAP) markers were used to assess genetic relationships and genetic variation among 36 germplasm resources from China and six cultivars from the United States. The results showed significant variation for 13 morphological characteristics among 42 tested seashore paspalum accessions, and that the phenotypic cv was, in turn, turf height > turf density > internode length > inflorescence density > leaf width > reproductive branch height > spikelet width > leaf length > spikelet number > inflorescence length > internode diameter > inflorescence width > spikelet length. According to the morphological characteristics and cluster analysis, 42 seashore paspalum accessions were divided into six morphological types. In total, 374 clear bands were amplified using 30 SRAP primer combinations; among these bands, 321 were polymorphic with 85.83% polymorphism. SRAP marker cluster analysis showed that 42 seashore paspalum accessions were grouped into seven major groups, with a genetic similarity coefficient ranging from 0.4385 to 0.9893 and genetic distance values ranging from 0.0108 to 0.8244. The high level of genetic diversity occurred among Chinese germplasm, and the genetic distance was relatively high between Chinese germplasm and cultivars introduced from the United States. The patterns in morphological trait variations and genetic diversity will be useful for the further exploitation and use of Chinese seashore paspalum resources.

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