scholarly journals Molecular markers based genetic relatedness studies in tissue culture propagated Japanese plum cultivars Santa Rosa and Frontier

2021 ◽  
Author(s):  
Manisha Thakur ◽  
Rakshandha Luharch ◽  
Vishal Sharma ◽  
Dharam Paul Sharma
Keyword(s):  
Molecular Markers ◽  
Genetic Relatedness ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Start Codon ◽  
Japanese Plum ◽  
Percent Similarity ◽  
Allelic Variations ◽  
Relationship Of

Abstract Santa Rosa and Frontier are the major Japanese plum cultivars grown throughout the world. The present investigation was performed to understand the genetic relatedness among in vitro propagated plum cultivars Santa Rosa and Frontier using PCR based molecular markers. For the study, three arbitrary markers viz. RAPD (Random amplified Polymorphic DNA), ISSR (Inter-Simple Sequence Repeats) and SCoT (Start Codon Targeted) were used. In RAPD analysis, 18 primers out of 28 amplified and generated 33 scorable bands. The allelic variations when analysed, revealed 84 percent similarity between these two cultivars with highest polymorphic information content of 0.78. Similarly, 15 ISSR primers produced 73 amplicons with an average of 4.86 amplicon per primer and similarity coefficient ranging from 62 to 67 percent. Seven SCoT primers out of 26 resulted in a total of twenty- six scorable bands with 24 polymorphic bands. Cluster analysis from all the three markers used broadly divided plum cultivars santa rosa and frontier into two major clusters containing in vitro shoots, their progenies and mother trees of respective genotypes. The study concluded that these three marker systems were found to be effective in revealing genetic relationship of these two commercially important plum cultivars.

Genetic Relatedness of Salmonella Serovars Isolated from Catfish (Clarias gariepinus) and Tilapia (Tilapia mossambica) Obtained from Wet Markets and Ponds in Penang, Malaysia

2016 ◽  
Vol 79 (4) ◽  
pp. 659-665 ◽  
Author(s):  
TITIK BUDIATI ◽  
GULAM RUSUL ◽  
WAN NADIAH WAN-ABDULLAH ◽  
LI-OON CHUAH ◽  
ROSMA AHMAD ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Random Amplified Polymorphic Dna ◽  
Clarias Gariepinus ◽  
Fish Feed ◽  
Commercial Fish ◽  
Tilapia Mossambica ◽  
Rapd Pcr ◽  
Salmonella Serovars ◽  
Relationship Of ◽  
Repetitive Extragenic Palindromic Pcr

ABSTRACT A total of 43 Salmonella enterica isolates belonging to different serovars (Salmonella Albany, Salmonella Agona, Salmonella Corvallis, Salmonella Stanley, Salmonella Typhimurium, Salmonella Mikawasima, and Salmonella Bovis-morbificans) were isolated from catfish (Clarias gariepinus) and tilapia (Tilapia mossambica) obtained from nine wet markets and eight ponds in Penang, Malaysia. Thirteen, 19, and 11 isolates were isolated from 9 of 32 catfish, 14 of 32 tilapia, and 11 of 44 water samples, respectively. Fish reared in ponds were fed chicken offal, spoiled eggs, and commercial fish feed. The genetic relatedness of these Salmonella isolates was determined by random amplified polymorphic DNA PCR (RAPD-PCR) using primer OPC2, repetitive extragenic palindromic PCR (REP-PCR), and pulsed-field gel electrophoresis (PFGE). Composite analysis of the RAPD-PCR, REP-PCR, and PFGE results showed that the Salmonella serovars could be differentiated into six clusters and 15 singletons. RAPD-PCR differentiated the Salmonella isolates into 11 clusters and 10 singletons, while REP-PCR differentiated them into 4 clusters and 1 singleton. PFGE differentiated the Salmonella isolates into seven clusters and seven singletons. The close genetic relationship of Salmonella isolates from catfish or tilapia obtained from different ponds, irrespective of the type of feed given, may be caused by several factors, such as the quality of the water, density of fish, and size of ponds.

Comparative analysis of diversity based on morpho-metric and molecular markers in chickpea over different environments

2018 ◽  
Author(s):  
Indu Rialch ◽  
Rama Kalia ◽  
H. K. Chaudhary ◽  
B. Kumar ◽  
J. C. Bhandari ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Agronomic Traits ◽  
Rapd Analysis ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Breeding Programme ◽  
Metric Traits

Ten morpho-agronomic traits and 80 random amplified polymorphic DNA (RAPD) molecular markers were used to survey genetic diversity in 25 chickpea genotypes. Analysis of variance revealed significant variability among different genotypes for morpho-metric traits. The cluster analysis done using morpho-metric traits grouped 25 genotypes into seven and six clusters in Environment I (Env. I) and Environment II (Env. II), respectively. Three genotypes viz., ICCV-96904, HPG-17, ICCV-95503 and L-HR-1 belonging to diverse clusters were identified divergent and may use in heterosis breeding programme. Of 80 random RAPD markers, 25 were found polymorphic. Three major clusters were identified using 25 polymorphic RAPD markers. The genetic similarity coefficient among genotypes ranged from 0.57 to 0.91. The average polymorphic information content (PIC) for 25 RAPD markers ranges from 0.12 to 0.40. D2-statistic, RAPD analysis and study of genotypes performance revealed sufficient genetic diversity among chickpea genotypes which would be useful in future breeding programme.

scholarly journals Characterization of genetic diversity of cactus species (Opuntia spp.) in Morocco by morphological traits and molecular markers

2017 ◽  
Vol 5 (2) ◽  
pp. 149-159 ◽  
Author(s):  
Y. El Kharrassi ◽  
M.A. Mazri ◽  
M.H. Sedra ◽  
A. Mabrouk ◽  
B . Nasser ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Morphological Traits ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Group Method ◽  
Rapd Primer ◽  
Opuntia Spp ◽  
Issr Primers

The genetic diversity within and among 124 accessions of Opuntia spp. collected from different regions of Morocco was assessed using morphological descriptors and molecular markers. Based on 10 morphological traits, the accessions were separated into 3 main clusters; each cluster was containing accessions from different regions and species. Polymerase chain reaction (PCR) was then performed on 22 accessions from different regions and species, with 10 inter-simple sequence repeat (ISSR) primers and one random amplified polymorphic DNA (RAPD) primer. ISSR primers produced 66 bands overall, 64 (96.9 %) of which were polymorphic while 6 bands were generated by the RAPD marker, all polymorphic. The polymorphic information content (PIC) values ranged from 0.62 to 0.97, with an average of 0.82. The dendrogram of genetic differences generated using the unweighted pair-group method using arithmetic averages (UPGMA) method showed 7 different clusters at a similarity of 0.76, which was confirmed by the principal component analysis (PCA). The main conclusion of our work is the high genetic similarity between Opuntia ficus indica and Opuntia megacantha species in Morocco. Our results will be useful for plant breeding and genetic resource conservation programs.

scholarly journals Genetic Diversity Among Colletotrichum falcatum Isolates Causing Red Rot of Sugarcane in Subtropical Region of India

2014 ◽  
Vol 6 (3) ◽  
pp. 308-315
Author(s):  
Ratinderbir KAUR ◽  
Bipen KUMAR ◽  
Yogesh VIKAL ◽  
Gulzar Singh SANGHERA
Keyword(s):  
Genetic Diversity ◽  
Genetic Relatedness ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Red Rot ◽  
Colletotrichum Falcatum ◽  
Molecular Characteristics ◽  
Molecular Polymorphism ◽  
Pathogenic Variability

Silver Genetic diversity of Colletotrichum falcatum causing red rot of sugarcane was assessed based on morphological, pathological and molecular characteristics especially from sub-tropical Indian conditions. Sixteen isolates of this pathogen were collected based on the extensive survey on prominent varieties grown in the region along with some elite selections. Morphological observations (colony colour, mycelium pattern and sporulation) grouped the isolates into two distinct types (C1: light type and C2: dark type). However, quantitative data on colony diameter showed five clusters for these isolates. Pathogenic characterization of these isolates on fourteen standard differentials formed six groups, ingroup 1: (CF-Pb-1) isolates Cf-157, Cf-249 and Cf-248 were the most virulent while group 6 (CF-Pb-6) isolates Cf-60 and Cf-247 were the least one. The genetic relatedness among the isolates using Random Amplified Polymorphic DNA (RAPD) analysis revealed sufficient molecular polymorphism, which in turn confirmed the variation in virulence of different isolates. The data categorized different isolates into two major clusters and five independent lineages. Polymorphic information content (PIC) ranged from 0.701 to 0.929. Isolate Cf-223 was found to be genetically most diverse among all the isolates. Present study inferred that morphological grouping of most of the isolates showed positive correlation with the pathogenic variability while molecular diversity did not showed such associations.

scholarly journals Keragaman genetik Anggrek Grammatophyllum scriptum asal biji dari hasil Kultur In Vitro berdasarkan penanda RAPD

Cassowary ◽  
2021 ◽  
Vol 4 (1) ◽  
pp. 10-18
Author(s):  
Zarima Wibawati ◽  
Amelia Sarungallo ◽  
Barahima Abbas
Keyword(s):  
Tissue Culture ◽  
Molecular Markers ◽  
Genetic Distance ◽  
In Vitro Culture ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Polymorphic Band ◽  
Genetic Character ◽  
Orchid Seed

Propagation through tissue culture by using orchid seed as explants will produce a lot of orchid plants. This study aims to measure the genetic character of orchid plantlets that were regenerated from seeds which have been resulted from in vitro culture. The genetic character of the original orchid plants produced from in vitro culture was determined using Random Amplified Polymorphic DNA (RAPD) molecular markers. The results showed that the primers used in the RAPD analysis showed a polymorphic band pattern of 14 DNA bands, with sizes between 500 bp - 8000 bp. The genetic distance of Grammatophyllum scriptum orchids that was regenerated from seeds is between 0.229 and 0.649.  The progenis produced from in vitro culture were clustered into seven groups at a dissimilarity coefficient of 45%.

Genetic relationships within and among Iberian fescues (Festuca L.) based on PCR-amplified markers

Genome ◽  
2006 ◽  
Vol 49 (9) ◽  
pp. 1170-1183 ◽  
Author(s):  
Pedro J.G. de Nova ◽  
Marcelino de la Cruz ◽  
Juan V. Monte ◽  
Consuelo Soler
Keyword(s):  
Molecular Markers ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Species Level ◽  
Lolium Rigidum ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Molecular Genetic Variation

The genus Festuca comprises approximately 450 species and is widely distributed around the world. The Iberian Penninsula, with more than 100 taxa colonizing very diverse habitats, is one of its main centers of diversification. This study was conducted to assess molecular genetic variation and genetic relatedness among 91 populations of 31 taxa of Iberian fescues, based on several molecular markers (random amplified polymorphic DNA, amplified fragment length polymorphisms, and trnL sequences). The analyses showed the paraphyletic origin of the broad-leaved (subgenus Festuca , sections Scariosae and Subbulbosae, and subgenus Schedonorus ) and the fine-leaved fescues (subgenus Festuca, sections Aulaxyper, Eskia, and Festuca). Schedonorus showed a weak relationship with Lolium rigidum and appeared to be the most recent of the broad-leaved clade. Section Eskia was the most ancient and Festuca the most recent of the fine-leaved clade. Festuca and Aulaxyper were the most related sections, in concordance with their taxonomic affinities. All taxa grouped into their sections, except F. ampla and F. capillifolia (section Festuca), which appeared to be more closely related to Aulaxyper and to a new independent section, respectively. Most populations clustered at the species level, but some subspecies and varieties mixed their populations. This study demonstrated the value in combining different molecular markers to uncover hidden genetic relationships between populations of Festuca.

scholarly journals Diversity and genetic relatedness among genotypes of Vitis spp. using microsatellite molecular markers

2013 ◽  
Vol 35 (3) ◽  
pp. 799-808 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Cosme Damião Cruz ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Molecular Markers ◽  
Microsatellite Markers ◽  
Information Content ◽  
Genetic Relatedness ◽  
Polymorphic Information Content ◽  
Germplasm Bank ◽  
Expected Heterozygosity ◽  
Vitis Spp

The purpose of this research was to study the genetic diversity and genetic relatedness of 60 genotypes of grapevines derived from the Germplasm Bank of Embrapa Semiárido, Juazeiro, BA, Brazil. Seven previously characterized microsatellite markers were used: VVS2, VVMD5, VVMD7, VVMD27, VVMD3, ssrVrZAG79 and ssrVrZAG62. The expected heterozygosity (He) and polymorphic information content (PIC) were calculated, and the cluster analysis were processed to generate a dendrogram using the algorithm UPGMA. The He ranged from 81.8% to 88.1%, with a mean of 84.8%. The loci VrZAG79 and VVMD7 were the most informative, with a PIC of 87 and 86%, respectively, while VrZAG62 was the least informative, with a PIC value of 80%. Cluster analysis by UPGMA method allowed separation of the genotypes according to their genealogy and identification of possible parentage for the cultivars 'Dominga', 'Isaura', 'CG 26916', 'CG28467' and 'Roni Redi'.

scholarly journals Establishment of an Efficient Micropropagation System for Humulus lupulus L. cv. Cascade and Confirmation of Genetic Uniformity of the Regenerated Plants through DNA Markers

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2268
Author(s):  
Doina Clapa ◽  
Monica Hârța
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Shoot Proliferation ◽  
Start Codon ◽  
Single Node ◽  
Genetic Uniformity ◽  
Planting Material ◽  
Regenerated Plants ◽  
Humulus Lupulus L ◽  
Different Types

The demand for virus-free hop planting material has increased in the last few years due to its multipurpose uses. The present study aimed to establish an effective protocol for clonal propagation of cv. Cascade using only the cytokinins as PGRs in all stages of micropropagation: (i) in vitro culture initiation using single-node micro-cuttings inoculated on modified Murashige and Skoog (MSm) medium solidified with Plant agar and supplemented with 0.5 mg L−1 6-benziyladenine (BA) with 76% recorded viability of nodal explants; (ii) in vitro multiplication of multinodal shoots on MSm medium gelled with Plant agar and supplemented with different types and concentrations of cytokinins: 2 mg L−1 kinetin (KIN), 0.7 mg L−1 1-(2-Chloro-4-pyridyl)-3-phenylurea) (1 CPPU), 2 mg L−1 meta-topoline (mT) and 0.5 mg L−1 BA, which was the best variant for shoot proliferation (9.48 ± 0.78 shoots/explant); (iii) rooting and acclimatization with the best results obtained by ex vitro rooting and acclimatization of plants in the same stage in perlite (96.00 ± 0.60% acclimatized rooted plants with 100% survival under greenhouse conditions). The true-to-type nature of in vitro raised plants with the mother plant was assessed by Random Amplified Polymorphic DNA (RAPD) and Start Codon Target Polymorphism (SCoT) molecular markers, and then their genetic uniformity were confirmed.

scholarly journals Genetic diversity analysis in a mini core collection of Damask rose (Rosa damascena Mill.) germplasm from Iran using URP and SCoT markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Atefeh Sadat Mostafavi ◽  
Mansour Omidi ◽  
Reza Azizinezhad ◽  
Alireza Etminan ◽  
Hassanali Naghdi Badi
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Core Collection ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Resolving Power ◽  
Start Codon ◽  
Rosa Damascena ◽  
Mini Core Collection ◽  
Damask Rose

Abstract Background Rosa damascena Mill is a well-known species of the rose family. It is famous for its essential oil content. The aim of the present study was to assess the genetic diversity and population structure of a mini core collection of the Iranian Damask rose germplasm. This involved the use of universal rice primers (URP) and start codon targeted (SCoT) molecular markers. Results Fourteen URP and twelve SCoT primers amplified 268 and 216 loci, with an average of 19.21 and 18.18 polymorphic fragments per primer, respectively. The polymorphic information content for URR and SCoT primers ranged from 0.38 to 0.48 and 0.11 to 0.45, with the resolving power ranging from 8.75 to 13.05 and 9.9 to 14.59, respectively. Clustering was based on neighbor-joining (NJ). The mini core collection contained 40 accessions and was divided into three distinct clusters, centered on both markers and on the combination of data. Conclusion Cluster analysis and principal coordinate analysis were consistent with genetic relationships derived by STRUCTURE analysis. The findings showed that patterns of grouping did not correlate with geographical origin. Both molecular markers demonstrated that the accessions were not genetically diverse as expected, thereby highlighting the possibility that gene flow occurred between populations.

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