scholarly journals Assessment of Genetic Relationship Among Landraces of Bangladeshi Ridge Gourd (Luffa acutangula Roxb.) Using RAPD Markers

2009 ◽  
Vol 1 (3) ◽  
pp. 615-623 ◽  
Author(s):  
S. Hoque ◽  
M. G. Rabbani
Keyword(s):  
Genetic Distance ◽  
Genetic Relationship ◽  
Genetic Relatedness ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Index ◽  
Group Method ◽  
Pair Group ◽  
Average Gene ◽  
Luffa Acutangula

Information on genetic relatedness among ridge gourd (Luffa acutangula) genotypes from Bangladesh is currently not reported. Twenty eight accessions collected from different parts of Bangladesh were studied using random amplified polymorphic DNA (RAPD) technique. Four selected decamer primers, out of sixteen screened, could generate a total of 27 RAPD fragments of which 22 were polymorphic (81.5%). The bands ranged from 50 to 1500 bp in size. Genetic variation statistics for all loci estimated the average gene diversity (h) value as 0.278 and the Shannon’s Information Index (I) as 0.415. Dendrogram based on unweighted pair-group method with arithmetic averages (UPGMA) segregated the accessions into five clusters. Cluster III was the largest with 13 members followed by cluster II, V, I and IV with 6, 4, 3 and 2 members, respectively. Accession LA27 and LA29 were found very close to each other with the highest inter-variety similarity index (96.05%) and the lowest genetic distance (0.077); whereas accession LA40 and LA72 were more distant to each other with the lowest inter-variety similarity index (44.43%) and the highest genetic distance (0.73). A DNA extraction method has been standardized. The marker was found to be useful tool for assessing genetic variations in Luffa acutangula. Keywords: Genetic relationship; Germplasm; Ridge gourd; Luffa acutangula; RAPD.  © 2009 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved. DOI: 10.3329/jsr.v1i3.1968               J. Sci. Res. 1 (3), 615-623 (2009) 

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)

scholarly journals Genetic diversity analysis in Brassica varieties through RAPD markers

1970 ◽  
Vol 34 (3) ◽  
pp. 493-503 ◽  
Author(s):  
KK Ghosh ◽  
ME Haque ◽  
S Parvin ◽  
F Akhter ◽  
MM Rahim
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Arithmetic Mean ◽  
Polymorphic Band ◽  
Group Method ◽  
Polymorphic Loci ◽  
Pair Group

This investigation was aimed at exploring the genetic diversity and relationship among nine Brassica varieties, namely BARI Sharisha-12, Agrani, Sampad, BINA Sharisha-4, BINA Sharisha-5, BARI Sharisha-13, Daulot, Rai-5, Alboglabra using Random Amplified Polymorphic DNA (RAPD) markers. In total, 59 reproducible DNA bands were generated by four arbitrary selected primers of which 58 (98.03%) bands were proved to be polymorphic. These bands ranged from 212 to 30686 bp in size. The highest proportion of polymorphic loci and gene diversity values were 37.29% and 0.1373, respectively, for BARI Sharisha-12 and the lowest proportion of polymorphic loci and gene diversity values were 8.47% and 0.0318, 8.47% and 0.0382 for BINA Sharisha-4 and Rai-5, respectively. A dendrogram was constructed using unweighted pair group method of arithmetic mean (UPGMA). The result of cluster analysis indicated that the 9 accessions were capable of being classified into 2 major groups. One group consists of BARI Sharisha-12, Agrani, Sampad, Daulot, Rai-5, Alboglabra. where Daulot and Rai-5 showed the lowest genetic distance of 0.049. And another group contains BINA Sharisha-4, BINA Sharisha-5, and BARI Sharisha-1 3, where BINA Sharisha-5 and BARI sharisha-13 showed genetic distance of 0.071. Key Words: RAPD, Brassica, genetic distance, polymorphic band. DOI: 10.3329/bjar.v34i3.3976 Bangladesh J. Agril. Res. 34(3) : 493-5032, September 2009

scholarly journals Genetic diversity analysis of tropical sugar beet (Beta vulgaris L.) varieties in Bangladesh using RAPD markers

Genetika ◽  
2016 ◽  
Vol 48 (1) ◽  
pp. 151-164
Author(s):  
Saidin Saclain ◽  
Abdul Latif ◽  
Babul Bala ◽  
Mithun Mallik ◽  
Shahidul Islam
Keyword(s):  
Genetic Variation ◽  
Sugar Beet ◽  
Genetic Distance ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Similarity Index ◽  
Genetic Distances ◽  
Group Method ◽  
Pair Group ◽  
Major Cluster

Knowledge on intra-specific genetic variation of an organism is important for its genetic improvement and conservation. In order to estimate genetic variation and relatedness in eleven tropical Sugar beet varieties we used randomly amplified polymorphic DNA (RAPD) markers. The RAPD analysis was performed using six decamer random primers, which amplified a total of 63 DNA fragments of which 43 (68.25%) were found polymorphic. The average polymorphic bands per primer was 7.17 and the overall gene diversity was 0.24. Among the 43 polymorphic loci studied, 2 were specific for 2K 310, 1 for Shubraha, 1 for Natura and 1 for HI-0473 varieties. Pair wise genetic distance and similarity indices were ranged from 0.12-0.51 and 66.73-92.91, respectively. Cauvery and 2K 310 were found to be the most distantly related with a higher genetic distance value (GD = 0.51) and lower similarity index (SI = 66.73), while Aranka and Serenada were the most closely related with their lower GD (0.12) and higher SI(92.91) values. In an unweighted pair group method of arithmetic mean dendrogram constructed on the basis of genetic distances, the eleven varieties grouped into two main clusters: 2K 310 alone was in one cluster whereas 10 other varieties grouped into a major cluster. This indicates that 2K 310 was distantly related with each of the other varieties. Distantly related varieties based on estimated genetic variation could be selected for future breeding program that could result in improvement of this crop.

scholarly journals Genetic Relationship Among Ten Promising Eggplant Varieties Using RAPD Markers

1970 ◽  
Vol 19 (2) ◽  
pp. 119-126 ◽  
Author(s):  
Md. Sanaullah Biswas ◽  
Md. Abdullah Yousuf Akhond ◽  
Md. Al-Amin ◽  
Mahmuda Khatun ◽  
Muhammed Rezwan Kabir
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Genetic Relationship ◽  
Plant Tissue ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Similarity Index ◽  
The Other ◽  
Upgma Dendrogram ◽  
Potential Tool

RAPD technique was used as a tool for assessing genetic diversity and varietal relationships among ten varieties of eggplant. Out of 21 primers screened four were selected. With these primers 76 clear and bright fragments were obtained of which 44 fragments considered polymorphic. The proportion of polymorphic loci and gene diversity values across all loci were 57.89% and 0.23, respectively. The UPGMA dendrogram based on genetic distance segregated the ten varieties of eggplant into two main clusters. Dohazari, Kazla, Nayantara and ISD-006 were grouped together in cluster I whereas Uttara, Islampuri, Khatkhatia, Singnath, BARI Begun-08 and Eggplant Line-083 into cluster II. Kazla and Nayantara variety pair was very close to each other with the highest intervarietal similarity index (92.54%) and lowest genetic distance (0.14). On the other hand, Khatkhatia and Nayantara pair was the lowest intervarietal similarity index (41.67%) with highest genetic distance (0.48). Therefore, identification of genetically distinct varieties using RAPD markers could be a potential tool for eggplant improvement. Key words: Eggplant, Polymorphism, Genetic relationship, RAPD D.O.I. 10.3329/ptcb.v19i2.5006 Plant Tissue Cult. & Biotech. 19(2): 119-126, 2009 (December)

scholarly journals MOLECULAR CHARACTERIZATION OF QUALITY PROTEIN MAIZE AND DOWNY MILDEW RESISTANCE LINES BASED ON SIMPLE SEQUENCE REPEATS (SSRs) MARKER

Zuriat ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
D. Ruswandi ◽  
N. Wicaksana ◽  
M. B. Pabendon ◽  
M. Azrai ◽  
M. Rachmadi ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Genetic Relationship ◽  
Genetic Relatedness ◽  
Genotypic Variation ◽  
Group Method ◽  
Maize Breeding ◽  
Pair Group ◽  
Group A ◽  
Ssrs Markers ◽  
Relationship Of

The information on germplasm diversity and genetic relatedness among elite breeding materials is an important element in maize breeding. Molecular characterization and genetic relationship of 11 QPM-DMR lines were analysed using thirty three SSRs markers. Genetic relationship was determined using Jaccard’s similarity coefficient, and dendogram was then constructed based on the unweighted pair-group method with arithmetical averages (UPGMA). Result showed that (i) all SSRs loci were informative for describing the genotypic variation as showed by their PIC, which ranged from 0.19 for umc1304 to 0.93 for phi112; (ii) the eleven maize inbred lines were clustered into one major group A and small groups B and C that corresponds well with the breeding programs adopted at different institutes of release, and (iii) thus, SSRs marker system is a valuable marker for varietals identification and for genetic diversity study of elite breeding materials.

Genomic variation and relationships in aerial yam (Dioscorea bulbifera L.) detected by random amplified polymorphic DNA

Genome ◽  
1996 ◽  
Vol 39 (1) ◽  
pp. 17-25 ◽  
Author(s):  
Juliane Ramser ◽  
Kurt Weising ◽  
Günter Kahl ◽  
Cristina López-Peralta ◽  
Rainer Wetzel
Keyword(s):  
Genetic Relatedness ◽  
Random Amplified Polymorphic Dna ◽  
Intraspecific Variability ◽  
Cesium Chloride ◽  
Morphological Characters ◽  
Genomic Variation ◽  
Group Method ◽  
Pair Group ◽  
Binary Character ◽  
Dioscorea Bulbifera

Random amplified polymorphic DNA (RAPD) markers were used to assess intraspecific variability and relationships in aerial yam (Dioscorea bulbifera L.). A total of 23 accessions from different geographic locations in Africa, Asia, and Polynesia were analyzed by 10 arbitrarily chosen GC-rich decamer primers. Using cesium chloride purified genomic template DNA, highly reproducible polymorphic fingerprints were generated by all 10 primers, resulting in a total of 375 informative characters. Only eight bands were monomorphic among all investigated accessions. A binary character matrix was generated by scoring for presence/absence of a band at a particular position, transformed into a matrix of pairwise distances using either the Jaccard or a simple matching coefficient, and analyzed by neighbour joining, UPGMA (unweighted pair group method with arithmetic averaging) cluster analysis, or split decomposition. All methods of data evaluation resulted in similar groupings that reflected the geographical origin of the samples. The African accessions formed a distinct isolated group, whereas Asian and Polynesian accessions proved to be more heterogeneous. With two exceptions (var. suavior and var. sativa), the RAPD data supported previous varietal classification based on morphological characters. Stepwise reduction of the number of evaluated characters did not affect branching patterns of the trees above a minimum threshold of 150. Key words : Dioscorea bulbifera, random amplified polymorphic DNA (RAPD), genetic variation, genetic relatedness.

scholarly journals Performance of salinity tolerance of F3 rice lines of BRRI dhan 29 × PBRC (STL-20) using RAPD markers

2019 ◽  
Vol 6 (2) ◽  
pp. 215-225
Author(s):  
Nazmul Islam Mazumder ◽  
Tania Sultana ◽  
Prtitish Chandra Paul ◽  
Dinesh Chandra Roy ◽  
Deboprio Roy Sushmoy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Salinity Tolerance ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Susceptible Variety ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
Tolerant Line

Twenty six rice lines of PBRC (salt tolerant line-20) × BRRI dhan-29 were used to evaluate salinity tolerance at the seedling stage and tested for salt tolerance using RAPD markers. Salinity screening was done using hydrophonic system at the greenhouse following IRRI standard protocol. Among the studied line, ten were moderately salinity tolerant, nine susceptible and rest of the lines highly susceptible. For assessing genetic diversity and relationship of F3 rice lines including two parents were tested against PCR-based Random Amplified Polymorphic DNA (RAPD) technique using three arbitrary decamer primers; OPA02, OPC01, and OPC12. Selected three primers generated a total of 14 bands. Out of 14 bands, 12 bands (86.67%) were polymorphic and 2 bands (13.33%) were monomorphic. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s (1972) genetic distance produced 2 main clusters of the 28 rice genotypes. Most of the moderately tolerant lines and PBRC (STL-20) (tolerant variety) were grouped in same cluster due to lower genetic distance, while maximum susceptible along with BRRI dhan29 (susceptible variety) showed higher genetic distance with PBRC (STL-20) and moderately tolerant lines. This result indicates that the lines which formed grouped together, they are less diversed. On the other hand the lines remain in different clusters or different groups, are much diversed. Thus RAPD perform a potentially simple, rapid and reliable method to evaluate genetic diversity and molecular characterization as well. Res. Agric., Livest. Fish.6(2): 215-225, August 2019

scholarly journals Molecular characterization of oil seed Brassica using RAPD markers

2020 ◽  
Vol 55 (1) ◽  
pp. 1-8
Author(s):  
M Islam ◽  
A Habib ◽  
S Khan ◽  
S Akter ◽  
B Goswami ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Arithmetic Means ◽  
Oil Seed ◽  
Pair Group ◽  
Brassica Spp ◽  
Breeding Programmes ◽  
High Level

Twelve varieties of oil seed Brassica spp. were characterized at molecular level using Random Amplified Polymorphic DNA (RAPD) primers to explore genetic diversity and to find out relationship among them. Twelve random primers used in the study generated 94 RAPD fragments and 53 (56.38%) of them were considered as polymorphic indicating high level of polymorphism within the materials. The size of amplified fragments ranged between 300-3000 bp. The values of pair-wise genetic distance ranged from 0.1613 to 0.5543. To find out phylogenetic relationships among the varieties, dendrogram based on Nei’s genetic distance was constructed using Unweighted Pair Group Method of Arithmetic Means (UPGMA) separating the 12 Brassica spp into two major clusters C1 and C2. This result will be useful for designing future breeding programmes for improvement of Brassica varieties. Bangladesh J. Sci. Ind. Res.55(1), 1-8, 2020

scholarly journals Study of relationships among twelve Phyllanthus species with the use of molecular markers

2010 ◽  
Vol 46 (No. 3) ◽  
pp. 135-141 ◽  
Author(s):  
G.R. Rout ◽  
S.K. Senapati ◽  
S. Aparajita
Keyword(s):  
Molecular Markers ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Index ◽  
Inter Simple Sequence Repeat ◽  
Morphological Characterization ◽  
Group Method ◽  
Pair Group ◽  
Group I ◽  
Marker Loci ◽  
Rapd And Issr

The present investigation was undertaken to describe the relationships among twelve species of Phyllanthus collected in India by help of molecular markers. In total, 259 marker loci were assessed, out of which 249 were polymorphic revealing 96.13% polymorphism. Nei's similarity index varied from 0.35 to 0.76 for RAPD (Random Amplified Polymorphic DNA) and from 0.31 to 0.76 for ISSR marker systems. Cluster analysis by the unweighted pair group method (UPGMA) of Dice coefficient of similarity generated dendrogram with more or less similar topology for both the analyses that offered a better explanation for diversity and affinities between the species. The phylogenetic tree obtained from both RAPD and ISSR (Inter Simple Sequence Repeat) markers has divided the 12 species into two groups: group I consisting of only one species Phyllanthus angustifolius (Sw.) Sw and group II with the rest of 11 species. Basically, these results were in compliance with notable morphological characterization. The present study revealed high variation among the species of Phyllanthus and will help to identify different Phyllanthus species.

scholarly journals Discrimination and Genetic Diversity among Cultivated Olives of Greece Using RAPD Markers

2003 ◽  
Vol 128 (5) ◽  
pp. 741-746 ◽  
Author(s):  
N. Nikoloudakis ◽  
G. Banilas ◽  
F. Gazis ◽  
P. Hatzopoulos ◽  
J. Metzidakis
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Fruit Size ◽  
Similarity Index ◽  
Group Method ◽  
Poor Correlation ◽  
Pair Group ◽  
Electrophoretic Patterns

Random amplified polymorphic DNA (RAPD) markers were used to study the genetic diversity and to discriminate among 33 Greek olive (Olea europaea L.) cultivars. Three feral forms from Crete and five foreign cultivars recently introduced into Greece were also included. Nineteen primers were selected which produced 64 reproducible polymorphic bands in the 41 olive genotypes studied, with an average of 3.4 informative markers per primer. The RAPD markers resulted in 135 distinct electrophoretic patterns, with an average of 7.1 patterns per primer. Based on either unique or combined patterns, all genotypes could be identified. Genetic similarities between genotypes were estimated using the Dice similarity index and these indicated that a high degree of diversity exists within the Greek olive germplasm. Using the unweighted pair-group method (UPGMA) most cultivars were clustered into two main groups according to their fruit size or commercial use (table or olive oil). However, poor correlation was detected between clustering of cultivars and their principal area of cultivation. RAPD marker data were subjected to nonmetric multidimentional scaling (NMDS) which produced results similar to those of the UPGMA analysis. The results presented here contribute to a comprehensive understanding of cultivated Greek olive germplasm and provide information that could be important for cultural purposes and breeding programs.

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