scholarly journals Genetic Diversity and Population Structure of Alnus cremastogyne as Revealed by Microsatellite Markers

Forests ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 278 ◽  
Author(s):  
Hong-Ying Guo ◽  
Ze-Liang Wang ◽  
Zhen Huang ◽  
Zhi Chen ◽  
Han-Bo Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Geographical Distribution ◽  
Mantel Test ◽  
Group Method ◽  
Arithmetic Means ◽  
Mountain Area ◽  
Pair Group ◽  
Hill Area ◽  
Population Genetic Variation ◽  
High Level

Alnus cremastogyne Burk. is a nonleguminous, nitrogen-fixing tree species. It is also the most important endemic species of Alnus Mill. in China, possessing important ecological functions. This study investigated population genetic variation in A. cremastogyne using 175 trees sampled from 14 populations native to Sichuan Province with 25 simple sequence repeat (SSR) markers. Our analysis showed that A. cremastogyne has an average of 5.83 alleles, 3.37 effective alleles, an expected heterozygosity of 0.63, and an observed heterozygosity of 0.739, indicating a relatively high level of genetic diversity. The A. cremastogyne populations in Liangshan Prefecture (Meigu, Mianning) showed the highest level of genetic diversity, whereas the Yanting population had the lowest. Our analysis also showed that the average genetic differentiation of 14 A. cremastogyne populations was 0.021. Analysis of molecular variance (AMOVA) revealed that 97% of the variation existed within populations; only 3% was among populations. Unweighted pair-group method with arithmetic means (UPGMA) clustering and genetic structure analysis showed that the 14 A. cremastogyne populations could be clearly divided into three clusters: Liangshan Prefecture population, Ganzi Prefecture population, the other population in the mountain area around the Sichuan Basin and central Sichuan hill area, indicating some geographical distribution. Further analysis using the Mantel test showed that this geographical distribution was significantly correlated with elevation.

scholarly journals Estimation of Genetic Diversity in Genus Mentha Collected From Azad Jammu And Kashmir, Pakistan

2019 ◽  
Author(s):  
Fozia Abasi ◽  
Israr Ahmad ◽  
Sami Ullah khan ◽  
Khawaja Shafique Ahmad ◽  
Aneela Ulfat ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Molecular Data ◽  
Group Method ◽  
Similarity Coefficients ◽  
Arithmetic Means ◽  
Jammu And Kashmir ◽  
Pair Group ◽  
High Level

ABSTRACTMints are perennial aromatic herbs used both for medicinal and aromatic purposes. Flora of Pakistan has reported six species of genus Mentha. Taxonomy of genus Mentha is more complex and confusing due to inter specific hybridization. The present research is the first documented report from Pakistan for the purpose to dissect Mentha specimens using molecular tools. A total of 17 SCoT and SSR markers used to dissect genetic diversity among 41 Mentha specimens. The results revealed substantial variation among Mentha specimens. The molecular data analyzed through NTSYS and Power marker software’s. Dendrogram constructed on the base of similarity coefficients generated using weighted pair group method of arithmetic means (UPGMA) recorded high level of polymorphism. Polymorphic Information Content (PIC) for molecular markers recorded in the range of 5-8. Mean genetic distance (GD) was estimated in the range from 0.35% to 100%. The minimum and maximum GD recorded in one combination each as P2-P4 and M41-P10. The present study was explored the efficiency of SCoT and SSR markers for evaluating the genetic diversity of medicinal plants. The present research was concluded that both morphological and molecular dendrogram determined considerable level of diversity among Mentha species. Furthermore, specific primers and DNA chloroplast technology could be needed for further molecular analysis to refine the data more up to varietal level.

scholarly journals Determination of genetic variations among different Trichoderma isolates using RAPD marker in Bangladesh

1970 ◽  
Vol 9 (1) ◽  
pp. 9-20 ◽  
Author(s):  
MSI Sagar ◽  
MB Meah ◽  
MM Rahman ◽  
AK Ghose
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Genetic Variations ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
High Level ◽  
Cluster 2

Some Trichoderma isolates were collected from different locations of Bangladesh for evaluating their bioefficiency by determining their genetic variations. PCR-based Random Amplified Polymorphic DNA (RAPD) Marker employing 3 decamer primers produced 29 scorable bands of which all (100%) were polymorphic. The co-efficient of gene differentiation (Gst) was 1.0000 reflecting the existence of high level of genetic diversity among the isolates. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s (1972) genetic distance produced 2 main clusters (16 isolates in cluster 1 and 19 isolates in cluster 2). The result indicating their genetic diversity has opened new possibility of using the most efficient and more isolates of Trichoderma in the preparation of effective biopesticide. Keywords: Genetic diversity; Trichoderma; RAPD DOI: http://dx.doi.org/10.3329/jbau.v9i1.8738 JBAU 2011; 9(1): 9-20

Genetic diversity and relationships among Secale L. based on RAMP markers

2004 ◽  
Vol 1 (2) ◽  
pp. 73-78 ◽  
Author(s):  
Shang Hai-Ying ◽  
Zheng You-Liang ◽  
Wei Yu-Ming ◽  
Wu Wei ◽  
Yan Ze-Hong
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Pcr Amplification ◽  
Group Method ◽  
Transitional Region ◽  
Arithmetic Average ◽  
Pair Group ◽  
Broad Leaf ◽  
Polymorphic Bands ◽  
High Level

AbstractGenetic diversity and relationships among 21 accessions of Secale L., including three species and 10 subspecies, were evaluated using RAMP markers. Forty-one out of 80 (50.5%) RAMP primers, which produced clear and polymorphic bands, were selected for PCR amplification of genomic DNA. A total of 446 bands were amplified from the 41 primers, and 428 of these bands (about 96%) were polymorphic. Three to 19 polymorphic bands could be amplified from each primer, with an average of 10.4 bands. The RAMP-based genetic similarity (GS) values among the 21 Secale accessions ranged from 0.266 to 0.658, with a mean of 0.449. A high level of genetic variation was found between or within the wild populations and the cultivars. Based on the GS matrix, a dendrogram was constructed using the unweighted pair group method with arithmetic average (UPGMA). All 21 accessions could be distinguished by RAMP markers. Clustering results showed that the genetic diversity of Secale based on RAMP markers was correlated with geographical distribution. Six rye cultivars, originating from Poland, Portugal, Mexico, Hungary, Armenia and Ukraine, were clustered into one group. The six countries are all located in the transitional region of broad-leaf forests between maritime and continental temperate zones, with narrow latitude span. In comparison, the other five cultivars from countries scattered over a region with large latitude span were distributed within different groups or subgroups. Genetic relationships based on RAMP markers had great deviation from the original taxonomy. Some subspecies of the same species were distributed within different groups, while some accessions of different species were closely clustered into one subgroup. These results suggest that RAMP markers could be an effective technique for detecting genetic diversity among Secale and give some useful information about its phylogenic relationships.

Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

1996 ◽  
Vol 26 (8) ◽  
pp. 1454-1462 ◽  
Author(s):  
Naoki Tani ◽  
Nobuhiro Tomaru ◽  
Masayuki Araki ◽  
Kihachiro Ohba
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Phylogenetic Trees ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Group Method ◽  
Stone Pine ◽  
Arithmetic Means ◽  
Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

scholarly journals Characterization and Identification of Pawpaw Cultivars and Advanced Selections by Simple Sequence Repeat Markers

2010 ◽  
Vol 135 (2) ◽  
pp. 143-149 ◽  
Author(s):  
Kirk W. Pomper ◽  
Jeremiah D. Lowe ◽  
Li Lu ◽  
Sheri B. Crabtree ◽  
Shandeep Dutta ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Marker ◽  
Genetic Erosion ◽  
Null Alleles ◽  
Group Method ◽  
Genomic Libraries ◽  
Pair Group ◽  
Marker Loci ◽  
High Level ◽  
In The Beginning

Pawpaw [Asimina triloba (L.) Dunal.], a tree fruit native to eastern North America, is in the beginning stages of commercialization. Cultivars available in the early 20th century have been lost, and significant genetic erosion may have occurred. Polymorphic microsatellite marker loci were developed from enriched genomic libraries. Five marker loci were used to fingerprint 28 cultivars and 13 selections. For the 41 genotypes, 102 alleles were amplified and major allele frequency (0.16–0.94), number of genotypes (2–27), and allele size (144–343 bp) varied greatly by locus. Four loci were highly polymorphic, as indicated by values for expected heterozygosity (He), observed heterozygosity (Ho), and polymorphism information content, but only two alleles were detected at locus Pp-C104. A high level of genetic diversity was observed in the studied genotypes. The Ho (0.68) and He (0.70) were similar and indicated few null alleles. In the 41 genotypes, 39 unique fingerprints were observed. These new microsatellite marker loci will be useful for cultivar fingerprinting, management of collections, and investigation of genetic diversity in collections and wild populations. Grouping of genotypes in an unweighted pair group method with arithmetic mean dendrogram was generally consistent with their origins.

scholarly journals Genetic DiversityAssessment in Ten Aromatic Rice Varieties of Bangladesh

2017 ◽  
Vol 27 (2) ◽  
pp. 217-225 ◽  
Author(s):  
Tahmina Islam ◽  
Shinthia Rahman ◽  
M Imdadul Hoque ◽  
RH Sarker
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa L ◽  
Group Method ◽  
Aromatic Rice ◽  
Arithmetic Means ◽  
Rice Varieties ◽  
Center Of Origin ◽  
Pair Group ◽  
Relationship Of ◽  
Selection Of

The availability of molecular marker systems allowed estimating the relationships among various taxa. This study was aimed at assessing the genetic diversity among ten aromatic rice (Oryza sativa L.) pools from Bangladesh by means of randomly amplified polymorphic DNA (RAPD) markers. These varieties were evaluated for polymorphisms after amplification with 10 decamer primers. A total of 60 RAPD fragments were generated among the assessed varieties with a polymorphism percentage of 80. Cluster analysis by the unweighted pair group method of arithmetic means (UPGMA) showed that these 10 varieties could be placed into two groups with a similarity ranging from 65 to 86% depicting adjacent association between Rajbhog and Kalijira‐12, whereas Maloti belongs to a separate group maintaining maximum distance from rest of the varieties. The analysis revealed that the intervarietal genetic relationship of several varieties is related to their center of origin. As expected, most of the varieties have a narrow genetic base. The present results could be used for the selection of possible parents to generate a mapping population and utilized by the breeders for assessing the genetic diversity of rice genotypes.Plant Tissue Cult. & Biotech. 27(2): 217-225, 2017 (December)

scholarly journals Genetic Diversity in Populations of Phytophthora citricola Associated with Horticultural Crops in California

Plant Disease ◽  
2007 ◽  
Vol 91 (12) ◽  
pp. 1556-1563 ◽  
Author(s):  
R. G. Bhat ◽  
G. T. Browne
Keyword(s):  
Genetic Diversity ◽  
Fragment Length Polymorphism ◽  
Group Method ◽  
Aflp Data ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Horticultural Crops ◽  
Pair Group ◽  
Phytophthora Citricola ◽  
High Level

California populations of the plant pathogen Phytophthora citricola were examined for amplified fragment length polymorphism (AFLP), pathogenicity on almond, and sensitivity to mefenoxam. The characterizations of AFLP variation and mefenoxam sensitivity were based on 86 isolates (44 from almond, 11 from avocado, 3 from strawberry, 18 from walnut, and 10 from six other hosts). Cluster analysis of the AFLP data using the unweighted pair group method indicated a high level of genetic diversity among the isolates, and four main clusters were identified—one dominated by isolates from almond, another including all isolates from avocado, and two including isolates from several hosts other than avocado. Analysis of molecular variance revealed that 38.4 and 24.9% of the AFLP variation were associated with host and geographical factors, respectively. Of 24 isolates, including those from almond, avocado, strawberry, and walnut, 22 were aggressive on almond shoots; there was no evidence of host specificity. All but 1 of the 86 isolates grew at different rates on V8 juice medium amended with mefenoxam at 1 ppm, indicating partial tolerance to the fungicide. Isolates of P. citricola from California populations are genetically diverse, and much of the variation is associated with host and geography. These populations are all potentially pathogenic on almond and tolerant to mefenoxam.

scholarly journals Performance of salinity tolerance of F3 rice lines of BRRI dhan 29 × PBRC (STL-20) using RAPD markers

2019 ◽  
Vol 6 (2) ◽  
pp. 215-225
Author(s):  
Nazmul Islam Mazumder ◽  
Tania Sultana ◽  
Prtitish Chandra Paul ◽  
Dinesh Chandra Roy ◽  
Deboprio Roy Sushmoy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Salinity Tolerance ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Susceptible Variety ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
Tolerant Line

Twenty six rice lines of PBRC (salt tolerant line-20) × BRRI dhan-29 were used to evaluate salinity tolerance at the seedling stage and tested for salt tolerance using RAPD markers. Salinity screening was done using hydrophonic system at the greenhouse following IRRI standard protocol. Among the studied line, ten were moderately salinity tolerant, nine susceptible and rest of the lines highly susceptible. For assessing genetic diversity and relationship of F3 rice lines including two parents were tested against PCR-based Random Amplified Polymorphic DNA (RAPD) technique using three arbitrary decamer primers; OPA02, OPC01, and OPC12. Selected three primers generated a total of 14 bands. Out of 14 bands, 12 bands (86.67%) were polymorphic and 2 bands (13.33%) were monomorphic. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s (1972) genetic distance produced 2 main clusters of the 28 rice genotypes. Most of the moderately tolerant lines and PBRC (STL-20) (tolerant variety) were grouped in same cluster due to lower genetic distance, while maximum susceptible along with BRRI dhan29 (susceptible variety) showed higher genetic distance with PBRC (STL-20) and moderately tolerant lines. This result indicates that the lines which formed grouped together, they are less diversed. On the other hand the lines remain in different clusters or different groups, are much diversed. Thus RAPD perform a potentially simple, rapid and reliable method to evaluate genetic diversity and molecular characterization as well. Res. Agric., Livest. Fish.6(2): 215-225, August 2019

scholarly journals Molecular characterization of oil seed Brassica using RAPD markers

2020 ◽  
Vol 55 (1) ◽  
pp. 1-8
Author(s):  
M Islam ◽  
A Habib ◽  
S Khan ◽  
S Akter ◽  
B Goswami ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Arithmetic Means ◽  
Oil Seed ◽  
Pair Group ◽  
Brassica Spp ◽  
Breeding Programmes ◽  
High Level

Twelve varieties of oil seed Brassica spp. were characterized at molecular level using Random Amplified Polymorphic DNA (RAPD) primers to explore genetic diversity and to find out relationship among them. Twelve random primers used in the study generated 94 RAPD fragments and 53 (56.38%) of them were considered as polymorphic indicating high level of polymorphism within the materials. The size of amplified fragments ranged between 300-3000 bp. The values of pair-wise genetic distance ranged from 0.1613 to 0.5543. To find out phylogenetic relationships among the varieties, dendrogram based on Nei’s genetic distance was constructed using Unweighted Pair Group Method of Arithmetic Means (UPGMA) separating the 12 Brassica spp into two major clusters C1 and C2. This result will be useful for designing future breeding programmes for improvement of Brassica varieties. Bangladesh J. Sci. Ind. Res.55(1), 1-8, 2020

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.

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