scholarly journals Genetic Variation and Structure of native and introduced Casuarina equisetifolia (L. Johnson) Provenances

2009 ◽  
Vol 58 (1-6) ◽  
pp. 79-85 ◽  
Author(s):  
G. H. Huang ◽  
C. L. Zhong ◽  
X. H. Su ◽  
Y. Zhang ◽  
K. Pinyopusarerk ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Fragment Length Polymorphism ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Mantel Test ◽  
Casuarina Equisetifolia ◽  
Breeding Programs ◽  
The Pacific ◽  
The Mean ◽  
Amova Analysis

AbstractCasuarina equisetifolia is an important tree species in tropical/subtropical zones of Asia, the Pacific and Africa. In this study, 220 individuals from seven native provenances and eleven introduced provenances of C. equisetifolia were analyzed to assess the genetic variation and structure using amplified fragment length polymorphism (AFLP) markers. A total of 465 bands were obtained by eight primer pairs, among which 153 were polymorphic. The mean NEI’s gene diversity H = 0.2113 calculated for 18 provenances and the total gene diversity HT = 0.4065 calculated for native provenances suggested abundant variation within provenances and species. High genetic divergence coefficient (GST = 0.4737) and low gene flow (Nm = 0.5555) detected among native provenances suggesting high differentiation of C. equisetifolia. An AMOVA analysis for native provenances revealed a high proportion (46.07%) of the total genetic variation distributed among provenances. The UPGMA clustering (r = 0.8028) and the Mantel test (r = 0.0716) for native provenances showed there was no correlation among genetic relationships and geographical distribution. The genetic information provided important implications for the future conservation and breeding programs of C. equisetifolia.

scholarly journals Diversity of Fraxinus ornus from Serbia and Montenegro as revealed by RAPDs

Genetika ◽  
2013 ◽  
Vol 45 (1) ◽  
pp. 51-62
Author(s):  
Srdjan Bojovic ◽  
Philippe Heizmann ◽  
Dragana Drazic ◽  
Dragan Kovacevic ◽  
Petar Marin ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Rapd Markers ◽  
Genetic Variance ◽  
Gene Diversity ◽  
Molecular Genetic ◽  
Mantel Test ◽  
Distance Matrice ◽  
Serbia And Montenegro ◽  
Outcrossing Species ◽  
The Mean

PCR-RAPD markers revealed individual variation in F. ornus. A total of 122 fragments were amplified using 7 primers and of these 97 fragments were polymorphic. The percentage of polymorphic loci was between 53.3% and 74.6% with an average of 63.1%. The mean gene diversity for all populations was 0.30 and the mean Shannon?s index was 0.44. Of the total genetic variation 87% was intra-population whilst 13% was inter-population. The Mantel test revealed significant correlation between genetic and geographical distance matrice. Results herein represent the first use of molecular genetic (DNA) markers to characterize genetic variation in F. ornus populations. The partition of total genetic variance indicates a relatively restricted population differentiation as expected in outcrossing species. Present and future information on genetic structure and variability in F. ornus needs to be incorporated into strategies for the preservation of genetic resources of tree species.

scholarly journals Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
Zulfahmi Zulfahmi ◽  
Parjanto Parjanto ◽  
Edi Purwanto ◽  
Ahmad Yunus
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Gene Diversity ◽  
In Situ Conservation ◽  
Genetic Material ◽  
Ex Situ ◽  
Breeding Programs ◽  
The Mean

Abstract. Zulfahmi, Parjanto, Purwanto E, Yunus A. 2021. Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia. Biodiversitas 22: 4431-4439. Information on genetic variation within and among populations of Eurycoma apiculata plants is important to develop strategies for their conservation, sustainable use, and genetic improvement. To date, no information on genetic variation within and among populations of the E. apiculata has been reported. This study aims to assess genetic diversity within and among populations of E. apiculata based on RAPD markers, and to determine populations to collect E. apiculata genetic material for conservation and breeding programs. Young leaves of E. apiculata were collected from six natural populations. Fifteen RAPD primers were used to assess the genetic diversity of each population. The data obtained were analyzed with POPGEN and Arlequin software. The amplification results of 15 selected primers produced 3-16 loci with all primers 100% polymorphic. At the species level, the mean allele per locus (Na), number of effective alleles (Ne), percentage of polymorphic loci (PPL), Nei’s gene diversity index (He) and Shannon information index (I) were 2.000, 1.244, 100%, 0.167, and 0.286, respectively. At the population level, the mean values for Na, Ne, PPL, He and I were 1.393, 1.312, 39.27%, 0.119, and 0.186, respectively. The highest value of gene diversity within population (He) was found in the Lingga-1 population and the lowest value was found in the Rumbio population. The value of genetic differentiation among populations (GST) of E. apiculata is 0.284, consistent with the results of the AMOVA analysis which found that genetic variation among populations was 23.14%, indicates that the genetic variation of E. apiculata was more stored within populations than among populations. The gene flow (Nm) value of E. apiculata was 1.259 migrants per generation among populations. The Nm value of this species was high category, and could inhibit genetic differentiation among populations. The clustering of E. apiculata population based on the UPGMA dendrogram and PCA was inconsistent with its geographic distribution, reflecting the possibility that genes migration occurred between islands in the past. The main finding of this study was the genetic variation of the E. apiculata mostly stored within the population. Therefore, the population with the highest genetic diversity is a priority for in-situ conservation, and collection of E. apiculata genetic material for ex-situ conservation and breeding programs should be carried out minimum from Lingga-1 and Pokomo populations.

Genetic Diversity of Wild Oat (Avena fatua)Populations from China and the United States

Weed Science ◽  
2007 ◽  
Vol 55 (2) ◽  
pp. 95-101 ◽  
Author(s):  
Runzhi Li ◽  
Shiwen Wang ◽  
Liusheng Duan ◽  
Zhaohu Li ◽  
Michael J. Christoffers ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
The United States ◽  
Mantel Test ◽  
Wild Oat ◽  
Chinese Populations ◽  
Nei's Distance ◽  
The Impact

Weed genetic diversity is important for understanding the ability of weeds to adapt to different environments and the impact of herbicide selection on weed populations. Genetic diversity within and among six wild oat populations in China varying in herbicide selection pressure and one population in North Dakota were surveyed using 64 polymorphic alleles resulting from 25 microsatellite loci. Mean Nei's gene diversity (h) for six wild oat populations from China was between 0.17 and 0.21, and total diversity (HT) was 0.23. A greater proportion of this diversity, however, was within (Hs= 0.19) rather than among (Gst= 0.15) populations. For the wild oat population from the United States,h= 0.24 andHT= 0.24 were comparable to the values for the six populations from China. Cluster analysis divided the seven populations into two groups, where one group was the United States population and the other group included the six Chinese populations. The genetic relationships among six populations from China were weakly correlated with their geographic distribution (r= 0.22) using the Mantel test. Minimal difference in gene diversity and small genetic distance (Nei's distance 0.07 or less) among six populations from China are consistent with wide dispersal of wild oat in the 1980s. Our results indicate that the wild oat populations in China are genetically diverse at a level similar to North America, and the genetic diversity of wild oat in the broad spatial scale is not substantially changed by environment, agronomic practices, or herbicide usage.

scholarly journals Genetic studies revealed differences between European and North American populations of Calypogeia azurea

2016 ◽  
Vol 42 (1) ◽  
pp. 19-26 ◽  
Author(s):  
Katarzyna Buczkowska ◽  
Alina Bączkiewicz ◽  
Patrycja Gonera
Keyword(s):  
Genetic Variation ◽  
North America ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Oil Bodies ◽  
Genetic Studies ◽  
Isozyme Loci ◽  
The Mean ◽  
Different Parts ◽  
Nei's Genetic Distance

Abstract Calypogeia azurea, a widespread, subboreal-montane liverwort species, is one of a few representatives of the Calypogeia genus that are characterized by the occurrence of blue oil bodies. The aim of the study was to investigate the genetic variation and population structure of C. azurea originating from different parts of its distribution range (Europe and North America). Plants of C. azurea were compared with C. peruviana, another Calypogeia species with blue oil bodies. In general, 339 gametophytes from 15 populations of C. azurea were examined. Total gene diversity (HT) estimated on the basis of nine isozyme loci of C. azurea at the species level was 0.201. The mean Nei’s genetic distance between European populations was equal to 0.083, whereas the mean genetic distance between populations originating from Europe and North America was 0.413. The analysis of molecular variance (AMOVA) showed that 69% of C. azurea genetic variation was distributed among regions (Europe and North America), 15% - among populations within regions, and 16% - within populations. Our study revealed that C. azurea showed genetic diversity within its geographic distribution. All examined samples classified as C. azurea differed in respect of isozyme patterns from C. peruviana.

scholarly journals Genetic diversity in wild and hatchery populations of stinging catfish (Heteropneustes fossilis Bloch) revealed by RAPD analysis

2012 ◽  
Vol 19 ◽  
pp. 81-87
Author(s):  
Md Nazrul Islam ◽  
Abhishak Basak ◽  
Dr Ashrafullah ◽  
Md Samsul Alam
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Gene Diversity ◽  
Similarity Index ◽  
Heteropneustes Fossilis ◽  
Wild Populations ◽  
Polymorphic Loci

Context: DNA fingerprinting using genetic markers such as Random Amplification of Polymorphic DNA (RAPD), Restriction Fragment Length Polymorphism (RFLP), microsatellite (Simple sequence repeat), Amplified Fragment Length Polymorphism (AFLP) etc. can be successfully used to reveal genetic variation within and among different populations. Objective: The aim of the present study was to assess genetic diversity in two wild and one hatchery populations of stinging catfish Heteropneustes fossilis by RAPD fingerprinting. Materials and Methods: A total of 90 live fish (H. fossilis), 30 from each source, were collected from a beel in Patuakhali, a beel in Jessore and Rupali Hatchery, Mymensingh. Genomic DNA was extracted from fin tissues. The concentration of DNA was estimated using a spectrophotometer. Fifteen decamer primers of random sequence from three kits (six from kit A, seven from kit B and two from kit C) (Operon technologies, Inc., Alameda, CA, USA) were screened on sub-samples of one randomly chosen H. fossilis DNA sample from the each population to test their suitability for amplifying RAPDs. The amplified products from each sample were separated by electrophoresis on 1.4% agarose gel containing ethidium bromide. The sizes of the bands were calculated using the software DNAFRAG and the sizes in base pair (bp) were used for identification of the bands (RAPD markers). The similarity index values (SI) between the RAPD fingerprint of any two individuals on the same gel were calculated from RAPD band sharing. Results: A total of 28 RAPD bands were obtained using four decamer random primers, among which 21 bands were polymorphic. The percentage of polymorphic loci, intra-population similarity indices and Nei's gene diversity values were 85.71%, 78.75 and 0.304±0.183 for Jessore population, 83.71%, 82.62 and 0.280±0.159 for Patuakhali population, 82.14%, 85.25 and 0.271±0.165 for Rupali hatchery population, respectively. The overall gene flow (Nm) among the populations was 5.755. The highest inter-similarity (Sij) was found between Patuakhali - Rupali hatchery populations. Among the three populations, the highest genetic distance (0.069) was found between Jessore and Patuakhali population. Considering polymorphic loci, intrapopulation similarity index and gene diversity the genetic variation in the Jessore population was higher than the other two populations. The genetic variation of the hatchery population was found to be lower than the two wild populations. Conclusion: The result of the present study can be used as baseline information regarding the genetic variation and population structure before undertaking any breeding programme. Study indicated that the genetic variation in the hatchery populations were slightly lower than those of the wild populations. DOI: http://dx.doi.org/10.3329/jbs.v19i0.13005 J. bio-sci. 19 81-87, 2011

scholarly journals Genetic diversity of three European Veratrum species revealed by Amplified Fragment Length Polymorphism

2017 ◽  
Vol 47 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Magdalena Szeliga ◽  
Joanna Ciura ◽  
Mirosław Tyrka
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Veratrum Album ◽  
Metabolic Properties

Abstract Chemical and genetic characterization of Veratrum species deposited in European collections is important for genepool preservation and identification of populations with desired metabolic properties. Veratrum album, V. lobelianum and V. nigrum are native to Europe, and in Poland are ranked as rare or threatened. Genetic variation of European Veratrum species was characterized by Amplified Fragment Length Polymorphism (AFLP) markers. The accumulation of jervine as a representative of steroidal alkaloids was measured in seeds. Distribution of 380 markers generated from eight primer combinations was useful for studying genetic relationships among and within species in the Veratrum genus and the most divergent populations were identified. Genetic variation between 12 populations of Veratrum species supports the classification of V. lobelianum as a subspecies of V. album. However, the results need further validation on extended material. A higher genetic diversity (22.3%) was observed between populations of V. nigrum as compared to V. album (14.5%). Contents of jervine allowed for discrimination of the studied Veratrum species and can be used as a potential chemotaxonomic marker. The highest jervine levels were found in V. album. V. nigrum seeds had only trace amounts and no jervine was detected in seeds of V. lobelianum.

scholarly journals Genetic Diversity of Arabica Coffee (Coffea arabicaL.) in Nicaragua as Estimated by Simple Sequence Repeat Markers

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Mulatu Geleta ◽  
Isabel Herrera ◽  
Arnulfo Monzón ◽  
Tomas Bryngelsson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Simple Sequence Repeat ◽  
Significant Contribution ◽  
Gene Diversity ◽  
Ex Situ ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Arabica Coffee ◽  
Simple Sequence

Coffea arabicaL. (arabica coffee), the only tetraploid species in the genusCoffea, represents the majority of the world’s coffee production and has a significant contribution to Nicaragua’s economy. The present paper was conducted to determine the genetic diversity of arabica coffee in Nicaragua for its conservation and breeding values. Twenty-six populations that represent eight varieties in Nicaragua were investigated using simple sequence repeat (SSR) markers. A total of 24 alleles were obtained from the 12 loci investigated across 260 individual plants. The total Nei’s gene diversity (HT) and the within-population gene diversity (HS) were 0.35 and 0.29, respectively, which is comparable with that previously reported from other countries and regions. Among the varieties, the highest diversity was recorded in the variety Catimor. Analysis of variance (AMOVA) revealed that about 87% of the total genetic variation was found within populations and the remaining 13% differentiate the populations (FST=0.13;P<0.001). The variation among the varieties was also significant. The genetic variation in Nicaraguan coffee is significant enough to be used in the breeding programs, and most of this variation can be conserved throughex situconservation of a low number of populations from each variety.

scholarly journals Estimation of genetic variation among related sugar beet genotypes by using RAPD

Genetika ◽  
2011 ◽  
Vol 43 (3) ◽  
pp. 575-582 ◽  
Author(s):  
Nevena Nagl ◽  
Ksenija Taski-Ajdukovic ◽  
Andrea Popovic ◽  
Zivko Curcic ◽  
Dario Danojevic ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Sugar Beet ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Polymorphism Analysis ◽  
Breeding Programs ◽  
Pair Group ◽  
Upgma Cluster Analysis ◽  
Cost Efficient

In marker assisted breeding programs, determination of genome polymorphism and development of suitable molecular markers is of the greatest importance. The aim of this research was development of RAPD markers, which will enable quick and cost efficient DNA polymorphism analysis among closely related sugar beet genotypes. The research was conducted on twelve sugar beet genotypes from population of closely related genotypes. Reactions with eight RAPD primers and five primer mixtures resulted in stable and reproducible bands in all samples, with 44 polymorphic and 14 monomorphic loci, and average of 6.13 bands per primer. In two-primer reactions nine new polymorphic bands were detected. Polymorphism information content (PIC) for each primer was calculated, while genetic variation was estimated by calculation of the number of polymorphic loci and their percentage, observed number of alleles, effective number of alleles, and Nei?s gene diversity. An unweighted pair group arithmetic mean method (UPGMA) cluster analysis showed that samples were divided in two groups with relatively high coefficient of similarity. The presented results showed that RAPD markers can be suitable for genetic diversity analysis in breeding material with high levels of homology and homozygosity.

scholarly journals Genetic Variation Within and Among Lowland Switchgrass Cultivars as Revealed With AFLP Polymorphisms

2020 ◽  
Vol 2 (1) ◽  
pp. 11-17
Author(s):  
Shiva Makaju ◽  
Yanqi Wu ◽  
Michael Anderson ◽  
Vijaya Kakani ◽  
Michael Smith ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Panicum Virgatum ◽  
Fragment Length Polymorphism ◽  
Hybrid Vigor ◽  
The Other ◽  
Crop Species ◽  
Breeding Programs ◽  
Panicum Virgatum L

Switchgrass (Panicum virgatum L.) has gained wider attention due to its recognition and use as a model herbaceous crop species for bioenergy production. Genetic diversity information in lowland switchgrass cultivars can help to specify cultivars to be used in the breeding programs aiming for hybrid vigor. The objective of this research was to analyze genetic variation within and among five lowland switchgrass cultivars using amplified fragment length polymorphism (AFLP) markers. AFLP polymorphisms indicated the presence of high genetic variation within lowland switchgrass cultivars with ‘Alamo’ exhibiting the highest genetic variation and ‘Performer’ the lowest. The Nei’s genetic diversity parameters revealed the lowest genetic distance between cultivars ‘Alamo’ and ‘Cimarron’ and the highest value between cultivars ‘Alamo’ and ‘Kanlow’. ‘Alamo’ and ‘Cimarron’ were clustered together while ‘BoMaster’, ‘Kanlow’, and ‘Performer’ were grouped into the other cluster. In addition, there were clusters with mixed genotypes. The findings of this study can be used to select diverse lines as parents for heterosis and inbreeding studies.

Identification and Analysis of Genetic Variation among Rose Cultivars Using Random Amplified Polymorphic DNA

2005 ◽  
Vol 60 (7-8) ◽  
pp. 611-617 ◽  
Author(s):  
Anuradha Mohapatra ◽  
Gyana Ranjan Rout
Keyword(s):  
Genetic Variation ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Plant Genetic Resources ◽  
Flower Colour ◽  
Morphological Characters ◽  
Breeding Programs ◽  
Rose Breeding

Identified germplasm is an important component for efficient and effective management of plant genetic resources. Traditionally, cultivars or species identification has relied on morphological characters like growth habit or floral morphology like flower colour and other characteristics of the plant. Studies were undertaken for identification and analysis of genetic variation within 34 rose cultivars through random amplified polymorphic DNA (RAPD) markers. Analysis was made by using twenty five decamer primers. Out of twenty five, ten primers were selected and used for identification and analysis of genetic relationships among 34 rose cultivars. A total of 162 distinct DNA fragments ranging from 0.1 to 3.4 kb was amplified by using 10 selected random decamer primers. The genetic similarity was evaluated on the basis of presence or absence of bands. The cluster analysis indicated that the 34 rose cultivars form 9 clusters. The first cluster consists of eight hybrid cultivars, three clusters having five cultivars each, one cluster having four cultivars, two clusters having three cultivars each and two clusters having one cultivar each. The genetic distance was very close within the cultivars. Thus, these RAPD markers have the potential for identification of clusters and characterization of genetic variation within the cultivars. This is also helpful in rose breeding programs and provides a major input into conservation biology.

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