scholarly journals Origin, Domestication, Dissemination and Genetic Diversity of Coconut: DNA information

CORD ◽  
2001 ◽  
Vol 17 (01) ◽  
pp. 34
Author(s):  
Lalith Perera
Keyword(s):  
Genetic Diversity ◽  
Fragment Length Polymorphism ◽  
Genomic Library ◽  
Conservation Strategies ◽  
Sri Lankan ◽  
Hierarchical Analysis ◽  
Microsatellite Primers ◽  
Aflp Data ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance

Information on origin, dissemination and levels and distribution of genetic diversity in coconuts will allow plant breeders and conservationists to select better breeding materials and formulate appropriate conservation strategies. PCR-based DNA profiling of coconut palms from Sri Lanka was initially conducted using both Amplified Fragment Length Polymorphism (AFLPs) and Microsatellites (SSRs). Thirty-nine microsatellite primers specific to coconut were developed by small insert genomic library construction. Eighteen of those primers were used to analyze the same set of Sri Lankan coconut materials. Overall, the results generated by both AFLPs and SSRs were in agreement. Most diversity was found in the tall variety (Typica) (0.92 and 0.62 for AFLPs and SSRs, respectively) rather than the intermediate (Aurantiaca) and dwarf (Nana) varieties (0.82 and 0.25 for AFLPs and SSRs, respectively). A hierarchical analysis of molecular variance (AMOVA) based on AFLP data was used to quantify and partition levels of variability  between and within form components. This revealed that for the inbreeding dwarf and intermediate forms most variation was observed between rather than within forms.  In contrast, the out-breeding tall forms exhibited as much variation within as between forms.

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 Genetic diversity in natural populations of Buriti (Mauritia flexuosa L. f.)

2011 ◽  
Vol 11 (3) ◽  
pp. 216-223 ◽  
Author(s):  
Liene Rocha Picanço Gomes ◽  
Maria Teresa Gomes Lopes ◽  
Jania Lilia da Silva Bentes ◽  
Willian Silva Barros ◽  
Pedro de Queiroz Costa Neto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Natural Populations ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Polymorphic Loci ◽  
Mauritia Flexuosa ◽  
Geographical Distances ◽  
Traditional Communities

This study aimed to characterize the genetic diversity of buriti populations by AFLP (Amplified Fragment Length Polymorphism) markers. The analysis was performed in four populations used by traditional communities in the state of Amazonia (Bom Jesus do Anamã, Lauro Sodré, Santa Luzia do Buiçuzinho, and Esperança II). From each population 30 plants were randomly selected. To obtain the markers four primer combinations were used. The percentage of polymorphic loci was estimated, the molecular variance among and within populations analyzed and a dendrogram constructed. The primers detected 339 polymorphic loci ranging from 81.1 % to 91.1 % among populations. Analysis of molecular variance attributed 77.18 % to variation within and 22.8 % to variation between populations. The dendrogram indicated the formation of two groups, showing that the populations of Bom Jesus do Anamã and Lauro Sodré are genetically most similar and thet the genetic and geographical distances are not correlated.

scholarly journals GENETIC DIVERSITY AMONG NATURAL POPULATIONS OF Keteleeria evelyniana Mast. IN CENTRAL HIGLANDS OF VIETNAM USING SSR MARKERS

2018 ◽  
Vol 56 (3) ◽  
pp. 275
Author(s):  
Tran Thi Lieu ◽  
Dinh Thi Phong ◽  
Vu Thi Thu Hien
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Natural Populations ◽  
Similarity Coefficient ◽  
Similarity Matrix ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Private Alleles ◽  
Softwood Species

Keteleeria evelyniana Mast. is a big softwood species with high economic values. Therefore, the number of these trees are rapidly decreasing due to rampant exploitation as well as its habitat loss and recently, the species is considered vulnerablein Vietnam. In this study, we assessed the genetic variation among seventy K. evelyniana samples of three natural populations in Lam Dong, Dak Lak and Kon Tum using 16 microsatellite markers. The results showed that thirteen markers were polymorphic. A total 39 DNA fragments were amplified, among them, thirty – five were polymorphic (accounting for 89.74%). Among studied populations, the level of genetic diversity at Lam Dong (Na = 2.063; Ne = 1.730; Ap = 0.375; I = 0.558; Ho = 0.459 and He = 0.367) was the highest. Analysis of molecular variance (AMOVA) showed that the total level of molecular changes between populations was 34.65% and between individuals in the same population was 65.35%. Private alleles (Ap) and inbreeding values (Fis) of K. evelyniana species were founded of all three populations in Lam Dong, Dak Lak and Kon Tum (0.375 and -0.234; 0.188 and -0.065; 0.063 and -0.047, respectively). The gene flow (Nm) also occurred among the K. evelyniana populations with the average of Nm = 5.423. A dendrogram (UPGMA) constructed based on the similarity matrix of 70 K. evelyniana samples divided into two main groups with their genetic similarity coefficient ranged from 76.5% (Ke26 and Ke44) to 99% (Ke23 and Ke25). The obtained results indicated the importance of conserving the genetic resources of K. evelyniana species in Tay Nguyen.

scholarly journals Discrimination and Genetic Diversity of Cephalotaxus Accessions Using AFLP Markers

2000 ◽  
Vol 125 (4) ◽  
pp. 404-412 ◽  
Author(s):  
Donglin Zhang ◽  
Michael A. Dirr ◽  
Robert A. Price
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Shade Tolerance ◽  
Fragment Length Polymorphism ◽  
Genetic Differences ◽  
Aflp Markers ◽  
Base Pairs ◽  
Aflp Data ◽  
Hybrid Species ◽  
Sun And Shade

Cephalotaxus Sieb. and Zucc. (plum yew) species and cultivars have become popular because of their sun and shade tolerance, resistance to deer browsing, disease and insect tolerance, and cold and heat adaptability. Unfortunately, the nomenclature and classification in the literature and nursery trade are confusing due to their extreme similarity in morphology. In this study, amplified fragment-length polymorphism (AFLP) markers were used to discriminate taxa and evaluate genetic differences among 90 Cephalotaxus accessions. A total of 403 useful markers between 75 and 500 base pairs (bps) was generated from three primer-pair combinations. Cluster analysis showed that the 90 accessions can be classified as four species, C. oliveri Mast., C. fortunei Hooker, C. harringtonia (Forbes) Koch., and C. ×sinensis (a hybrid species); four varieties, C. fortunei var. alpina Li, C. harringtonia var. koreana (Nakai) Rehd., C. harringtonia var. nana (Nakai) Hornibr., and C. harringtonia var. wilsoniana (Hayata) Kitamura; and eight cultivars. Suggested names are provided for mislabeled or misidentified taxa. The Cephalotaxus AFLP data serve as a guide to researchers and growers for identification and genetic differences of a taxon, and a model to establish a cultivar library against which later introductions or problematic collections can be cross-referenced.

Preliminary Investigation of Genetic Variation within and between Cultivated and Natural Populations of Banksia coccinea and Banksia menziesii

1998 ◽  
Vol 46 (4) ◽  
pp. 547 ◽  
Author(s):  
M. A. Rieger ◽  
M. Sedgley
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Full Range ◽  
Preliminary Investigation ◽  
Natural Populations ◽  
South Australia ◽  
Randomly Amplified Polymorphic Dna ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Cultivated Populations

The randomly amplified polymorphic DNA (RAPD) technique followed by analysis of molecular variance (AMOVA) was used to determine the level of variation within and between commercial plantations of Banksia coccinea R.Br. and B. menziesii R.Br. in South Australia and natural populations in Western Australia. For B. coccinea, the majority of variation was within populations (66.1%), while between all populations accounted for 20.8%. The variation between cultivated and natural populations was 13.2%. There was close clustering between the cultivated populations, which appeared to be most closely related to the inland natural populations. In contrast, the variation between cultivated and natural populations for B. menziesii was 0.4% with the majority of the variation within populations (93.2%) and 6.4% between all populations. The cultivated and natural populations formed a single cohesive cluster. These data indicate that the full range of natural genetic diversity of B. menziesii appears to occur in the cultivated plantations, but this was not the case for B. coccinea.

Genetic Diversity of Cambuci (Campomanesia Phaea) Revealed by Microsatellite Markers

2021 ◽  
Author(s):  
Rafael Oliveira Moreira ◽  
Eduardo de Andrade Bressan ◽  
Horst Bremer Neto ◽  
Angelo Pedro Jacomino ◽  
Antonio Figueira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Microsatellite Markers ◽  
Native Species ◽  
Genetic Parameters ◽  
Genomic Library ◽  
Conservation Strategies ◽  
Paulo State ◽  
Allele Number ◽  
Expected Heterozygosity

Abstract Campomanesia phaea (Myrtaceae), known as cambuci, is a native species from the Brazilian Atlantic Forest with great potential to be developed as a new fruit crop. Microsatellite markers were developed for cambuci to characterize the genetic diversity and to investigate the genetic structure of a group of accessions originally collected at the presumed center of diversity of the species. The work involved the collection of 145 accessions from five regional groups (Juquitiba, Paraibuna, Mogi das Cruzes, Ribeirão Pires, and Salesópolis) in São Paulo state, Brazil. Fourteen loci were identified in an enriched genomic library developed from one of these accessions. Six out of 14 loci revealed to be polymorphic, disclosing 26 alleles. Based on the allele frequencies, the calculated genetic parameters of the five groups indicated an average allele number per loci (A) of 3.83, with the expected heterozygosity (He) of 0.57 and the observed heterozygosity (Ho) of 0.54. The analysis of the genetic structure indicated that most of the genetic diversity is found within each population (HS = 0.57), whereas the genetic diversity among populations was low (GST = 0.19). The genetic diversity parameter of Nei was considered low for the cambuci analyzed populations, with no evidence of inbreeding. Based on Darwin analysis, we chose 18 accessions from the five regional populations to compose a core collection that includes most of the genetic diversity found in this study. Our findings may contribute to define better conservation strategies and genetic breeding approaches for this native species in Brazil.

Population structure of Moniliophthora perniciosa in the main cacao producing departments of Colombia

Plant Disease ◽  
2021 ◽  
Author(s):  
Yeirme Jaimes ◽  
Carolina Gonzalez ◽  
Jairo Rojas ◽  
Jessica Johana Rivera ◽  
Christian Cilas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Geographic Origin ◽  
Genetic Change ◽  
Linkage Disequilibrium Analysis ◽  
Host Genotype ◽  
Dispersal Patterns ◽  
Moniliophthora Perniciosa ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance

The witches’ broom (Moniliophthora perniciosa) is considered as one of the main threats for cacao production and, consequently, for chocolate production worldwide.. In this work, the genetic diversity and population structure of M. perniciosa were analyzed for 59 isolates collected in five departments of Colombia and using 10 microsatellite markers. Analyses revealed 35 multilocus genotypes (MLGs) and clonal populations structure according to linkage disequilibrium analysis. One of the objectives of this study was to determine whether populations were differentiated by geographic origin or T. cacao host genotype. Analysis of molecular variance, Discriminant Analysis of Principal Components (DAPC) and Bruvo genetic distance suggested that the genetic structure was driven by geographic origin and not by T. cacao genotype. The results of this study were consistent with previous findings obtained in other cocoa producing countries. Important insights were discussed regarding the dispersal patterns of the pathogen in Colombia and the genetic change of its populations due to different environmental conditions.

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 diversity in natural populations of noble crayfish (Astacus astacus L.) in north-western Poland on the basis of combined SSR and AFLP data

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7301
Author(s):  
Remigiusz Panicz ◽  
Łukasz Napora-Rutkowski ◽  
Sławomir Keszka ◽  
Lidia Skuza ◽  
Magdalena Szenejko ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Natural Populations ◽  
Conservation Strategies ◽  
Astacus Astacus ◽  
Aflp Data ◽  
Inbreeding Coefficients ◽  
Noble Crayfish ◽  
Total Variability ◽  
Northwestern Poland

Background Conservation of noble crayfish (Astacus astacus) populations is becoming particularly important since the number of individuals is rapidly declining across the distribution range of the species in Europe. Five crayfish populations in northwestern Poland have been constantly monitored for two decades. However, the genetic structure of these populations has not been analysed, although this information is important to devise effective conservation strategies. Methods Noble crayfish were collected in the autumn of 2014 by scuba diving in Lakes Graniczne, Babinki, Biwakowe, Sęki and Kwisno, all of which are situated in the Bytów Lakeland of northwestern Poland. Genetic diversity of the five populations was assessed based on allele variability in nine SSR regions and six AFLP primer combinations. Results Microsatellite results analysed with AMOVA showed that the diversity between populations corresponds to 18% of total variability, which was confirmed by similar results obtained using AFLP. Additionally, significant genetic diversity was revealed by high average FST values. All of the studied crayfish populations significantly deviated from the expected Hardy–Weinberg genetic equilibrium and were characterised by negative values of inbreeding coefficient (FIS). Discussion The invariably negative inbreeding coefficients (FIS) suggest a low number of mating individuals, a possible consequence of the phenomenon known as genetic bottleneck. However, additional comprehensive analyses are needed to assess the genetic structure, origin and vulnerability of the remaining populations of noble crayfish in the Bytów Lakeland of northwestern Poland, which have high conservation value and are particularly important as a live genetic bank for breeding and restitution purposes.

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