scholarly journals Degenerate primed randomly amplified polymorphic DNA (DP-RAPD) fingerprinting of bacteriophages of Vibrio harveyi from shrimp hatcheries in Southern India

2021 ◽  
Author(s):  
Thiyagarajan Sanjeevi ◽  
Chrisolite B ◽  
Alavandi S.V
Keyword(s):  
Genetic Relatedness ◽  
Vibrio Harveyi ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Electron Microscopic ◽  
Rapd Fingerprinting ◽  
Pair Group ◽  
Transmission Electron ◽  
Sucrose Fermentation ◽  
Contractile Tail

Vibrio harveyi is a significant pathogen of shrimp. Seventy-six bacteriophages infecting luminescent V. harveyi were isolated from a total of 194 water samples drawn from various sources of shrimp hatcheries located in South East coast and Andaman island of India. Degenerate primed randomly amplified polymorphic DNA (DP- RAPD) fingerprinting of these bacteriophages was carried out to determine their genetic relatedness. Similarity matrix based on Dice coefficient followed by construction of dendrogram by unweighted pair group method with arithmetic averages (UPGMA) revealed 12 major clusters. One phage was randomly selected from each of these major clusters for transmission electron microscopic observations. Eleven of them had an icosahedral head (46-115 nm) with a long non- contractile tail (132-329 nm), belonging to the Siphoviridae family and two phages had a short tail (15-27 nm), belonging to the family Podoviridae. The phylogenetic analysis of the phages using DP-RAPD fingerprinting correlated to some extent to the phenotypic nature of the host specifically with regard to sucrose fermentation and source of isolation. However, phages specifically infecting V. harveyi and those belonging to different families did not cluster together in the DP-PCR cluster analysis. Hence, the genetic diversity of phages infecting same host with respect to phenotypic difference was revealed by the DP-RAPD applied in this study.

scholarly journals Molecular Diversity and Genetic Relatedness of Candida albicans Isolates from Birds in Hungary

2021 ◽  
Vol 186 (2) ◽  
pp. 237-244
Author(s):  
M. Domán ◽  
L. Makrai ◽  
Gy. Lengyel ◽  
R. Kovács ◽  
L. Majoros ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Molecular Diversity ◽  
Genetic Relatedness ◽  
Group Method ◽  
Pair Group ◽  
Degree Of Separation ◽  
Avian Origin ◽  
Species Specific ◽  
Sequence Types ◽  
Unweighted Pair Group Method

AbstractThe molecular epidemiology of Candida albicans infections in animals has been rarely studied. In this study, multilocus sequence typing was used to characterise the genetic diversity and population structure of 24 avian origin C. albicans isolates collected from different birds with candidiasis and compared to human isolates. Fourteen diploid sequence types (DSTs) including six new DSTs were determined. Cluster analysis revealed that isolates grouped into 8 clades. Bird isolates mainly belonged to minor clades and Clade 15 with DST 172 was the most common (11 isolates; 45.8%). The remaining isolates were clustered into Clade 7 (5 isolates; 20.8%), Clade 10 (4 isolates; 16.6%), Clade 8 (2 isolates; 8.3%), Clade 4 (1 isolate; 4.2%) and Clade 16 (1 isolate; 4.2%). Unweighted pair group method with arithmetic averages (UPGMA) and eBURST analyses showed that the genetic construction of avian origin C. albicans population is fairly diverse. Although species-specific lineages were not found, some degree of separation in the evolution of bird and human strains could be observed.

scholarly journals Discrimination among Cultivars of Cabbage Using Randomly Amplified Polymorphic DNA Markers

HortScience ◽  
2000 ◽  
Vol 35 (6) ◽  
pp. 1155-1158 ◽  
Author(s):  
Rogério L. Cansian ◽  
Sergio Echeverrigaray
Keyword(s):  
Rapd Markers ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Base Pairs ◽  
Arithmetic Average ◽  
Pair Group ◽  
Similarity Indices ◽  
Upgma Cluster Analysis ◽  
Group A

Randomly amplified polymorphic DNA (RAPD) markers were used to discriminate among 16 commercial cultivars of cabbage (Brassica oleracea L. Capitata Group). A set of 18 decamer primers was selected from 100 random sequences and used to characterize cultivars and to evaluate distances. The selected primers produced 105 (54%) polymorphic bands ranging in size from 100 and 2500 base pairs, out of a total of 195 bands, which allowed for discrimination of all cultivars. Similarity indices between cultivars were computed from RAPD data, and ranged from 0.72 to 0.87 with an average of 0.82. Unweighted pair-group method with arithmetic average (UPGMA) cluster analysis revealed two groups, one formed by two cultivars recommended for summer cropping, and the other by 14 cultivars. This large group was additionally divided into two subgroups. RAPD analysis provides a quick and reliable alternative for the identification of cabbage cultivars and for determination of the relationships among them.

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.

Genetic relatedness among cultivated and wild mulberry (Moraceae: Morus) as revealed by inter-simple sequence repeat analysis in China

2006 ◽  
Vol 86 (1) ◽  
pp. 251-257 ◽  
Author(s):  
Zhao Weiguo ◽  
Zhou Zhihua ◽  
Miao Xuexia ◽  
Wang Sibao ◽  
Zhang Lin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Pair Group ◽  
Simple Sequence

The genetic diversity of 27 mulberry (Morus spp.) genotypes mainly from China was investigated using inter-simple sequence repeat (ISSR) markers to assist in addressing breeding objectives and conserving existing genetic resources. Of the 22 primers screened, 15 produced highly reproducible ISSR bands. Using these 15 primers, 138 discernible DNA fragments were generated with 126 (91.3%) being polymorphic, indicating considerable genetic variation among the mulberry genotypes studied. Genetic similarity ranged from 0.6014 between Yu 2 and Yu 711 to 0.9493 between Cuizhisang and Dejiang 10. The phenetic dendrogram based on ISSR data generated by the unweighed pair group method with arithmetical averages (UPGMA) method grouped the 27 accessions into two major clusters: cluster I, cultivated mulberry species (M. multicaulis Perr., M. alba Linn., M. atropurpurea oxb., M. bombycis Kiodz., M. australis Poir., M. rotundiloba Kiodz., M. alba var. pendula Dipp., M. alba var. macrophylla Loud., and M. alba var. venose Delile.); and cluster II, wild mulberry species (M. cathayana Hemsl., M. laevigata Wall., M. wittiorum Hand-Mazz., M. nigra Linn., and M. mongolica Schneid.). Our molecular analyses agree with the existing morphological classification of Morus and clarify the genetic relationships among mulberry species. Key words: Morus L., genetic diversity, inter-simple sequence repeat, relatedness

Rediscovery of historical Vitis vinifera varieties from the South Anatolia region by using amplified fragment length polymorphism and simple sequence repeat DNA fingerprinting methods

Genome ◽  
2013 ◽  
Vol 56 (5) ◽  
pp. 295-302 ◽  
Author(s):  
Kaan Yilancioglu ◽  
Selim Cetiner
Keyword(s):  
Vitis Vinifera ◽  
Fragment Length ◽  
Genetic Relatedness ◽  
Genetic Erosion ◽  
Principal Component ◽  
Distinct Group ◽  
Group Method ◽  
Local Cultivars ◽  
Pair Group ◽  
Selected Subset

Anatolia played an important role in the diversification and spread of economically important Vitis vinifera varieties. Although several biodiversity studies have been conducted with local cultivars in different regions of Anatolia, our aim is to gain a better knowledge on the biodiversity of endangered historical V. vinifera varieties in the northern Adana region of southern Anatolia, particularly those potentially displaying viticulture characteristics. We also demonstrate the genetic relatedness in a selected subset of widely cultivated and commercialized V. vinifera collection cultivars, which were obtained from the National Grapevine Germplasm located at the Institute of Viticulture, Turkey. In the present study, microsatellites were used in narrowing the sample size from 72 accessions down to a collection of 27 varieties. Amplified fragment length polymorphisms were then employed to determine genetic relatedness among this collection and local V. vinifera cultivars. The unweighted pair group method with arithmetic mean cluster and principal component analyses revealed that Saimbeyli local cultivars form a distinct group, which is distantly related to a selected subset of V. vinifera collection varieties from all over Turkey. To our knowledge, this is the first study conducted with these cultivars. Further preservation and use of these potential viticultural varieties will be helpful to avoid genetic erosion and to promote continued agriculture in the region.

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 Isolation and characterisation of Vibrio alginolyticus lytic bacteriophage φVa-1 from brackishwater clam Meritrix meritrix in India

2017 ◽  
Vol 64 (3) ◽  
Author(s):  
E. C. Abhilash ◽  
S. V. Alavandi
Keyword(s):  
Hexagonal Structure ◽  
Vibrio Alginolyticus ◽  
Lytic Bacteriophage ◽  
Electron Microscopic ◽  
Tryptone Soya Agar ◽  
Double Stranded Dna ◽  
Transmission Electron ◽  
The Family ◽  
Contractile Tail ◽  
Overlay Technique

The Gram negative bacterium Vibrio alginolyticus is generally found in marine and brackishwater systems. A lytic bacteriophage capable of specifically infecting V. alginolyticus was isolated from the brackishwater clam (Meretrix meretrix) using agar overlay technique. The phage produced plaques 3 mm in dia, which increased to 5 mm overnight on tryptone soya agar (TSA) plates and the optimum temperature and pH was found to be 32°C and 7.5 respectively. The phage was designated as φVa-1 and nucleic acid characterisation confirmed that the phage has double stranded DNA. Transmission electron microscopic observations revealed that the bacteriophage had hexagonal structure with a long contractile tail andthe phage was found to belong to the family Myoviridae.

scholarly journals Molecular Analysis of Hybrids among the Ornamental Eucalypts Eucalyptus macrocarpa, E. pyriformis, and E. youngiana

2001 ◽  
Vol 126 (3) ◽  
pp. 336-339 ◽  
Author(s):  
Kirsty Neaylon ◽  
Kate L. Delaporte ◽  
Margaret Sedgley ◽  
Graham G. Collins ◽  
John G. Conran
Keyword(s):  
Genetic Similarity ◽  
Minimum Spanning Tree ◽  
Molecular Data ◽  
Pcr Analysis ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Chain Reaction ◽  
Mature Trees ◽  
Pair Group ◽  
Polymerase Chain

The potential for hybridization among three species of Eucalyptus L'Hér in the Series Macrocarpae, E. macrocarpa Hook (Mottlecah), E. pyriformis Turcz. (pear-fruited mallee), and E. youngiana F. Muell. (large-fruited mallee), was investigated using molecular data generated by randomly amplified polymorphic DNA (RAPD)-polymerase chain reaction (PCR) analysis. Samples of DNA from seedlings derived from controlled pollinations, and from different individuals from each species, were amplified with six different 10-mer primers. The presence or absence of RAPD fragments was used to generate a dendrogram based on genetic similarity, an ordination derived by multidimensional scaling (MDS), and a minimum spanning tree (MST) to show the relative links and dissimilarities between the individuals tested. Two clusters were identified on the unweighted pair-group method arithmetric average dendrogram. The first included all of the E. macrocarpa genotypes and all but one of the E. macrocarpa hybrids. The second included all of the E. youngiana and E. pyriformis genotypes and their hybrids. The MDS ordinations placed the hybrid seedlings between the parent species. From the 30 progeny investigated, 28 were assessed from the molecular data to be hybrids from controlled pollinations. The remaining two seedlings appeared to be derived from self-pollination. The parentage of two mature trees, thought to be natural hybrids involving the three species, was also investigated. One was confirmed as a cross between E. youngiana and E. pyriformis, but the second was less certain because of its low genetic similarity to all other individuals, and may be a hybrid involving species not included in this study.

scholarly journals 555 Estimation of Genetic Diversity among Citrullus Accessions using RAPD Markers

HortScience ◽  
2000 ◽  
Vol 35 (3) ◽  
pp. 491D-491
Author(s):  
Amnon Levi ◽  
Claude E. Thomas ◽  
Anthony P. Keinath ◽  
Todd C. Wehner
Keyword(s):  
Genetic Similarity ◽  
Rapd Markers ◽  
Genetic Relatedness ◽  
Plant Introduction ◽  
Group Method ◽  
Similarity Coefficients ◽  
High Confidence ◽  
Core Collections ◽  
The Third ◽  
Pair Group

Genetic relatedness was estimated among 42 U.S. plant introduction (PI) accessions of the genus Citrullus (37 PIs of which were reported to have disease resistance and five watermelon cultivars) using 30 RAPD primers. These primers produced 662 RAPD markers that could be scored with high confidence. Based on these markers, genetic similarity coefficients were calculated, and a dendrogram was constructed using the unweighted pair-group method with arithmatic average (UPGMA). The analysis delineated three major clusters. The first cluster consisted of a group of five watermelon cultivars, a group of C. lanatus var. lanatus accessions and a group of C. lanatus var. lanatus accessions that contained some C. lanatus var. citroides genes. The second cluster consisted of the C. lanatus var. citroides accessions, while the third cluster consisted of the C. colocynthis accessions. The two C. lanatus clusters differentiated from each other and from the C. colocynthis cluster at the level of 58.8% and 38.9% genetic similarity. Our results indicate that closely related Citrullus PIs may have resistances to the same diseases. Thus, molecular markers may be a useful tool in the development of core collections of Citrullus PIs with resistance to diseases.

scholarly journals Development of Sequence-characterized Amplified Region Markers for the Identification of Grapevine Cultivars

HortScience ◽  
2015 ◽  
Vol 50 (12) ◽  
pp. 1744-1750
Author(s):  
Kang Hee Cho ◽  
Jung Ho Noh ◽  
Seo Jun Park ◽  
Se Hee Kim ◽  
Dae-Hyun Kim ◽  
...  
Keyword(s):  
Rapd Markers ◽  
Morphological Characteristics ◽  
Polymorphic Band ◽  
Group Method ◽  
Scar Markers ◽  
Randomly Amplified Polymorphic Dna ◽  
Genetic Fingerprinting ◽  
Sequence Characterized Amplified Region ◽  
Pair Group ◽  
Average Similarity

Grapevine cultivars have traditionally been identified based on the morphological characteristics, but the identification of closely related cultivars has been difficult because of their similar pedigree backgrounds. In this study, we developed DNA markers for genetic fingerprinting in 37 grapevine cultivars, including 20 cultivars bred in Korea. A total of 180 randomly amplified polymorphic DNA (RAPD) markers were obtained using 30 different primers. The number of polymorphic bands ranged from three (OPG-08 and OPU-19) to nine (OPV-01 and UBC116), with an average of six. RAPD markers were used in cluster analysis performed with the unweighted pair-group method of arithmetic averages (UPGMA). The average similarity value was 0.69 and the dendrogram clustered the 37 grapevine cultivars into five clusters. The relationships among the grapevine cultivars were consistent with the known pedigrees of the cultivars. The 50 RAPD fragments selected were sequenced for the development of sequence-characterized amplified region (SCAR) markers. As a result, 16 of 50 fragments were successfully converted into SCAR markers. A single polymorphic band, the same size as the RAPD fragments or smaller, was amplified depending on the primer combinations in the 14 SCAR markers, and codominant polymorphisms were detected using the SCAR markers G119_412 and GB17_732. Among these markers, combination of 11 SCAR markers, GG05_281, G116_319, G146_365, G119_412, GW04_463, G169_515, G116_539, GV04_618, GV01_678, GG05_689, and GB17_732, provided sufficient polymorphisms to distinguish the grapevine cultivars investigated in this study. These newly developed markers could be a fast and reliable tool for identifying grapevine cultivars.

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