scholarly journals Genetic diversity in wild and hatchery populations of stinging catfish (Heteropneustes fossilis Bloch) revealed by RAPD analysis

2012 ◽  
Vol 19 ◽  
pp. 81-87
Author(s):  
Md Nazrul Islam ◽  
Abhishak Basak ◽  
Dr Ashrafullah ◽  
Md Samsul Alam
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Gene Diversity ◽  
Similarity Index ◽  
Heteropneustes Fossilis ◽  
Wild Populations ◽  
Polymorphic Loci

Context: DNA fingerprinting using genetic markers such as Random Amplification of Polymorphic DNA (RAPD), Restriction Fragment Length Polymorphism (RFLP), microsatellite (Simple sequence repeat), Amplified Fragment Length Polymorphism (AFLP) etc. can be successfully used to reveal genetic variation within and among different populations. Objective: The aim of the present study was to assess genetic diversity in two wild and one hatchery populations of stinging catfish Heteropneustes fossilis by RAPD fingerprinting. Materials and Methods: A total of 90 live fish (H. fossilis), 30 from each source, were collected from a beel in Patuakhali, a beel in Jessore and Rupali Hatchery, Mymensingh. Genomic DNA was extracted from fin tissues. The concentration of DNA was estimated using a spectrophotometer. Fifteen decamer primers of random sequence from three kits (six from kit A, seven from kit B and two from kit C) (Operon technologies, Inc., Alameda, CA, USA) were screened on sub-samples of one randomly chosen H. fossilis DNA sample from the each population to test their suitability for amplifying RAPDs. The amplified products from each sample were separated by electrophoresis on 1.4% agarose gel containing ethidium bromide. The sizes of the bands were calculated using the software DNAFRAG and the sizes in base pair (bp) were used for identification of the bands (RAPD markers). The similarity index values (SI) between the RAPD fingerprint of any two individuals on the same gel were calculated from RAPD band sharing. Results: A total of 28 RAPD bands were obtained using four decamer random primers, among which 21 bands were polymorphic. The percentage of polymorphic loci, intra-population similarity indices and Nei's gene diversity values were 85.71%, 78.75 and 0.304±0.183 for Jessore population, 83.71%, 82.62 and 0.280±0.159 for Patuakhali population, 82.14%, 85.25 and 0.271±0.165 for Rupali hatchery population, respectively. The overall gene flow (Nm) among the populations was 5.755. The highest inter-similarity (Sij) was found between Patuakhali - Rupali hatchery populations. Among the three populations, the highest genetic distance (0.069) was found between Jessore and Patuakhali population. Considering polymorphic loci, intrapopulation similarity index and gene diversity the genetic variation in the Jessore population was higher than the other two populations. The genetic variation of the hatchery population was found to be lower than the two wild populations. Conclusion: The result of the present study can be used as baseline information regarding the genetic variation and population structure before undertaking any breeding programme. Study indicated that the genetic variation in the hatchery populations were slightly lower than those of the wild populations. DOI: http://dx.doi.org/10.3329/jbs.v19i0.13005 J. bio-sci. 19 81-87, 2011

scholarly journals AFLP Analysis for Genetic Diversity in Capsicum Annuum and Related Species

2006 ◽  
Vol 1 (3) ◽  
pp. 1934578X0600100
Author(s):  
Sanjog T. Thul ◽  
Ajit K. Shasany ◽  
Mahendra P. Darokar ◽  
Suman P. S. Khanuja
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Great Degree ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Variation Analysis ◽  
Average Similarity ◽  
Geographical Locations

Intra- and inter-specific genetic variation analysis was conducted using amplified fragment length polymorphism (AFLP) profiling in Capsicum accessions in the germplasms collected from different geographical locations in India. A total of 24 accessions were investigated belonging to six species, namely C. annuum, C. baccatum, C. chinence, C. eximium, C. frutescens and C. luteum. Average similarity within the 15 accessions of C. annuum was highest (100%) between accessions CIMAP/CA45 and CIMAP/CA49 obtained from IISR, Kerala and 43% among the species CIMAP/CC1 and CIMAP/CB2. In this analysis, accessions were clustered more pronouncedly according to their geographical locations than to their taxonomic labels. A great degree of intermixing of present day domesticated chillies is evident from the present study.

scholarly journals Genetic diversity of three European Veratrum species revealed by Amplified Fragment Length Polymorphism

2017 ◽  
Vol 47 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Magdalena Szeliga ◽  
Joanna Ciura ◽  
Mirosław Tyrka
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Veratrum Album ◽  
Metabolic Properties

Abstract Chemical and genetic characterization of Veratrum species deposited in European collections is important for genepool preservation and identification of populations with desired metabolic properties. Veratrum album, V. lobelianum and V. nigrum are native to Europe, and in Poland are ranked as rare or threatened. Genetic variation of European Veratrum species was characterized by Amplified Fragment Length Polymorphism (AFLP) markers. The accumulation of jervine as a representative of steroidal alkaloids was measured in seeds. Distribution of 380 markers generated from eight primer combinations was useful for studying genetic relationships among and within species in the Veratrum genus and the most divergent populations were identified. Genetic variation between 12 populations of Veratrum species supports the classification of V. lobelianum as a subspecies of V. album. However, the results need further validation on extended material. A higher genetic diversity (22.3%) was observed between populations of V. nigrum as compared to V. album (14.5%). Contents of jervine allowed for discrimination of the studied Veratrum species and can be used as a potential chemotaxonomic marker. The highest jervine levels were found in V. album. V. nigrum seeds had only trace amounts and no jervine was detected in seeds of V. lobelianum.

Genetic diversity of side-oats grama [Bouteloua curtipendula (Michx.) Torr.] populations as revealed by amplified fragment length polymorphism markers

2013 ◽  
Vol 93 (6) ◽  
pp. 1105-1114 ◽  
Author(s):  
B. Biligetu ◽  
M. P. Schellenberg ◽  
Yong-Bi Fu
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Population Diversity ◽  
Genetic Enhancement ◽  
Aflp Analysis ◽  
Wild Populations ◽  
Bouteloua Curtipendula

Biligetu, B., Schellenberg, M. P. and Fu, Y.B. 2013. Genetic diversity of side-oats grama [Bouteloua curtipendula (Michx.) Torr.] populations as revealed by amplified fragment length polymorphism markers. Can. J. Plant Sci. 93: 1105–1114. Side-oats grama [Bouteloua curtipendula (Michx.) Torr.] is a warm-season grass widely distributed in North America and is considered as an important grass for reclamation and summer forage production in drier regions. This study assessed genetic diversity of nine wild populations of side-oats grama grass, their corresponding balanced multiple-site composite (BMSC), and a population selected for forage type (FT), using the amplified fragment length polymorphism (AFLP) technique. Five AFLP primer pairs were employed to genotype 157 plants, and 312 polymorphic AFLP bands were detected. The frequencies of AFLP bands ranged from 0.01 to 0.99, and averaged 0.39. The AFLP analysis revealed 6% of the total AFLP variation present among the nine wild populations and 94% of variation within populations. The Minto population had the largest within-population diversity, while the FT population the lowest based on AFLP band richness and polymorphic loci. The BMSC population displayed significant genetic differentiation from the wild populations, but still captured substantial genetic diversity. Bayesian cluster analysis using BAPS and STRUCTURE programs revealed three and four optimal clusters of populations that explained 9.8 and 9.5% of the total AFLP variation, respectively. A genetic clustering of individual plants displayed no clear genetic separations among wild, FT, and BMSC populations, but the FT population showed some level of genetic shift, indicating the initial impact of artificial selection. These findings are significant for our understanding of the genetic diversity of side-oats grama. Large genetic variation present within populations provides a potential for further genetic enhancement.

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 Genetic variation between Colletotrichum lindemuthianum isolates

2017 ◽  
Vol 38 (SI 2 - 6th Conf EFPP 2002) ◽  
pp. 378-380
Author(s):  
K.I. Ansari ◽  
N. Palacios ◽  
C. Araya ◽  
T. Langin ◽  
D. Egan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Geographic Origin ◽  
Colletotrichum Lindemuthianum ◽  
Molecular Profile ◽  
Aflp Analysis ◽  
Huge Variation

We characterized the genetic diversity of seventy-three C. lindemuthianum isolates collected from 10 different countries by Amplified Fragment Length Polymorphism (AFLP) analysis. The results of this research highlighted the fact that there is huge variation in the genetic diversity between isolates from different countries. The molecular profile of the isolates showed correlation with geographic origin of the isolates.

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

Genetic diversity of fringed brome (Bromus ciliatus) as determined by amplified fragment length polymorphism

2005 ◽  
Vol 83 (10) ◽  
pp. 1322-1328 ◽  
Author(s):  
Yong-Bi Fu ◽  
Bruce E. Coulman ◽  
Yasas S.N. Ferdinandez ◽  
Jacques Cayouette ◽  
Paul M. Peterson
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Habitat Restoration ◽  
Fragment Length Polymorphism ◽  
Natural Populations ◽  
Germplasm Conservation ◽  
Amplified Fragment Length Polymorphism ◽  
Large Area ◽  
Geographic Origins

Fringed brome ( Bromus ciliatus L.) is found in native stands throughout a large area of North America. Little is known about the genetic diversity of this species. The amplified fragment length polymorphism (AFLP) technique was applied to assess the genetic diversity of 16 fringed brome populations sampled in Canada from the provinces of Alberta, British Columbia, Quebec, and Saskatchewan. Four AFLP primer pairs were employed to screen 82 samples with four to six samples per population and 83 polymorphic AFLP bands scored for each sample. The frequencies of the scored bands in all assayed samples ranged from 0.01 to 0.99 and averaged 0.53. Analysis of molecular variance revealed that 52.6% of the total AFLP variation resided among the 16 populations and 20.6% among the four provinces. The five Quebec populations appeared to be genetically the most diverse and distinct. The AFLP variability observed was significantly associated with the geographic origins of the fringed brome populations. These findings are useful for sampling fringed brome germplasm from natural populations for germplasm conservation and should facilitate the development of genetically diverse regional cultivars for habitat restoration and revegetation.

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