Diversity and spatial structure of clones in Vaccinium uliginosum populations

2005 ◽  
Vol 83 (2) ◽  
pp. 211-218 ◽  
Author(s):  
T Albert ◽  
O Raspé ◽  
A -L Jacquemart
Keyword(s):  
Genetic Diversity ◽  
Seedling Recruitment ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Distances ◽  
Mean Value ◽  
Growth Strategy ◽  
Structured Populations ◽  
Mean Values ◽  
Vaccinium Uliginosum

In Belgium, a total of three Vaccinium species with a shrub or dwarf shrub growth form can be found: Vaccinium myrtillus L., Vaccinium vitis-idaea L., and Vaccinium uliginosum L. Vaccinium uliginosum is the only one of these for which the extent of clonality is unknown. Therefore, the clonal structure of two V. uliginosum populations was inferred from random amplified polymorphic DNA (RAPD) markers. Among the 47 sampled patches, 61 clones were identified. The mean values of the number of clones divided by the number of samples (G/N), the Simpson's index (D), and the genotypic evenness (E) were 0.28, 0.95, and 0.96, respectively. Vaccinium uliginosum exhibited a typical phalanx growth strategy that resulted in structured populations at the ramet level, that is, ramets belonging to the same clone were closely associated and formed distinct clumps. However, at the clone level, populations were not structured, that is, genetic distances between pairs of clones were not correlated with the spatial distances between the clones within a population. Genetic diversity was as high as that in nonclonal species (mean value of Shannon's diversity index (Ho) = 0.647). In accord with the life history traits of V. uliginosum (long-lived species with a mixed breeding system and potentially high seed dispersal), most of the genetic variation was found within populations.Key words: genetic diversity, genetic structure, seedling recruitment, vegetative propagation, Ericaceae.

scholarly journals Intra-line and inter-line genetic diversity in sire lines of the Old Kladruber horse based on microsatellite analysis of DNA

2011 ◽  
Vol 56 (No. 4) ◽  
pp. 163-175 ◽  
Author(s):  
L. Vostrý ◽  
O. Kracíková ◽  
B. Hofmanová ◽  
V. Czerneková ◽  
T. Kott ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Analysis ◽  
Genetic Difference ◽  
Principal Component ◽  
Genetic Distances ◽  
Mean Value ◽  
Pedigree Information ◽  
Mean Values ◽  
The Mean ◽  
Coefficient Of Relationship

The Old Kladruber horse is the oldest original Czech horse breed &ndash; gene resource, with pedigree records spanning three centuries. Because the population is closed, there is a concern about the loss of genetic variation. The genetic diversity within and amongst sire lines was evaluated using microsatellite markers and based on pedigree information. The DNA analysis, covering 16 microsatellite loci, revealed that the genetic diversity (observed heterozygosity = 0.637, genetic diversity = 0.678 and the mean number of alleles = 8.25) for the Old Kladruber horse is consistent with other populations of horses. Inter-line genetic difference in sire lines reached the mean value (the F<sub>ST</sub> values ranged from 0.020 to 0.017). Differences amongst the sire lines were identified using genetic distances and principal component analysis. One gene cluster comprised black variation sire lines, while the second cluster included the sire lines of the grey variation. In the subjects monitored, the average inbreeding coefficient of 0.076 was estimated on the basis of pedigree information. The highest mean values of the coefficient of relationship were estimated within the colour variations. When comparing the genetic distance and the average coefficient of relationship, differences were found out. These results are useful for the development of breeding strategies which consider classical horse breeding as well as recent achievements of population and conservation genetics.

scholarly journals Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

2021 ◽  
Vol 13 (12) ◽  
pp. 6830
Author(s):  
Murat Guney ◽  
Salih Kafkas ◽  
Hakan Keles ◽  
Mozhgan Zarifikhosroshahi ◽  
Muhammet Ali Gundesli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plant Genetic Resources ◽  
Juglans Regia ◽  
Genetic Distances ◽  
Mean Value ◽  
Central Anatolia ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

Genetic Diversity Analysis of Salvadora Oleoides Decne: An Evergreen Dry Land Fruit Tree of Rajasthan, India

2021 ◽  
Author(s):  
Juleri M Upendra ◽  
Shari Nair ◽  
Satyawada R Rao ◽  
Harchand R Dagla
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Splice Junction ◽  
Genetic Distances ◽  
Climatic Conditions ◽  
Fruit Tree ◽  
Group Method ◽  
Dry Land ◽  
Intron Splice ◽  
Semi Arid

Abstract Genetic diversity of Salvadora oleoides Decne is analyzed by cumulative data of 10 Random Amplified Polymorphic DNA (RAPD), 10 Inter Simple Sequence Repeats (ISSR) and 7 Intron Splice Junction (ISJ) markers. The plant is an evergreen fruit tree and well distributed in semi-arid and sub-humid climatic conditions of Rajasthan, India. RAPD, ISSR and ISJ primers accounted for 84.4%, 85.3%, 85.9% polymorphism. Average 0.23 PIC is accounted for RAPD, ISSR and ISJ primers. The genetic similarity ranged between 0.42-0.89. Analysis of molecular variance (AMOVA) revealed higher variation (73%) at intra-population than inter-population (27%) level. Genetic distances based on Un-weighted Pair Group Method with Arithmetic mean (UPGMA) dendrogram and Principal Coordinate Analysis (PCoA) is correlated with physical distances or climatic conditions of Salvadora oleoides Decne in a semi-arid and sub-humid environment of Rajasthan. The present investigation may help in the understanding of gene flow systems between physical distances and environmental heterogeneity of the populations for better management of Salvadora oleoides Decne in the region.

Detection of genetic diversity in rough fescue (Festuca campestris Rydb) populations of southern Alberta and British Columbia, Canada, using RAPD markers

2008 ◽  
Vol 88 (2) ◽  
pp. 307-312
Author(s):  
Zhao Mengli ◽  
Han Bing ◽  
Walter D Willms
Keyword(s):  
Genetic Diversity ◽  
British Columbia ◽  
Genetic Distance ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Distance ◽  
Genetic Distances ◽  
Gene Frequencies ◽  
Southern Alberta ◽  
Potential Adaptation ◽  
Rough Fescue

Mountain rough fescue (Festuca campestris Rydb.) is a tufted native grass in southern Alberta and British Columbia, Canada, and has attracted interest for use in reclamation. However, its seed is often available from only a few localized sources and may not be adapted for areas removed from the collection site. We conducted a study to determine the genetic variability among rough fescue populations to assess its potential adaptation. Thirty plants were collected from each of six populations and analyzed using Random Amplified Polymorphic DNA (RAPD). One population (Kamloops, BC) was separated by several mountain ranges from the five easterly Alberta populations.The Kamloops population was also separated from the Alberta populations by genetic distance in two clusters. Of the total genetic variation present in the data, 21% was found among populations while the remaining (79%) was found within populations. Nei’s genetic distances among populations were related to their geographical distances. Genetic differences among populations appeared to be caused primarily by differences in gene frequencies rather than rare genes. Also, genetic diversity appeared to increase from west to east suggesting that the more easterly populations had greater adaptation potential. We speculate that the more easterly populations are less likely to share genes since the prevailing winds are from the west. Germplasm from the more easterly populations may be used with suitable precautions within Alberta and possibly around Kamloops. Key words: Genetic distance, geographic distance, reclamation, potential adaptation

scholarly journals Assessment of genetic diversity among surian Toona sinensis Roem in progenies test using random amplified polymorphic DNA markers

2018 ◽  
Vol 22 (1) ◽  
pp. 22
Author(s):  
Jayusman Jayusman ◽  
Muhammad Na’iem ◽  
Sapto Indrioko ◽  
Eko Bhakti Hardiyanto ◽  
ILG Nurcahyaningsih
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Management Strategies ◽  
Genetic Distances ◽  
Sampled Data ◽  
Toona Sinensis ◽  
The Mean ◽  
Individual Trees

Surian Toona sinensis Roem is one of the most widely planted species in Indonesia. This study aimed to estimate the genetic diversity between a number of surian populations in a progeny test using RAPD markers, with the goal of proposing management strategies for a surian breeding program. Ninety-six individual trees from 8 populations of surian were chosen as samples for analysis. Eleven polymorphic primers (OP-B3, OP-B4, OP-B10, OP-H3, OP-Y6, OP-Y7, OP-Y8, OP-Y10, OP-Y11, OP-Y14, and OP-06) producing reproducible bands were analyzed for the 96 trees, with six trees per family sampled. Data were analyzed using GenAlEx 6.3, NTSYS 2.02. The observed percentage of polymorphic loci ranged from 18.2% to 50%. The mean level of genetic diversity among the surian populations was considered to be moderate (He 0.304). Cluster analysis grouped the genotypes into two main clusters, at similarity levels of 0.68 and 0.46. The first two axes of the PCoA explained 46.16% and 25.54% of the total variation, respectively. The grouping of samples into clusters and subclusters did not correspond with family and their distances, but the grouping was in line with the genetic distances of the samples.

scholarly journals Assessment of Genetic Diversity in Cultivated Tomato (Solanum Lycopersicum L.) Genotypes Using Rapd Primers

2013 ◽  
Vol 21 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Saida Sharifova ◽  
Sabina Mehdiyeva ◽  
Konstantinos Theodorikas ◽  
Konstantinos Roubos
Keyword(s):  
Genetic Diversity ◽  
Rapd Analysis ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Arithmetic Mean ◽  
Similarity Coefficient ◽  
Group Method ◽  
Solanum Lycopersicum L ◽  
Pair Group ◽  
Upgma Cluster Analysis

Abstract Random Amplified Polymorphic DNA (RAPD) analysis was carried out on 19 Azerbaijan tomato genotypes, both cultivars and local populations. A total of 26 amplified products were revealed by 6 primers. The genetic similarity among evaluated genotypes ranged from 0.188 to 1.000. The lowest similarity was observed between cultivars ‘Azerbaijan’ and ‘Shakar’ (0.188), while the highest between ‘Elnur’ and ‘Garatag’ (1.000). The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis based on Jaccard’s similarity coefficient divided genotypes into four main groups. The first group was the largest and consisted of 12 genotypes, while the fourth group was the smallest consisted of 1 genotype only. The most polymorphic primer was OPB-18 that presented a genetic diversity index of 0.823, while the least informative was primer OPG-17 with an index of 0.349. The average genetic diversity calculated from RAPD data was 0.665.

scholarly journals Using Random Amplified Polymorphic DNA (RAPD) analysis to investigation of genetic diversity, and relationships among a set of clinical Aspergillus fumigatus isolates

2014 ◽  
Vol 8 (1) ◽  
pp. 46-54
Author(s):  
Batool Omran Theeb ◽  
Abdulkareem Jasim Hashim ◽  
Akeel Hussain Ali Al-Assi
Keyword(s):  
Genetic Diversity ◽  
Aspergillus Fumigatus ◽  
Genetic Relatedness ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
Close Relation ◽  
Genetic Distances ◽  
Universal Primers ◽  
Characteristic Banding ◽  
High Level

This study is an attempt to determine the genetic diversity and relationships among fourteen local isolate isolated from patients with Aspergillosis (Aspergillus fumigatus) by using the Random Amplified Polymorphic DNA (RAPD) technique. Twelve universal primers used in this study produced 94 bands across fourteen isolates. Of these bands, 67 bands or 71.2% were polymorphic. The size of the amplified bands ranged between 100-2000 bp. The genetic polymorphism value of each primer was determined and ranged between 33-100%. In terms of unique banding patterns, determine the finger print for six isolates the most characteristic banding pattern was for the (AFU1, AFU2, AFU3, AFU4, AFU8 and AFU14) with primer (OP F-16 , OP I-06, OP F-16, OP X-01, OP X-01and OP A-06). Genetic distances ranged from 0.12419 to 0.64404 among A. fumigatus isolates. Cluster analyses were performed to construct a dendrogram among studied A. fumigatus isolates. The cluster analysis places most of the A.fumigatus isolates isolated from patient come from yhe same area into a close relation (subcluster) showing a high level of genetic relatedness and were distinct from isolates from another area (the other subcluster). Interestingly, a number of isolates originating from the same sources did form well defined groups, indicating association between the RAPD patterns and the geographic origin of the isolates. The information generated from this study can be used in the future for controlling of Aspergillosis programs.

Genetic diversity among geographically separated populations of Nepenthes mirabilis

Biologia ◽  
2006 ◽  
Vol 61 (3) ◽  
Author(s):  
Arunrat Chaveerach ◽  
Alongkod Tanomtong ◽  
Runglawan Sudmoon ◽  
Tawatchai Tanee
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Geographical Area ◽  
Inter Simple Sequence Repeat ◽  
Genetic Distances ◽  
High Genetic Diversity ◽  
Total Genetic Diversity ◽  
Environmental Variations ◽  
Diversity Profile ◽  
Great Genetic Diversity

AbstractThe distribution of Nepenthes mirabilis ranges from Northeast (NE) to South (S) Thailand. Eleven individuals from NE, S and Suen Jatujak market in Bangkok, Central (C) Thailand, were collected and divided into four populations according to their geographical areas. These four populations were analyzed to determine a genetic diversity profile using thirteen inter-simple sequence repeat markers. The individuals produced 75.18% polymorphic banding profiles. The Shannon’s index was used to estimate genetic diversity. Total genetic diversity (H T) and inter-population genetic diversity (H S) were 0.854 and 0.678, respectively. The degree of genetic differentiation (G ST) of the species populations is 0.206, whereas the gene flow (Nm) among all the various geographical area populations is 1.016. Both the dendrogram and the results of the Shannon’s diversity index suggest great genetic diversity. These results support the broad range of distribution sites of Nepenthes mirabilis, which would require high genetic diversity to adapt to the environmental variations that can be found between NE, C, and S Thailand. ANOVA shows that the genetic diversity in each population is not significantly different (P > 0.05). Mantel tests reveal that geographical distance is an important factor for affecting the genetic distances among populations.

Genetic variation in two Chamaecrista species (Leguminosae), one endangered and narrowly distributed and another widespread in the Serra do Espinhaço, Brazil

2007 ◽  
Vol 85 (7) ◽  
pp. 629-636 ◽  
Author(s):  
Reinaldo Moreira da Silva ◽  
G. Wilson Fernandes ◽  
Maria Bernadete Lovato
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Habitat Destruction ◽  
Conservation Strategies ◽  
Lower Percentage ◽  
Endemic Plant ◽  
Endemic Plant Species ◽  
Two Populations ◽  
Shannon’S Diversity Index

The Serra do Espinhaço in Brazil is under continuous and increasing levels of human disturbance. It has a large number of endemic plant species such as Chamaecrista semaphora (Irwin and Barneby), an endangered species with extremely narrow range. We studied the genetic diversity of C. semaphora and compared it with Chamaecrista mucronata (Spreng.) Irwin and Barneby, a widespread congeneric species distributed over the entire Serra do Espinhaço, in an attempt to provide information for conservation strategies. Two populations of C. mucronata and the only two known populations of C. semaphora from Serra do Cipó were screened for variability using random amplified polymorphic DNA (RAPD) markers. Populations of C. semaphora exhibited a lower percentage of polymorphic markers (16.9%) and Shannon’s Diversity Index (H′pop = 0.124) than C. mucronata populations (43.3% and H′pop = 0.299). Most of the genetic variability of both species studied was distributed within populations; C. semaphora populations (ΦST = 0.198) were less divergent than C. mucronata populations (ΦST = 0.378). The risk of extinction for C. semaphora is large owing to its low level of genetic diversity compared with its widespread congener and because of increasing habitat destruction. Both populations of C. semaphora urgently need protection to maximize the genetic diversity of this species and diminish further substantial loss within the populations.

Parasite (Schistosoma mansoni) and host (Biomphalaria glabrata) genetic diversity: population structure in a fragmented landscape

Parasitology ◽  
2001 ◽  
Vol 122 (5) ◽  
pp. 545-554 ◽  
Author(s):  
C. SIRE ◽  
J. LANGAND ◽  
V. BARRAL ◽  
A. THÉRON
Keyword(s):  
Genetic Diversity ◽  
Schistosoma Mansoni ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rattus Rattus ◽  
Biomphalaria Glabrata ◽  
Genetic Distances ◽  
Snail Host ◽  
Fragmented Landscape ◽  
Geographical Distances

Random amplified polymorphic DNA (RAPD) markers were used to quantify genetic diversity within and between 5 populations ofSchistosoma mansoniwithin its definitive host (Rattus rattus) and the 5 corresponding populations of the snail intermediate host (Biomphalaria glabrata) from a limited endemic area of murine schistosomiasis on the island of Guadeloupe. Analysis of molecular variance (AMOVA) and canonical correspondence analysis (CCA) were used to test the significance of genetic differentiation between populations. Both methods gave similar results. Of total gene diversity, 15.1% (AMOVA) and 18.8% (CCA) was partitioned between localities forS. mansoniwith an absence of association between genetic and geographical distances. Geographical localities accounted for 20.5% (CCA) of the total diversity forB. glabratapopulations. The genetic distances between pairs of parasite populations were not correlated with the genetic distances between the corresponding pairs of snail host populations. Such strong patterns of local differentiation of both parasite and snail populations are consistent with predictions based on metapopulation dynamics and may have implications on host–parasite susceptibility relationship through local adaptation processes.

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