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 and Origin of Slovene Common Bean (Phaseolus vulgaris L.) Germplasm as Revealed by AFLP Markers and Phaseolin Analysis

2006 ◽  
Vol 131 (2) ◽  
pp. 242-249 ◽  
Author(s):  
Jelka Šustar-Vozlič ◽  
Marko Maras ◽  
Branka Javornik ◽  
Vladimir Meglič
Keyword(s):  
Genetic Diversity ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Seed Protein ◽  
Fragment Length Polymorphism ◽  
Aflp Markers ◽  
Group Method ◽  
Phaseolus Vulgaris L ◽  
Pair Group ◽  
High Level

There is a long tradition of common bean cultivation in Slovenia, which has resulted in the development of numerous landraces in addition to newly established cultivars. The genetic diversity of 100 accessions from the Genebank of the Agricultural Institute of Slovenia (AIS) were evaluated with amplified fragment length polymorphism (AFLP) markers and phaseolin seed protein. Twenty-seven standard accessions of known Mesoamerican and Andean origin, 10 wild Phaseolus vulgaris accessions and two related species, P. coccineus L. and P. lunatus L., were also included. Ten AFLP primer combinations produced 303 polymorphic bands, indicating a relatively high level of genetic diversity. Based on the marker data, unweighted pair group method with arithmethic mean (UPGMA) analysis and principal coordinate analysis (PCoA) all P. vulgaris accessions were separated into three well-defined groups. Two groups consisted of accessions of Mesoamerican and Andean origin, while the third was comprised of only four wild P. vulgaris accessions. A set of Slovene accessions formed a well-defined sub-group within the Andean cluster, showing their unique genetic structure. These data were supported by phaseolin analysis, which also revealed additional variants of “C” and “T” phaseolin types. The results are in agreement with previous findings concerning diversification of common bean germplasm introduced in Europe.

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 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 Investigating the Spatiotemporal Genetic Structure of Phytophthora capsici in Michigan

2001 ◽  
Vol 91 (10) ◽  
pp. 973-980 ◽  
Author(s):  
K. H. Lamour ◽  
M. K. Hausbeck
Keyword(s):  
Fragment Length Polymorphism ◽  
Aflp Marker ◽  
Phytophthora Capsici ◽  
Group Method ◽  
Analysis Of Molecular Variance ◽  
Arithmetic Average ◽  
Pair Group ◽  
Average Cluster ◽  
Over Time ◽  
F Statistics

Phytophthora capsici isolates were recovered from pepper and cucurbit hosts at seven locations in Michigan from 1998 to 2000. Isolates were characterized for compatibility type (CT), mefenoxam sensitivity (MS), and amplified fragment length polymorphism (AFLP) marker profiles. In total, 94 AFLP bands were resolved. Individual populations were highly variable. Within populations, 39 to 49% of the AFLP bands were polymorphic and estimated heterozygosities ranged from 0.16 to 0.19. Of the 646 isolates fingerprinted, 70% (454) had unique AFLP profiles. No clones were recovered between years or locations. Pairwise F statistics (ΦST) between populations from different locations ranged from 0.18 to 0.40. A tree based on unweighted pair-group method with arithmetic average cluster analysis indicates discrete clusters based on location. Isolates from the same location showed no clustering based on the year of sampling. Analysis of molecular variance partitioned variability among (40%) and within populations (60%). The overall estimated ΦST was 0.34 (SD = 0.03). A1/A2 CT ratios were ≈1:1, and MS frequencies were similar between years for the two locations sampled over time. These data suggest that P. capsici persists in discrete outcrossing populations and that gene flow among locations in Michigan is infrequent.

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.

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 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 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 Genetic Diversity and Dynamics of Sinorhizobium meliloti Populations Nodulating Different Alfalfa Cultivars in Italian Soils

2000 ◽  
Vol 66 (11) ◽  
pp. 4785-4789 ◽  
Author(s):  
Maria Carelli ◽  
Stefano Gnocchi ◽  
Silvia Fancelli ◽  
Alessio Mengoni ◽  
Donatella Paffetti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Polymorphism ◽  
Genetic Structure ◽  
Sinorhizobium Meliloti ◽  
Dna Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
High Level ◽  
Rhizobium Population

ABSTRACT We analyzed the genetic diversity of 531 Sinorhizobium meliloti strains isolated from nodules of Medicago sativa cultivars in two different Italian soils during 4 years of plant growth. The isolates were analyzed for DNA polymorphism with the random amplified polymorphic DNA method. The populations showed a high level of genetic polymorphism distributed throughout all the isolates, with 440 different haplotypes. Analysis of molecular variance allowed us to relate the genetic structure of the symbiotic population to various factors, including soil type, alfalfa cultivar, individual plants within a cultivar, and time. Some of these factors significantly affected the genetic structure of the population, and their relative influence changed with time. At the beginning of the experiment, the soil of origin and, even more, the cultivar significantly influenced the distribution of genetic variability of S. meliloti. After 3 years, the rhizobium population was altered; it showed a genetic structure based mainly on differences among plants, while the effects of soil and cultivar were not significant.

Genetic Diversity of Iranian Clones of Common Reed (Phragmites australis) Based on Morphological Traits and RAPD Markers

Weed Science ◽  
2011 ◽  
Vol 59 (3) ◽  
pp. 366-375 ◽  
Author(s):  
Marjan Diyanat ◽  
Ali A. S. Booshehri ◽  
Hassan M. Alizadeh ◽  
Mohammad R. Naghavi ◽  
Hamid R. Mashhadi
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Common Reed ◽  
Group Method ◽  
Successful Management ◽  
Morphological Comparison ◽  
Pair Group ◽  
High Level ◽  
Methods Of Control

The genetic diversity of 39 clones of common reed originating from different geographical areas of Iran were evaluated using morphological and RAPD analyses. High level of morphological variation was observed among clones. The 16 primers used in this study amplified 149 scorable RAPD loci among which 123 were polymorphic (83.1%). A dendrogram was prepared on the basis of a similarity matrix of RAPD data using the unweighted pair-group method with arithmetic averages (UPGMA) algorithm and separated the 39 clones into four groups, which mainly were in accordance with geographical origins. The results of the morphological comparison mostly corresponded with the results of RAPD analysis. It is possible that these variations among clones will affect successful management of common reed using chemical or the other methods of control.

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