scholarly journals Description and analysis of genetic diversity among squash accessions

2009 ◽  
Vol 52 (2) ◽  
pp. 271-283 ◽  
Author(s):  
Athanasios L. Tsivelikas ◽  
Olga Koutita ◽  
Anastasia Anastasiadou ◽  
George N. Skaracis ◽  
Ekaterini Traka-Mavrona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Clustering Algorithm ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Molecular Data ◽  
Optimal Number ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group

In this work, the part of the squash core collection, maintained in the Greek Gene Bank, was assessed using the morphological and molecular data. Sixteen incompletely classified accessions of the squash were characterized along with an evaluation of their resistance against two isolates of Fusarium oxysporum. A molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers was also performed, revealing high level of polymorphism. To study the genetic diversity among the squash accessions, a clustering procedure using Unweighed Pair Group Method and Arithmetic Average (UPGMA) algorithm was also adopted. Two independent dendrograms, one for the morphophysiological and one for molecular data were obtained, classifying the accessions into two and three main clusters, respectively. Despite the different number of the clusters there were many similarities between these two dendrograms, and a third dendrogram resulting from their combination was also produced, based on Gower's distance and UPGMA clustering algorithm. In order to determine the optimal number of clusters, the upper tail approach was applied. The more reliable clustering of the accessions was accomplished using RAPD markers as well as the combination of the two different data sets, classifying the accessions into three significantly different groups. These groups corresponded to the three different cultivated species of C. maxima Duch., C. moschata Duch., and C. pepo L. The same results were also obtained using Principal Component Analysis.

The use of RAPD markers to distinguish among juniper and cedar cultivars

2000 ◽  
Vol 78 (5) ◽  
pp. 655-659 ◽  
Author(s):  
Tom Hsiang ◽  
Junbin Huang
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Unknown Origin ◽  
Genetic Distances ◽  
Group Method ◽  
Pair Group ◽  
Juniperus Chinensis ◽  
Juniperus Scopulorum ◽  
Close Relatives

Two species of Chamaecyparis and six cultivars each of Juniperus chinensis L. and Juniperus scopulorum Sarg. (Cupressaceae) were subjected to random amplified polymorphic DNA (RAPD) analysis using seven primers. Unweighted pair group method with averages (UPGMA) and principal component analyses of genetic distances between cultivars showed that 42 polymorphic RAPD bands could distinguish among all cultivars and properly group them by species and genera. Where the origin of a specific juniper cultivar is uncertain, analysis of genetic distance can pinpoint close relatives. For example, we were unable to trace the origin of J. chinensis 'Alps', and we initially thought it was a mislabeled J. chinensis 'Blue Alps'. However, we found 'Alps' to be closer to J. chinensis 'Fairview' and 'Mountbatten' than to 'Blue Alps'. Similarly, 'Wichita Blue' has an unknown origin, but it had the highest genetic similarity with 'Medora'.Key words: juniper, cedar, RAPD, cultivars, phylogenetics.

scholarly journals Evaluation of Genetic Diversity among Persian Fig Cultivars by Morphological Traits and RAPD Markers

HortScience ◽  
2018 ◽  
Vol 53 (5) ◽  
pp. 613-619 ◽  
Author(s):  
Ghazal Baziar ◽  
Moslem Jafari ◽  
Mansoureh Sadat Sharifi Noori ◽  
Samira Samarfard
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Hierarchical Cluster ◽  
Fruit Trees ◽  
Group Method ◽  
Fars Province ◽  
Pair Group

Ficus carica L. is one of the most ancient fruit trees cultivated in Persia (Iran). The conservation and characterization of fig genetic resources is essential for sustainable fig production and food security. Given these considerations, this study characterizes the genetic variability of 21 edible F. carica cultivars in the Fars Province using random amplified polymorphic DNA (RAPD) markers. The collected cultivars were also characterized for their morphological features. A total of 16 RAPD primers produced 229 reproducible bands, of which, 170 loci (74.43%) were polymorphic with an average polymorphic information content (PIC) value of 0.899. Genetic analysis using an unweighted pair-group method with arithmetic averaging (UPGMA) revealed genetic structure and relationships among the local germplasms. The dendrogram resulting from UPGMA hierarchical cluster analysis separated the fig cultivars into five groups. These results demonstrate that analysis of molecular variance allows for the partitioning of genetic variation between fig groups and illustrates greater variation within fig groups and subgroups. RAPD-based classification often corresponded with the morphological similarities and differences of the collected fig cultivars. This study suggests that RAPD markers are suitable for analysis of diversity and cultivars’ fingerprinting. Accordingly, understanding of the genetic diversity and population structure of F. carica in Iran may provide insight into the conservation and management of this species.

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

RAPD analysis of cultivated and wild yellow nutsedge (Cyperus esculentusL.)

Weed Science ◽  
1998 ◽  
Vol 46 (3) ◽  
pp. 318-321 ◽  
Author(s):  
Paloma Abad ◽  
Bernardo Pascual ◽  
José V. Maroto ◽  
Salvador López-Galarza ◽  
María J. Vicente ◽  
...  
Keyword(s):  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Wild Populations ◽  
Arithmetic Average ◽  
Yellow Nutsedge ◽  
Pair Group ◽  
High Level ◽  
Unweighted Pair Group Method

Cultivated and weedy clones of yellow nutsedge were analyzed using random amplified polymorphic DNA (RAPD) markers to assess the polymorphism within the species and determine if this approach was suitable for identification of cultivar and wild populations. The RAPD markers unambiguously identified all studied clones. Nei-Li similarities were computed and used in an unweighted pair group method using arithmetic average (UPGMA) cluster analyses. Cultivated and weedy clones were clustered in two groups, but two cultivated clones were more closely related to weedy clones than to cultivated clones. The results showed a high level of genetic variability among the clones tested, particularly among the cultivated ones. Identification of yellow nutsedge cultivars and analysis of genetic diversity within and among weedy populations is possible by using only a small number of primers. In this study, seven selected primers discriminated among the 10 tested clones.

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 Genetic diversity of Pleurotus ostreatus (Jacq.) P. Kumm. strains in Java based on random amplified polymorphic DNA markers

2021 ◽  
Vol 22 (6) ◽  
Author(s):  
NURAENI EKOWATI ◽  
ARIS MUMPUNI ◽  
JUNI SAFITRI MULJOWATI ◽  
NUNIEK INA RATNANINGTYAS ◽  
ARDHINI RIN MAHARNING
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Dna Markers ◽  
Pleurotus Ostreatus ◽  
Genetic Similarity ◽  
Random Amplified Polymorphic Dna ◽  
Dna Amplification ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group

Abstract. Ekowati N, Mumpuni A, Muljowati JS, Ratnaningtyas NI, Maharning AR. 2021. Genetic diversity of Pleurotus ostreatus (Jacq.) P. Kumm. strains in Java based on Random Amplified Polymorphic DNA markers.  Biodiversitas 22: 3488-3493. Genetic variation in a fungal population can occur due to mutation and recombination, resulting in changes in the nucleotides that encode specific DNA sequences. Strains with a high genetic distance and good production capabilities can be used to develop genetic breeding. This study aimed to investigate genetic relationship among Pleurotus ostreatus strains cultivated in Java (Bogor, Cianjur, Tasikmalaya, Purwokerto, Yogyakarta, Tawangmangu, Malang, and Madiun) based on random amplified polymorphic DNA (RAPD) markers.  The research method consisted of DNA isolation and DNA amplification using six primers, i.e. OPA2, OPA3, OPA4, OPA7, OPA9, and OPA10. DNA band data were analyzed using NTSYSpc21 software to determine the level of genetic similarity, based on the Unweighted Pair Group Method with Arithmetic Average Algorithm (UPGMA). In all, 101 amplified DNA bands were obtained, with sizes ranging from 136 to 2320 bp and 96.0% of the bands were polymorphic. Based on cluster analysis, it shows that three clusters were formed. There were genetic variations and relationships among eight P. ostreatus strains in Java with a genetic similarity varying from 37-98%.

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.

scholarly journals Genetic Diversity and Relationships in Malus sp. Germplasm Collections as Determined by Randomly Amplified Polymorphic DNA

2001 ◽  
Vol 126 (3) ◽  
pp. 318-328 ◽  
Author(s):  
Nnadozie C. Oraguzie ◽  
Sue E. Gardiner ◽  
Heather C.M. Basset ◽  
Mirko Stefanati ◽  
Rod D. Ball ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Scatter Plot ◽  
Arithmetic Average ◽  
Germplasm Collections ◽  
Food Research ◽  
Pair Group ◽  
Upgma Cluster Analysis

Four subsets of apple (Malus Mill.) germplasm representing modern and old cultivars from the repository and apple genetics population of the Horticulture and Food Research Institute of New Zealand Limited were used in this study. A total of 155 genotypes randomly chosen from the four subsets were analyzed for random amplified polymorphic DNA (RAPD) variation. Nine decamer primers generated a total of 43 fragments, 42 of which were polymorphic across the 155 genotypes. Pairwise distances were calculated between germplasm subsets using the distance metric algorithm in S-PLUS, and used to examine intra-and inter-subset variance components by analysis of molecular variation (AMOVAR). A phenogram based on unweighted pair group method with arithmetic average (UPGMA) cluster analysis was constructed from the pairwise distances and a scatter plot was generated from principal coordinate analysis. The AMOVAR showed that most of the variation in the germplasm (94.6%) was found within subsets, suggesting that there is significant variation among the germplasm. The grouping of genotypes based on the phenogram and scatter plot generally did not reflect the pedigree or provenance of the genotypes. It is possible that more RAPD markers are needed for determining genetic relationships in apple germplasm. Nevertheless, the variation observed in the study suggests that the current practice of sublining populations in the first generation to control inbreeding may not be necessary in subsequent generations. If these results are confirmed by fully informative molecular markers, germplasm managers should reassess the structure of their genetics populations. There may be a need to combine sublines in order to capture the maximum genetic diversity available and to streamline breeding efforts.

scholarly journals GENETIC VARIABILITY OF INDONESIAN PAPAYA ACCESSIONS AS REVEALED BY RANDOM AMPLIFIED POLYMORPHIC DNA AND MORPHOLOGICAL CHARACTERIZATION

2019 ◽  
Vol 20 (1) ◽  
pp. 1
Author(s):  
Riry Prihatini ◽  
Tri Budiyanti ◽  
Noflindawati Noflindawati
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Accurate Method ◽  
Morphological Characters ◽  
Morphological Characterization ◽  
Fruit Shape ◽  
Morphological Data ◽  
Group Method ◽  
Pair Group

<p class="abstrakinggris">Diverse papaya (<em>Carica</em> sp.) accessions are found in many regions in Indonesia, but their genetic diversity have not yet been studied. Random Amplified Polymorphic DNA (RAPD) is a simple yet accurate method that can be used to examine the genetic diversity of papaya. The study aimed to examine the genetic diversity of Indonesian papaya accessions using RAPD markers and morphological characters. The RAPD was applied on 23 papaya accessions using 30 primers. The appearing bands were further analyzed with the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and Principal Component Analysis (PCA). The molecular results were then compared to the fruit morphological data, including fruit shape, size, flesh color, texture, and flavor. The RAPD analysis revealed that the 23 papaya accessions clustered into six main clades with Dice-Sorensen coefficient similarity ranged from 0.71 to 0.98. The first group consisted of 11 accessions, including both the hybrids and local accessions. The second group consisted of eight accessions especially six Indonesian hybrids, a Mexican Hybrid and a Hawaiian hybrid. The other four groups had a single member namely Sicincin Panjang, Lokal Sumani, Cariso, and Carica. The molecular grouping, however, did not align with the fruit character grouping. Overall, it was implied that the Indonesian papaya accessions were genetically narrow, of which some accessions were closely related to Hawaiian and Mexican accessions. These results can be used as a reference on papaya crossbreeding program in Indonesia.</p>

scholarly journals Climate Change and Fading Genetic Resources of Parkia biglobosa (Jacq.) in Nigeria Based on SSR Markers

2019 ◽  
Author(s):  
Jacob Popoola ◽  
James Agbolade ◽  
Abiodun Ajiboye ◽  
Omotolani Akinola ◽  
Francis Lewu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Principal Component ◽  
Sub Saharan Africa ◽  
Group Method ◽  
Parkia Biglobosa ◽  
Arithmetic Average ◽  
Ecological Zones ◽  
Pair Group

African locust bean (Parkia biglobosa (Jacq.) is a multi-purpose economic tree with genetic potentials in sub-Saharan Africa. Its cultivation and production is declining with increased aging and genetically threatened throughout its natural ranges. Research efforts are needed to change the present scenario to sustainable cultivation and utilization, hence this present study. This study was aimed at evaluating genetic diversity and geographical spread relationships of twenty landraces collected from different ecological zones of Nigeria using simple sequence repeat (SSR) markers. Ten SSR markers were screened and five primers (PbL02, PbL03, PbL04, PbL05 and PbL09) were selected based on clear amplification products and reproducible scorable bands. The SSR primers detected a total of 55 alleles ranged from 10 to 14 alleles with a mean of 11. The percentage polymorphisms were high and ranged from 68.75 % in PbL04 to 84.21 % in PbL05 with a mean of 74.16 %. The polymorphic information content (PIC) was in the range of 0.31 in PbL02 to 0.37 in PbL09. The genetic diversity and heterozygosity values ranged from 0.39 to 0.50 and 0.00 to 0.68 while the average genetic distance for all pair wise comparisons was 0.31.The first five Principal Component (PC) accounted for 70.20 % of the total variation out of which PC1 (31.50%) and PC2 (19.20%) extracted 49.70% molecular similarity. The dendrogram resulted in separation of the 19 landraces into three major clusters based on unweighted pair group method with arithmetic average. Cluster I comprised of five landraces: ABNo130 and BENo023; OYNo11, KANo125 and NiNo262 while cluster II had only one (BANo116). Cluster III was diverse comprising 13 landraces: ZANo188, KNNo162, KENo220, GMNo076 and EbNo260, ADNo64, EdNo164, KANo137, KENo217, KwNo270, NiNo241, OsNo206 and PLNo120. The homogeneity of alleles among the studied landraces suggested suspicion of loss of genetic intra-specific variation among the landraces of P. biglobosa which calls for concerted efforts toward better cultivation, conservation, management, utilization and genetic improvement of the species in Nigeria.

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