Rapd variation of late-maturing sorghum [ Sorghum bicolor (L.) Moench] landraces from Ethiopia

2007 ◽  
Vol 55 (3) ◽  
pp. 375-382 ◽  
Author(s):  
S. Mamo ◽  
A. Ayana ◽  
T. Tesso
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Sorghum Bicolor ◽  
Rapd Markers ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
The Mean ◽  
Polymorphic Bands ◽  
High Degree ◽  
Sorghum Bicolor L

A study on the extent and pattern of genetic variability in late-maturing sorghum [ Sorghum bicolor (L.) Moench] landraces collected from the Wello and Hararge areas of Ethiopia was conducted using random amplified polymorphic DNA (RAPD) markers for 70 individuals representing 14 populations. Four oligonucleotide primers generated a total of 55 polymorphic bands with 13–19 bands per primer and a mean of 16 bands across the 70 individuals. The value of the Shannon diversity index among the populations (0.26) and between the two regions (0.24) was low to moderate, despite the high degree of polymorphic bands per primer. The mean genetic distance (0.25) between the populations was found to be low. The low genetic variation may be due to the reduced population size of late-maturing sorghum landraces in the two regions of Ethiopia because of farmers’ decisions in the process of planting, managing, harvesting and processing their crops. Partitioning of the genetic variation into variation between and within the population revealed that 92.9% and 7.10% of the variation was found to be between and within the populations, respectively. Cluster analysis of genetic distance estimates further confirmed a low level of differentiation in late-maturing sorghum populations both between and within the regions. The implications of the results for genetic conservation purposes are discussed.

scholarly journals Phylogenetic Assessment of Garcinia Species Using RAPD Markers

2018 ◽  
Vol 15 (4) ◽  
pp. 949-955
Author(s):  
Madappa Machamada Bheemaiah ◽  
Bopaiah Ajikuttira Kushalappa ◽  
Grace Prabhakar
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Tree Species ◽  
Rapd Markers ◽  
Genetic Relatedness ◽  
Random Amplified Polymorphic Dna ◽  
Cophenetic Correlation ◽  
The Matrix ◽  
Cophenetic Correlation Coefficient ◽  
Polymorphic Bands

The plants in the Garcinia species are economically important. Phylogenetic investigation is needed for these tree species to boost breeding and conservation programmes. Six Garcinia species were investigated for their phylogenetic relationship using Random Amplified Polymorphic DNA(RAPD) markers. A standardised procedure was developed for isolation of DNA from the leaf samples of G. cambogia, G. indica, G. xanthochymus, G. morella, G. mangostana and G. livingstonei. Phylogenetic investigation is needed for these tree species to boost breeding and conservation programmes. A standardised procedure was developed for isolation of DNA from the leaf samples of G. cambogia, G. indica, G. xanthochymus, G. morella, G. mangostana and G. livingstonei. The DNA samples were subjected to PCR using 8 random primers. 269 polymorphic bands were obtained and scored to develop the values for the genetic distance. The dendrogram was developed using the software dendroUPGMA and the Cophenetic correlation coefficient of 0.801 is obtained. G. cambogia and G. livingstonei are closely placed with a score of 24% followed by G. morella. It had a 30% index score to G. cambogia and G. livingstonei but is followed by just 31% score with G. indica. G.mangostana is connected at 33.5% dissimilarity to the above groups showing it is an introduced variety. G. xanthochymus is the last link with 37% score in the matrix. The data represented is the first of the type for the species. This will help in further DNA related work in these species. The genetic relatedness among these species is reported and this can be utilised in marker analysis for other Garcinia species.

scholarly journals Evaluation of genetic diversity of Brassica napus germplasm from China and Europe assessed by RAPD markers

2011 ◽  
Vol 49 (No. 3) ◽  
pp. 106-113 ◽  
Author(s):  
Shengwu Hu ◽  
J. Ovesná ◽  
L. Kučera ◽  
V. Kučera ◽  
M. Vyvadilová
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Rapd Markers ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Pairwise Distance ◽  
Winter Rape ◽  
The Third ◽  
Best Fit

The genetic diversity and the relationships among rapeseed germplasm, including a collection of 20 Chinese, 25 Czech, 2 German, 2 French, and 1 English cultivars and breeding materials were evaluated using random amplified polymorphic DNA (RAPD) markers. A total of 79 different polymorphic amplification products were obtained using10 selected decamer primers. RAPDs revealed a significant level of polymorphism among the accessions. The diversity index (DI) ranged from 1.390 to 3.491, showing a sufficient potential of selected primers to differentiate among studied genotypes. Three different metrics were used to assess genetic diversity. The best fit between a priori knowledge about germplasm origin and a posteriori grouping was found using Hamman metrics. Cluster analysis based on Hamman pairwise distance comparison divided the studied accessions into three main clusters. The first group included only accessions fromChina, the second group only that fromEurope with the exception of Zhongshuang No. 2, a Chinese winter rape possessing European cultivars in the pedigree. The third group included accessions both fromChina andEurope. The results indicate the occurrence of a considerable genetic variation between Chinese and European accessions.

scholarly journals Assessment of Genetic Diversity in Five Nicaraguan Populations of Cedrela odorata L. (Meliaceae) using RAPD Markers

Encuentro ◽  
2016 ◽  
pp. 28-39
Author(s):  
Arlen Tijerino ◽  
Lourdes Callejas ◽  
David A. Cerda-Granados
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Rapd Markers ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Natural Populations ◽  
Cedrela Odorata ◽  
Total Genetic Diversity ◽  
Geographical Distances ◽  
The Mean

The goal of this study was to assess the genetic diversity of Nicaraguan populations of Cedrela odorata using Random Amplified Polymorphic DNA (RAPD) markers. Thus, genomic DNA was isolated from leaf samples collected from ninety-two trees belonging to five Nicaraguan natural populations of C. odorata. The mean number of alleles per locus, effective number of alleles per locus, percentage of polymorphic loci, genetic diversity (He ) of Nei and diversity index (Ho ) of Shannon were estimated for each population assuming that the populations were in HardyWeinberg equilibrium. Total genetic diversity was partitioned in intrapopulational and interpopulational diversity using Nei’s genetic differentiation (GST) and through an Analysis of Molecular Variance (AMOVA). The ΦST matrix was used to construct a dendrogram by the neighbor-joining method. According to values of both He and Ho , Esquipulas (Deparment of Matagalpa) presented the lowest diversity level; while La Trinidad (Department of Estelí) showed the highest diversity level. Genetic differentiation was calculated obtaining a GST value of 13.36%. AMOVA also showed a similar differentiation value ΦST =13.81%). Neighbour-joining dendrogram clustered the five populations in two groups, where the group formed by La Trinidad and El Refugio (Department of Granada) presented the biggest differentiation. Correlation between genetic and geographical distances was not found.

scholarly journals Genetic variation and molecular relationships among eight taxa of Desmodium Desv. based on RAPD markers

2017 ◽  
Vol 24 (2) ◽  
pp. 149-154
Author(s):  
M. Oliur Rahman ◽  
Md. Zahidur Rahman ◽  
Sonia Khan Sony ◽  
Mohammad Nurul Islam
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Rapd Markers ◽  
Genetic Relatedness ◽  
Random Amplified Polymorphic Dna ◽  
Banding Patterns ◽  
Upgma Dendrogram ◽  
Close Proximity ◽  
Plant Taxon ◽  
Molecular Relationships

Genetic variation and molecular relationships among eight taxa of Desmodium Desv. were assessed on the basis of random amplified polymorphic DNA (RAPD) markers. The banding patterns of eight taxa namely, Desmodium gangeticum (L.) DC., D. heterocarpon (L.) DC., D. heterophyllum (Willd.) DC., D. motorium (Houtt.) Merr., D. pulchellum (L.) Benth., D. triflorum (L.) DC., D. triquetrum (L.) DC. and D. triquetrumsubsp. alatum (DC.) Prain were compared. A total of 81 DNA fragments were detected by 11 primers. Among the taxa studied D. triquetrum and D. triquetrum subsp. alatum were found to be most closely related followed by close proximity between D. gangeticum and D. motorium. The highest genetic distance was observed between D. triflorum and D. heterophyllum followed by D. heterocarpon and D. heterophyllum. UPGMA dendrogram was constructed to show the genetic relatedness among the taxa employed and the tree revealed a close proximity among D. pulchellum, D. gangeticum and D. motorium. In contrast, D. heterophyllum was found distantly related with rest of the taxa.Bangladesh J. Plant Taxon. 24(2): 149–154.

scholarly journals Detection and analysis of genetic variation in Salicornieae (Chenopodiaceae) using random amplified polymorphic DNA (RAPD) markers

Taxon ◽  
1995 ◽  
Vol 44 (1) ◽  
pp. 53-63 ◽  
Author(s):  
T. Luque ◽  
C. Ruiz ◽  
J. Avalos ◽  
I. L. Calderón ◽  
M. E. Figueroa
Keyword(s):  
Genetic Variation ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna

Evaluation of Genetic Diversity in Castor (Ricinus communis L.) using RAPD Markes

2011 ◽  
Vol 343-344 ◽  
pp. 981-987
Author(s):  
Feng Juan Li ◽  
Chang Lu Wang ◽  
Dong He ◽  
Ya Qiong Liu ◽  
Mian Hua Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Genetic Distance ◽  
Oil Content ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Ricinus Communis ◽  
Major Group ◽  
Ricinus Communis L ◽  
Polymorphic Bands

RAPD markers are used to study the genetic diversity of the main planting on 37 castor varieties widely cultivated in china according to the oil content and other characteristic of different castor varieties. Genetic distance of 37 Chinese castor varieties is studied by RAPD markers analysis. RAPD analysis shows that a total of 122 bands are amplified from random primers of 20 S series, including 71 polymorphic bands with polymorphic rate of 58.20%. 37 castor beans are divided into four major groups in the phylogenetic tree. One castor germplasm is included in1, 2, 3 groups respectively, and two sub-groups are included in the 4 major group.

Direct comparison of levels of genetic variation in tomato detected by a GACA-containing microsatellite probe and by random amplified polymorphic DNA

Genome ◽  
1994 ◽  
Vol 37 (3) ◽  
pp. 375-381 ◽  
Author(s):  
W. Rus-Kortekaas ◽  
M. J. M. Smulders ◽  
P. Arens ◽  
B. Vosman
Keyword(s):  
Tissue Culture ◽  
Genetic Variation ◽  
Somaclonal Variation ◽  
Random Amplified Polymorphic Dna ◽  
Dna Fingerprint ◽  
Pairwise Comparisons ◽  
Lycopersicon Pennellii ◽  
Lycopersicon Species ◽  
Polymorphic Bands ◽  
Simple Sequence

In this study, a direct comparison was made of the ability of four selected random amplified polymorphic DNA (RAPD) primers and a GACA-containing microsatellite probe to detect genetic variation in Lycopersicon. Of the 89 RAPD primers initially tested, 85 showed differences between a representative of Lycopersicon pennellii and L. esculentum, but only 4 distinguished among three L. esculentum cultivars. These four primers were subsequently tested on representatives of six Lycopersicon species. In pairwise comparisons of species, all or 14 of the 15 combinations could be distinguished by single primers. When the primers were tested on 15 L. esculentum cultivars, 90 of the 105 combinations could be distinguished by the four primers together. Finally, none of 118 tested primers showed reproducible differences among calli or progeny of régénérants from tissue culture, although some of the plants had inherited morphological mutations. The probe pWVA16, which detects GACA-containing microsatellites, could distinguish in TaqI-digested DNA the representatives of Lycopersicon species as well as all the L. esculentum cultivars tested. The probe was unable to detect polymorphisms among calli and the progeny of regenerants from tissue culture. An analysis of the results showed that the four selected RAPD primers were able to detect polymorphic bands among species at a frequency of 80%, and among cultivars at a frequency of 44%. In contrast, the microsatellite probe detected polymorphic bands at a frequency of 100 and 95%, respectively. The GACA-containing probe did not detect any common bands among the representatives of the six species, while band sharing with RAPDs was 48%. These results indicate that the two methods detect two types of DNA that differ in their degree of variability.Key words: DNA fingerprint, RAPD, simple sequence, somaclonal variation, tissue culture.

scholarly journals Assessment of genetic diversity among surian Toona sinensis Roem in progenies test using random amplified polymorphic DNA markers

2018 ◽  
Vol 22 (1) ◽  
pp. 22
Author(s):  
Jayusman Jayusman ◽  
Muhammad Na’iem ◽  
Sapto Indrioko ◽  
Eko Bhakti Hardiyanto ◽  
ILG Nurcahyaningsih
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Management Strategies ◽  
Genetic Distances ◽  
Sampled Data ◽  
Toona Sinensis ◽  
The Mean ◽  
Individual Trees

Surian Toona sinensis Roem is one of the most widely planted species in Indonesia. This study aimed to estimate the genetic diversity between a number of surian populations in a progeny test using RAPD markers, with the goal of proposing management strategies for a surian breeding program. Ninety-six individual trees from 8 populations of surian were chosen as samples for analysis. Eleven polymorphic primers (OP-B3, OP-B4, OP-B10, OP-H3, OP-Y6, OP-Y7, OP-Y8, OP-Y10, OP-Y11, OP-Y14, and OP-06) producing reproducible bands were analyzed for the 96 trees, with six trees per family sampled. Data were analyzed using GenAlEx 6.3, NTSYS 2.02. The observed percentage of polymorphic loci ranged from 18.2% to 50%. The mean level of genetic diversity among the surian populations was considered to be moderate (He 0.304). Cluster analysis grouped the genotypes into two main clusters, at similarity levels of 0.68 and 0.46. The first two axes of the PCoA explained 46.16% and 25.54% of the total variation, respectively. The grouping of samples into clusters and subclusters did not correspond with family and their distances, but the grouping was in line with the genetic distances of the samples.

scholarly journals Genetic studies revealed differences between European and North American populations of Calypogeia azurea

2016 ◽  
Vol 42 (1) ◽  
pp. 19-26 ◽  
Author(s):  
Katarzyna Buczkowska ◽  
Alina Bączkiewicz ◽  
Patrycja Gonera
Keyword(s):  
Genetic Variation ◽  
North America ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Oil Bodies ◽  
Genetic Studies ◽  
Isozyme Loci ◽  
The Mean ◽  
Different Parts ◽  
Nei's Genetic Distance

Abstract Calypogeia azurea, a widespread, subboreal-montane liverwort species, is one of a few representatives of the Calypogeia genus that are characterized by the occurrence of blue oil bodies. The aim of the study was to investigate the genetic variation and population structure of C. azurea originating from different parts of its distribution range (Europe and North America). Plants of C. azurea were compared with C. peruviana, another Calypogeia species with blue oil bodies. In general, 339 gametophytes from 15 populations of C. azurea were examined. Total gene diversity (HT) estimated on the basis of nine isozyme loci of C. azurea at the species level was 0.201. The mean Nei’s genetic distance between European populations was equal to 0.083, whereas the mean genetic distance between populations originating from Europe and North America was 0.413. The analysis of molecular variance (AMOVA) showed that 69% of C. azurea genetic variation was distributed among regions (Europe and North America), 15% - among populations within regions, and 16% - within populations. Our study revealed that C. azurea showed genetic diversity within its geographic distribution. All examined samples classified as C. azurea differed in respect of isozyme patterns from C. peruviana.

Molecular Diversity Analysis of Lentil (Lens culinaris Medik.) through RAPD Markers

2012 ◽  
Vol 22 (1) ◽  
pp. 51-58 ◽  
Author(s):  
M.E. Hoque ◽  
M.M. Hasan
Keyword(s):  
Genetic Distance ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Group Method ◽  
Diversity Analysis ◽  
Pair Group ◽  
Molecular Genetic Diversity

Random Amplified Polymorphic DNA (RAPD) markers were used to study the molecular genetic diversity analysis among six BARI released lentil varieties viz. BARI masur-1, BARI masur-2, BARI masur-3, BARI masur-4, BARI masur-5 and BARI masur-6. PCR amplified products were visualized on 1.0% agarose gel and the band for each primer were scored. Ten RAPD markers were used in this study. Out of them 7 primers showed amplification of 53 DNA fragments with 60.37% of them being polymorphic. The highest number of polymorphic loci was noticed in the variety BARI masur-3. The same variety also showed maximum Nei’s gene diversity value (0.0552). The highest Nei’s genetic distance (0.5002) was observed in BARI masur-1 vs. BARI masur-5 whereas, the lowest genetic distance (0.0692) was found in BARI masur-1 vs. BARI masur-2. The unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Nei’s genetic distance grouped the six cultivars into two main clusters. BARI masur-1, BARI masur-2 and BARI masur-3 were in cluster I and BARI masur-4, BARI masur-5 and BARI masur-6 were in cluster II. The cultivar BARI masur-4 was closest to the cultivar BARI masur-6 with the lowest genetic distance (0.0972) and the highest genetic distance (0.5002) was found between BARI masur-1 and BARI masur-5. The RAPD markers were found to be useful in molecular characterization of lentil varieties which could be utilized by the breeders for the improvement of lentil cultivars. DOI: http://dx.doi.org/10.3329/ptcb.v22i1.11260 Plant Tissue Cult. & Biotech. 22(1): 51-58, 2012 (June)

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