scholarly journals An identification tool for the Australian weedy Sporobolus species based on random amplified polymorphic DNA (RAPD) profiles

2005 ◽  
Vol 56 (2) ◽  
pp. 157 ◽  
Author(s):  
Sangita Shrestha ◽  
Stephen W. Adkins ◽  
Glenn C. Graham ◽  
Donald S. Loch
Keyword(s):  
Genetic Diversity ◽  
Genetic Markers ◽  
Native Species ◽  
Random Amplified Polymorphic Dna ◽  
Data Matrix ◽  
High Genetic Diversity ◽  
Considerable Difficulty ◽  
Major Cluster ◽  
Weedy Species ◽  
Species Specific

Based on morphological features alone, there is considerable difficulty in identifying the 5 most economically damaging weed species of Sporobolus [viz. S. pyramidalis P. Beauv., S. natalensis (Steud.) Dur and Schinz, S. fertilis (Steud.) Clayton, S. africanus (Poir.) Robyns and Tourney, and S. jacquemontii Kunth.] found in Australia. A polymerase chain reaction (PCR)-based random amplified of polymorphic DNA (RAPD) technique was used to create a series of genetic markers that could positively identify the 5 major weeds from the other less damaging weedy and native Sporobolus species. In the initial RAPD profiling experiment, using arbitrarily selected primers and involving 12 species of Sporobolus, 12 genetic markers were found that, when used in combination, could consistently identify the 5 weedy species from all others. Of these 12 markers, the most diagnostic were UBC51490 for S. pyramidalis and S. natalensis; UBC43310, 2000, 2100 for S. fertilis and S. africanus; and OPA20850 and UBC43470 for S. jacquemontii. Species-specific markers could be found only for S. jacquemontii. In an effort to understand why there was difficulty in obtaining species-specific markers for some of the weedy species, a RAPD data matrix was created using 40 RAPD products. These 40 products amplified by 6 random primers from 45 individuals belonging to 12 species, were then subjected to numerical taxonomy and multivariate system (NTSYS pc version 1.70) analysis. The RAPD similarity matrix generated from the analysis indicated that S. pyramidalis was genetically more similar to S. natalensis than to other species of the ‘S. indicus complex’. Similarly, S. jacquemontii was more similar to S. pyramidalis, and S. fertilis was more similar to S. africanus than to other species of the complex. Sporobolus pyramidalis, S. jacquemontii, S. africanus, and S. creber exhibited a low within-species genetic diversity, whereas high genetic diversity was observed within S. natalensis, S. fertilis, S. sessilis, S. elongates, and S. laxus. Cluster analysis placed all of the introduced species (major and minor weedy species) into one major cluster, with S. pyramidalis and S. natalensis in one distinct subcluster and S. fertilis and S. africanus in another. The native species formed separate clusters in the phenograms. The close genetic similarity of S. pyramidalis to S. natalensis, and S. fertilis to S. africanus may explain the difficulty in obtaining RAPD species-specific markers. The importance of these results will be within the Australian dairy and beef industries and will aid in the development of integrated management strategy for these weeds.

DNA-Based Marker Systems to Determine Genetic Diversity of Weedy Species and Their Application to Biocontrol

Weed Science ◽  
1995 ◽  
Vol 43 (3) ◽  
pp. 504-513 ◽  
Author(s):  
Scott J. Nissen ◽  
Robert A. Masters ◽  
Donald J. Lee ◽  
Martha L. Rowe
Keyword(s):  
Genetic Diversity ◽  
Biological Control ◽  
Weed Control ◽  
Random Amplified Polymorphic Dna ◽  
Biological Weed Control ◽  
Multiple Introductions ◽  
Introduced Populations ◽  
Length Polymorphisms ◽  
Geographic Origins ◽  
Weedy Species

DNA-based molecular markers may provide information about introduced weedy species that would be useful in biological weed control efforts. Chloroplast DNA restriction fragment length polymorphisms (cpDNA RFLP) and random amplified polymorphic DNA (RAPD) analysis are two DNA-based marker techniques that can provide estimates of genetic variation in native and introduced populations of weedy species. Profiles provided by these techniques could furnish the necessary information to determine the geographic origins of introduced species and provide evidence for multiple introductions. Although DNA-based markers would not necessarily identify the genetic basis for host-pest compatibility, they would enable identification of specific host genotypes. Current criteria for selecting a weedy species as a target for biological control are primarily political and economic. The importance of genetic diversity and population structure in determining the vulnerability of plant populations to insects or diseases has not been fully appreciated. Estimates of genetic diversity based on DNA marker analysis could be used as one criteria for determining which plants are targeted for biological control. The success of biological weed control efforts has been limited by the high levels of genetic diversity occurring in target weed specks and the lack of biocontrol agent and target weed compatibilities. DNA-based markers may be used to increase our understanding of these factors and contribute to the success of biological weed control by helping to target the most vulnerable species and provide more realistic expectations of the potential for success given available resources.

scholarly journals Using Random Amplified Polymorphic DNA to Assess Genetic Diversity and Structure of NaturalCalophyllum brasiliense(Clusiaceae) Populations in Riparian Forests

2014 ◽  
Vol 2014 ◽  
pp. 1-8
Author(s):  
Evânia Galvão Mendonça ◽  
Anderson Marcos de Souza ◽  
Fábio de Almeida Vieira ◽  
Regiane Abjaud Estopa ◽  
Cristiane Aparecida Fioravante Reis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Random Amplified Polymorphic Dna ◽  
Natural Populations ◽  
Rio Grande ◽  
Shannon Index ◽  
High Genetic Diversity ◽  
Family Structures ◽  
Genetic Diversity And Structure ◽  
Kinship Coefficients

The objective of this study was to assess the genetic variability in two natural populations ofCalophyllum brasilienselocated along two different rivers in the state of Minas Gerais, Brazil, using RAPD molecular markers. Eighty-two polymorphic fragments were amplified using 27 primers. The values obtained for Shannon index (I) were 0.513 and 0.530 for the populations located on the margins of the Rio Grande and Rio das Mortes, respectively, demonstrating the high genetic diversity in the studied populations. Nei’s genetic diversity (He) was 0.341 for the Rio Grande population and 0.357 for the Rio das Mortes population. These results were not significantly different between populations and suggest a large proportion of heterozygote individuals within both populations. AMOVA showed that 70.42% of the genetic variability is found within populations and 29.58% is found among populations (ФST=0.2958). The analysis of kinship coefficients detected the existence of family structures in both populations. Average kinship coefficients between neighboring individuals were 0.053 (P<0.001) in Rio das Mortes and 0.040 (P<0.001) in Rio Grande. This could be due to restricted pollen and seed dispersal and the history of anthropogenic disturbance in the area. These factors are likely to contribute to the relatedness observed among these genotypes.

scholarly journals Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10327
Author(s):  
Ricardo M. Landínez-García ◽  
Juan Carlos Narváez ◽  
Edna J. Márquez
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Freshwater Fish ◽  
Microsatellite Loci ◽  
Natural Populations ◽  
Genetic Stock ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Genetic Stocks ◽  
Species Specific

Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.

scholarly journals Molecular techniques in the assessment of genetic relationships between populations of Consolida (Ranunculaceae)

Caryologia ◽  
2021 ◽  
Vol 74 (2) ◽  
pp. 149-161
Author(s):  
Jing Ma ◽  
Wenyan Fan ◽  
Shujun Jiang ◽  
Xiling Yang ◽  
Wenshuai Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Morphological Characters ◽  
Mantel Test ◽  
Molecular Techniques ◽  
Group Method ◽  
Plant Resources ◽  
High Genetic Diversity

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. The genus Consolida (DC.) Gray (Ranuculaceae) belongs to tribe Delphinieae. It comprises approximately 52 species, including the members of the genus Aconitella Spach. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Consolida genetic diversity. Therefore, we collected and analyzed 19 species from 12 provinces of regions. Overall, one hundred and twenty-seven plant specimens were collected. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and principal component analysis (PCA) divided Consolida species into two groups. All primers produced polymorphic amplicons though the extent of polymorphism varied with each primer. The primer OPA-06 was found to be most powerful and efficient as it generated a total of 24 bands of which 24 were polymorphic. The Mantel test showed correlation (r = 0.34, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Consolida species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Consolida species. Our aims were 1) to assess genetic diversity among Consolida species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa.

scholarly journals Genetic Similarity of Commerson’s Anchovy across Segara Anakan Cilacap Assessed Using Randomly Amplified Polymorphic DNA (RAPD) Markers

Jurnal Biota ◽  
2021 ◽  
Vol 7 (1) ◽  
pp. 42-50
Author(s):  
Muhammad Khoerol Anam ◽  
Adi Amurwanto ◽  
Kusbiyanto Kusbiyanto ◽  
Hendro Pramono ◽  
M Husein Sastranegara ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Differences ◽  
Population Genetic Study ◽  
Randomly Amplified Polymorphic Dna ◽  
High Genetic Diversity ◽  
Impressive Result

Segara Anakan areas can be divided into three different regions according to their salinity. Salinity differences suggested that Commerson’s anchovy population in that area can be divided into three subpopulations due to genetic differences. Genetic differences among subpopulation can be assessed through a population genetic study using random amplified polymorphic DNA. This study aims to evaluate the genetic variation and differences of Commerson's anchovy (Stolephorus commersonnii) collected at three different water salinities in Segara Anakan estuary Cilacap Indonesia. Total genomic DNA was isolated using the Chelex method. Genetic diversity and differences were assessed using RAPD markers and were analyzed statistically using an analysis of molecular variance, as implemented in Arlequin software.  The results showed that high genetic diversity was observed within the subpopulations. However, no significant genetic differences were observed among subpopulations which indicate genetic similarity. A high number of offspring are likely to cause high genetic variation within subpopulations.  Adult and larvae migration is the cause of genetics similarity across Segara Anakan. Another impressive result is that water salinity did not affect the genetic characteristic of Commerson,s anchovy. Genetic similarity of Commerson’s anchovy indicates that Segara Anakan forms a single genetic conservation unit.

scholarly journals Molecular identification and genetic diversity in Hypericum L.: A high value medicinal plant using RAPD markers markers

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 393-405
Author(s):  
Dezhong Bi ◽  
Dan Chen ◽  
Majid Khayatnezhad ◽  
Zohreh Hashjin ◽  
Zifa Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characters ◽  
Mantel Test ◽  
High Genetic Diversity ◽  
Genetic Structure Of Populations ◽  
Geographical Distances ◽  
Species Adaptability ◽  
Hypericum Species

Genus Hypericum (Guttiferae, Hypericoideae) is perennial, belonging to the Hypericaceae family, having 484 species in forms of trees, shrubs, and herbs, distributed in 36 taxonomic sections. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Hypericum genetic diversity. Therefore, we collected and analyzed six species from five provinces of Iran regions. Overall, seventy plant specimens were collected. Our aims were 1) to assess genetic diversity among Hypericum species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. H. dogonbadanicum depicted unbiased expected heterozygosity (UHe) in the range of 0.10. Shannon information was high (0.32) in H. perforaturm. H. dogonbadanicum showed the lowest value, 0.17. The observed number of alleles (Na) ranged from 0.22 to 0.53 in H. dogonbadanicum and H. elongaturn. Gene flow (Nm) was relatively low (0.87) in Hypericum. The Mantel test showed correlation (r = 0.45, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Hypericum species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Hypericum species.

scholarly journals Evaluation of genetic diversity in geranium (Geraniaceae) using RAPD marker

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 363-378
Author(s):  
Juan Yin ◽  
Majid Khayatnezhad ◽  
Abdul Shakoor
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Morphological Characters ◽  
Mantel Test ◽  
Group Method ◽  
Plant Resources ◽  
High Genetic Diversity ◽  
Pair Group ◽  
Genetic Structure Of Populations

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Geranium genetic diversity. Therefore, we collected and analyzed thirteen species from nine provinces. Overall, one hundred and twenty-five plant specimens were collected. Our aims were 1) to assess genetic diversity among Geranium species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and multidimensional scaling divided Geranium species into two groups. G. sylvaticum depicted unbiased expected heterozygosity (UHe) in the range of 0.11. Shannon information was high (0.38) in G. columbinum. G. sylvaticum showed the lowest value, 0.14. The observed number of alleles (Na) ranged from 0.25 to 0.55 in G. persicum and G. tuberosum. The effective number of alleles (Ne) was in the range of 1.020-1.430 for G. tuberosum and G. collinum. Gene flow (Nm) was relatively low (0.33) in Geranium. The Mantel test showed correlation (r = 0.27, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Geranium species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Geranium species.

scholarly journals Assessment of genetic diversity using DNA markers among Brassica rapa var. yellow sarson germplasm lines collected from Eastern Uttar Pradesh and Uttarakhand hills

2016 ◽  
Vol 8 (3) ◽  
pp. 1333-1340
Author(s):  
Harsha Harsha ◽  
Jitendra Kumar Meena ◽  
Ram Bhajan ◽  
Usha Pant ◽  
Mohammed Talha
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Principal Coordinate Analysis ◽  
Molecular Profile ◽  
Polymorphic Band ◽  
Germplasm Management ◽  
High Genetic Diversity

The genetic diversity and the relatedness among thirty-one germplasm lines of yellow sarson collected from eastern UP were evaluated using morphological characters and Random Amplified Polymorphic DNA (RAPD) markers. Molecular parameters, viz. A total number of bands, average polymorphic band, average percent polymorphism, average polymorphic information content (PIC), Jaccard’s similarity coefficient, Principal Coordinate Analysis (PCA) and dendrogram generated using RAPD markers. A total of 148 different polymorphic amplification products were obtained using 10 selected decamer primers. The Jaccard similarity coefficient ranged from 0.557-0.899. Maximum polymorphism detected was 100 %.The range of amplification was from 190bp to 9 kb. Some unique bands were also reported with different primers that can be used for the identification of particular accession. PYSC-11-11 and PYSC-11-36 genotypes showed a maximum number of unique loci of different size. 31 germplasm lines grouped into two major clusters I and II based on RAPD profiling. Morphological characterization was done on the basis of leaf, petal and beak characteristics. The similarity value among the germplasm lines ranged from 0.222 to 1.000 using morphological descriptors. The dendrogram generated grouped the germplasm accession into two major groups at 44% similarity value. The cluster analysis was comparable up to some extent with Principal Coordinate Analysis (PCA) of two and three-dimensional plots. The variability revealed by morphological and molecular profile were found to be non-comparable. This study indicated the presence of high genetic diversity among collected yellow sarson germplasm, which could be used for developing for breeding and germplasm management purposes.

scholarly journals Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?

2015 ◽  
Author(s):  
Emiliano Trucchi ◽  
Benoit Facon ◽  
Paolo Gratton ◽  
Emiliano Mori ◽  
Nils Chr. Stenseth ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Dynamics ◽  
Leading Edge ◽  
High Genetic Diversity ◽  
Hystrix Cristata ◽  
The North ◽  
Fundamental Information ◽  
Genome Wide ◽  
Crested Porcupine ◽  
Species Specific

AbstractStudying the evolutionary dynamics of an alien species surviving and continuing to expand after several generations can provide fundamental information on the relevant features of clearly successful invasions. Here, we tackle this task by investigating the dynamics of the genetic diversity in invasive crested porcupine (Hystrix cristata) populations, introduced to Italy about 1500 years ago, which are still growing in size, distribution range and ecological niche. Using genome-wide RAD markers, we describe the structure of the genetic diversity and the demographic dynamics of the H. cristata invasive populations and compare their genetic diversity with that of native African populations of both H. cristata and its sister species, H. africaeaustralis. First, we demonstrate that genetic diversity is lower in both the invasive Italian and the North Africa source range relative to other native populations from Sub-Saharan and South Africa. Second, we find evidence of multiple introduction events in the invasive range followed by very limited gene flow. Through coalescence-based demographic reconstructions, we also show that the bottleneck at introduction was mild and did not affect the introduced genetic diversity. Finally, we reveal that the current spatial expansion at the northern boundary of the range is following a leading-edge model characterized by a general reduction of genetic diversity towards the edge of the expanding range. We conclude that the level of genome-wide diversity of H. cristata invasive populations is less important in explaining its successful invasion than species-specific life-history traits or the phylogeographic history in the native source range.

scholarly journals Genetic diversity of Lonicera L. (Caprifoliaceae) estimated by molecular markers and morphological characters

Genetika ◽  
2021 ◽  
Vol 53 (2) ◽  
pp. 651-662
Author(s):  
Xin Ma ◽  
Huailiang Tian ◽  
Haiou Xia ◽  
Z Zeenat
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characters ◽  
Mantel Test ◽  
High Genetic Diversity ◽  
Changing Environments ◽  
Genetic Structure Of Populations ◽  
Geographical Distances ◽  
Species Adaptability

Members of Lonicera are characterized by opposite, narrowly elliptic to obovate leaves, white, yellow, reddish, or purple-red corolla with capitate stigma and undulate calyx margin. In Flora Iranica, Wendelbo (1965) classified 19 species of the Lonicera into two subgenera (Chamaecerasus and Lonicera) and three sections, namely Isoxylosteum, Isika and Coeloxylosteum. The four studied species belong to subgenus Chamaecerasus and sections Isika and Coeloxylosteum. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Lonicera genetic diversity. Therefore, we collected and analyzed three species from 2 provinces regions. Overall, 45 plant specimens were collected. Our aims were 1) to assess genetic diversity among Lonicera species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. The Mantel test showed correlation (r=0.66, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Lonicera species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Lonicera species.

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