Genetic Diversity and Population Structure of Diploid and Polyploid Species of Isoëtes in East Asia Based on Amplified Fragment Length Polymorphism Markers

2009 ◽  
Vol 170 (4) ◽  
pp. 496-504 ◽  
Author(s):  
Changkyun Kim ◽  
Hyunchur Shin ◽  
Hong‐Keun Choi
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
East Asia ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Polyploid Species

Assessing genetic variability among Brazilian strains ofXanthomonas axonopodispv.manihotisthrough restriction fragment length polymorphism and amplified fragment length polymorphism analyses

1999 ◽  
Vol 45 (9) ◽  
pp. 754-763 ◽  
Author(s):  
S Restrepo ◽  
T L Valle ◽  
M C Duque ◽  
V Verdier
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Bacterial Blight ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Restriction Fragment Length

Xanthomonas axonopodis pv.manihotis (Xam) causes bacterial blight, a major disease of cassava, which is a starchy root crop that feeds about 500 million people throughout the world. To better select resistant cassava germplasm, we examined the population structure of Xam in Brazil, Latin America's largest producer of cassava, and a major center of diversity for the crop. The 79 strains collected between 1941 and 1996 from three edaphoclimatic zones were analyzed by restriction fragment length polymorphism (RFLP), using a probe linked to a Xam pathogenicity gene (pthB). Thirty-eight haplotypes were identified, and geographical differentiation for the Xam strains was demonstrated. Strains from subtropical zone (ECZ 6) showed high genetic diversity in most of the sites from which they were collected. They also showed migration from site to site. RFLP and amplified fragment length polymorphism (AFLP) analyses were carried out on 37 Xam strains and compared; the AFLP assays were performed using eight primer combinations. A multiple correspondence analysis, used to assess genetic relatedness among strains and estimate genetic diversity, indicated that the Brazilian Xam population showed high diversity. No correlation was found between AFLP and RFLP data, but the two techniques provided complementary information on the genetic diversity of Xam. Most strains were highly aggressive on a susceptible cultivar. The genetic analysis presented here contributes to a better understanding of the Xam population structure in Brazil and will help select strains of the pathogen for screening cassava germplasm resistant to the disease.Key words: cassava bacterial blight, resistance, genetic diversity, molecular characterization.

scholarly journals Genetic Diversity of Vibrio cholerae in Chesapeake Bay Determined by Amplified Fragment Length Polymorphism Fingerprinting

2000 ◽  
Vol 66 (1) ◽  
pp. 140-147 ◽  
Author(s):  
Sunny C. Jiang ◽  
Valerie Louis ◽  
Nipa Choopun ◽  
Anjana Sharma ◽  
Anwar Huq ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Evolution ◽  
Chesapeake Bay ◽  
Vibrio Cholerae ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Environmental Conditions ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism

ABSTRACT Vibrio cholerae is indigenous to the aquatic environment, and serotype non-O1 strains are readily isolated from coastal waters. However, in comparison with intensive studies of the O1 group, relatively little effort has been made to analyze the population structure and molecular evolution of non-O1 V. cholerae. In this study, high-resolution genomic DNA fingerprinting, amplified fragment length polymorphism (AFLP), was used to characterize the temporal and spatial genetic diversity of 67 V. choleraestrains isolated from Chesapeake Bay during April through July 1998, at four different sampling sites. Isolation of V. choleraeduring the winter months (January through March) was unsuccessful, as observed in earlier studies (J. H. L. Kaper, R. R. Colwell, and S. W. Joseph, Appl. Environ. Microbiol. 37:91–103, 1979). AFLP fingerprints subjected to similarity analysis yielded a grouping of isolates into three large clusters, reflecting time of the year when the strains were isolated. April and May isolates were closely related, while July isolates were genetically diverse and did not cluster with the isolates obtained earlier in the year. The results suggest that the population structure of V. choleraeundergoes a shift in genotype that is linked to changes in environmental conditions. From January to July, the water temperature increased from 3°C to 27.5°C, bacterial direct counts increased nearly an order of magnitude, and the chlorophyll aconcentration tripled (or even quadrupled at some sites). No correlation was observed between genetic similarity among isolates and geographical source of isolation, since isolates found at a single sampling site were genetically diverse and genetically identical isolates were found at several of the sampling sites. Thus, V. cholerae populations may be transported by surface currents throughout the entire Bay, or, more likely, similar environmental conditions may be selected for a specific genotype. The dynamic nature of the population structure of this bacterial species in Chesapeake Bay provides new insight into the ecology and molecular evolution ofV. cholerae in the natural environment.

AFLP analyses of genetic variation of Eupatorium adenophorum (Asteraceae) populations in China

2009 ◽  
Vol 89 (1) ◽  
pp. 119-126 ◽  
Author(s):  
W. K. Huang ◽  
F. H. Wan ◽  
J. Y. Guo ◽  
B. D. Gao ◽  
B. Y. Xie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Shannon Index ◽  
Eupatorium Adenophorum ◽  
Data Set

The Eupatorium adenophorum is one of the most widespread invasive alien species in China. In the present study, the genetic variation and population structure of this species were analyzed using amplified fragment length polymorphism (AFLP) markers. Nine primer pairs were selected for the analysis and 685 bands were produced, among which 474 bands were polymorphic (PPB = 69.2%). Diversity levels within populations were relatively high (mean expected heterozygosity = 0.188, mean Shannon index = 0.296). Regression analysis showed a significant positive relationship between Shannon genetic diversity and altitude (R2 = 0.31). However, there was a negative correlation between Shannon genetic diversity and latitude (R2 = 0.16), as well as between Shannon genetic diversity and longitude (R2 = 0.45). Cluster analysis grouped the majority of the weed populations into three main clusters that corresponded with the geographic regions. At the regional level, the AMOVA indicated that about 70% of the variations in the data set were from genotypic variations within populations, 13.3% of the variations were due to regional differences, and the remaining 16.6% were due to differences among populations within the provincial regions. The results imply that most individuals tested in the present study should have been produced through seeds, and the process of colonization resulted in progressive loss of genetic diversity from the southwest to the northeast of China. Key words: Amplified fragment length polymorphism, invasive species, Eupatorium adenophorum, diversity, genetic variation, population structure

scholarly journals Assessment of the Genetic Diversity and Population Structure of Lotus Cultivars Grown in China by Amplified Fragment Length Polymorphism

2011 ◽  
Vol 136 (5) ◽  
pp. 339-349 ◽  
Author(s):  
Jie Fu ◽  
Qiaoyan Xiang ◽  
Xianbao Zeng ◽  
Mei Yang ◽  
Ying Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Group I ◽  
Population Structure Analysis ◽  
Morphological Criteria

To assess the genetic diversity among lotus (Nelumbo) accessions and evaluate the correlation between genetic variation and morphological classification, we sampled 138 accessions: two of N. lutea, 112 of N. nucifera, 17 of hybrids between N. nucifera and N. lutea, and seven Japanese cultivars. The 11 selected combinations of amplified fragment length polymorphism (AFLP) primers produced 138 polymorphic loci, and the percentage of polymorphism was 28.7%. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram clustered all the accessions into two groups: Group I comprised N. lutea and its hybrids with N. nucifera; Group II included N. nucifera and its hybrids with N. lutea and Japanese cultivars. Population structure analysis identified four main clusters: N. lutea clustered mainly in C1, whereas N. nucifera clustered in C2, C3, and C4, which was consistent with the UPGMA and principal coordinate analysis results. The Japanese cultivars were related more closely to N. nucifera (genetic similarity coefficient = 0.74) than to N. lutea (0.46); hence, the Japanese cultivars can be classified as N. nucifera. Moreover, rhizome lotuses formed a separate subclade, whereas seed lotuses were interspersed among flower lotuses, which demonstrated that rhizome lotuses were distinct from flower and seed lotuses. Plant size, flower color, and other morphological criteria used commonly to classify lotuses were correlated with genetic variation to a certain extent but not sufficiently for accurate classification. It appears that it is necessary to use both DNA markers and morphological characteristics to classify lotus species and cultivars.

scholarly journals Fluorescent amplified fragment length polymorphism (fAFLP) analyses and genetic diversity in Litopenaeus vannamei (Penaeidae)

2005 ◽  
Vol 28 (2) ◽  
pp. 267-270 ◽  
Author(s):  
Michelle Mantovani Gonçalves ◽  
Manoel Victor Franco Lemos ◽  
Pedro Manoel Galetti Junior ◽  
Patrícia Domingues de Freitas ◽  
Manuel Antonio Andrade Furtado Neto
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Litopenaeus Vannamei ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism
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