scholarly journals Diversitatea moleculară a două ecotipuri de Datura inoxia provenite din vestul şi estul României

2020 ◽  
Author(s):  
Cristina Chelu ◽  
◽  
Carmen Varlam ◽  
Gheorghe Titescu ◽  
Gallia Butnaru ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Genetic Similarity ◽  
Molecular Diversity ◽  
Rapd Analysis ◽  
Genomic Variation ◽  
Origin And Evolution ◽  
Random Primers ◽  
Datura Inoxia

Molecular Diversity of two Ecotypes of Datura inoxia Originating from Western and Eastern Romania. To characterize genomic variation among genotypes, we have performed RAPD analysis using ten random primers. The results yielded 88 bands out of which 39 were polymorphic. The primers US1 and US7 showed 87.71% and 72.72% polymorphism respectively. The least polymorphism was shown by primer US9 (12.50%). The primer US15 did not produce any bands suggesting the absence of matching sequences in the genomic DNA. The dendrogram classified ecotypes into two clusters (A and B); cluster B possess three sub-clusters: B1 - Socodor 2; B2 - Flamura 1 and Flamura 2, and B3 - Flamura 3. Overall, the values of genetic similarity between ecotypes were low pointing out their particular origin and “evolution”.

Precise Detection and Tracing of Trichoderma hamatum 382 in Compost-Amended Potting Mixes by Using Molecular Markers

1999 ◽  
Vol 65 (12) ◽  
pp. 5421-5426 ◽  
Author(s):  
Pervaiz A. Abbasi ◽  
Sally A. Miller ◽  
Tea Meulia ◽  
Harry A. J. Hoitink ◽  
Jin-Man Kim
Keyword(s):  
Genomic Dna ◽  
Biocontrol Agent ◽  
Rapd Analysis ◽  
Simple Procedure ◽  
Low Molecular Weight ◽  
Dna Fragments ◽  
Pcr Assay ◽  
Sequence Characterized Amplified Region ◽  
Random Primers ◽  
Trichoderma Hamatum

ABSTRACT Randomly amplified polymorphic DNA (RAPD) analysis and the PCR assay were used in combination with dilution plating on a semiselective medium to detect and enumerate propagules of Trichoderma hamatum 382, a biocontrol agent utilized in compost-amended mixes. Distinct and reproducible fingerprints were obtained upon amplification of purified genomic DNA of T. hamatum 382 with the random primers OPE-16, OPH-19, and OPH-20. Three amplified DNA fragments of 0.35 (OPE-160.35), 0.6 (OPH-190.6), and 0.65 (OPH-200.65) kb were diagnostic for T. hamatum 382, clearly distinguishing it from 53 isolates of four other Trichoderma spp. tested. Some isolates of T. hamatum shared these low-molecular-weight fragments with T. hamatum 382. However, RAPD analysis of isolates of T. hamatum with all three random primers used in consecutive PCR tests distinguishedT. hamatum 382 from other isolates of T. hamatum. These three RAPD amplicons were cloned and sequenced, and pairs of oligonucleotide primers for each cloned fragment were designed. Use of the primers in the PCR assay resulted in the amplification of DNA fragments of the same size as the cloned RAPD fragments from genomic DNA of T. hamatum 382. A combination of dilution plating on a semiselective medium forTrichoderma spp. and PCR, with the RAPD primers OPH-19, OPE-16, and OPH-20 or the three sequence-characterized primers, was used successfully to verify the presence of T. hamatum 382 propagules in nine different soil, compost, and potting mix samples. All 23 Trichoderma isolates recovered on semiselective medium from commercial potting mixes fortified with T. hamatum 382 were identified as T. hamatum 382, whereas 274 Trichoderma isolates recovered from the other nine samples were negative in the PCR assay. Thus, this highly specific combination of techniques allowed detection and enumeration of propagules of T. hamatum 382 in fortified compost-amended potting mixes. Sequence-characterized amplified region markers also facilitated the development of a very simple procedure to amplify DNA of T. hamatum 382 directly from fortified compost-amended potting mixes.

Assessment of polymorphism using RAPD in the generalized hemiparasitic plant Helicanthes elasticus (Desv.)Danser collected from six different hosts

2021 ◽  
Vol 16 (7) ◽  
pp. 141-149
Author(s):  
T.G. Ajithkumar ◽  
Mathew Lizzy ◽  
K.N. Sunil Kumar
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Rapd Analysis ◽  
Anacardium Occidentale ◽  
Random Primers ◽  
Citrus Maxima ◽  
Polymorphic Bands

RAPD analysis was carried out to determine genetic diversity that occurred among the selected accessions of H.elasticus obtained from six different hosts. All together 10 random primers were used for the RAPD assay, of which primer S11 produced 12 amplified bands in which 10 are polymorphic. Primer S9 produced the least number of amplified fragments. 10 primers together resulted in 88 amplified fragments, of which 26 are found to be polymorphic. Considerable polymorphism was shown by 3 primers that can be represented in a descending order S11>S79>S10. Accessions of H.elasticus obtained from Anacardium occidentale and Citrus maxima produced more polymorphic bands with S11. The overall polymorphism obtained in the selected samples of this hemiparasite was 29.54 indicating that genetic similarity was more among these samples rather than genetic diversity.

Phylogenetic relationships of five morphological groups of hexaploid wheat (Triticum aestivum L. em Thell.) based on RAPD analysis

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 724-727 ◽  
Author(s):  
Wenguang Cao ◽  
G Scoles ◽  
P Hucl ◽  
R N Chibbar
Keyword(s):  
Hexaploid Wheat ◽  
Phylogenetic Relationships ◽  
Genetic Similarity ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Triticum Aestivum L ◽  
Similarity Coefficients ◽  
Morphological Classification ◽  
Wild Wheat

The genetic relationships among the five groups of hexaploid wheat: common, spelta, macha, vavilovii, and semi-wild wheat (SWW) are not clear. Random amplified polymorphic DNA (RAPD) analysis was used to assess phylogenetic relationships among these five morphological groups of hexaploid wheat. RAPD data were analyzed using the NTSYS-PC computer program to generate Jaccard genetic similarity coefficients. A dendrogram based on RAPD analysis grouped 15 accessions into five distinct clusters. These results are in agreement with those based on morphological classification, suggesting that common wheat is most closely related to SWW, followed by spelta, vavilovii, and macha.Key words: RAPD, macha, spelta, vavilovii, semi-wild wheat, phylogenetic relationships.

scholarly journals The use of random amplified polymorphic DNA to evaluate the genetic variability of Ponkan mandarin (Citrus reticulata Blanco) accessions

2000 ◽  
Vol 23 (1) ◽  
pp. 169-172 ◽  
Author(s):  
Helvécio Della Coletta Filho ◽  
Marcos Antonio Machado ◽  
M. Luiza P.N. Targon ◽  
Jorgino Pompeu Jr.
Keyword(s):  
Genetic Variability ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Point Mutations ◽  
The Other ◽  
Citrus Reticulata ◽  
Random Primers ◽  
Citrus Reticulata Blanco ◽  
Ponkan Mandarin

RAPD analysis of 19 Ponkan mandarin accessions was performed using 25 random primers. Of 112 amplification products selected, only 32 were polymorphic across five accessions. The absence of genetic variability among the other 14 accessions suggested that they were either clonal propagations with different local names, or that they had undetectable genetic variability, such as point mutations which cannot be detected by RAPD.

scholarly journals RAPD-based analysis of differences between male and female genotypes of Asparagus officinalis

2012 ◽  
Vol 39 (No. 1) ◽  
pp. 33-37 ◽  
Author(s):  
Y. Ii ◽  
A. Uragami ◽  
Y. Uno ◽  
M. Kanechi ◽  
N. Inagaki
Keyword(s):  
Molecular Markers ◽  
Sex Determination ◽  
Genomic Dna ◽  
Asparagus Officinalis ◽  
Breeding Line ◽  
Male And Female ◽  
Future Studies ◽  
Random Primers

Asparagus (Asparagus officinalis L.) plants are dioecious. All-male cultivars are desired because of their higher yields. To increase the proportion of male individuals planted in the field and expedite the breeding of all-male cultivars in asparagus, development of generally applicable molecular markers to distinguish male and female individuals is required. Bulked genomic DNA samples from ten male (XY) and ten female (XX) plants was screened with 10-bp random primers. Of the 188 primers tested, the primer T35R54 produced a 1600-bp fragment observed only in male individuals. The specificity of this T35R54-1600 marker was verified using DNA from one supermale (YY) and one female (XX) breeding line and their four F<sub>1</sub> progenies (XY). The T35R54-1600 marker fragment was observed in both supermale and all-male lines. The sequence of the T35R54 primer (5'-TTCACGGTGG-3') was absent among the sequences of primers or amplified fragments from previous studies. Therefore, this marker could be useful as a sex-related marker in future studies to increase the reliability of sex determination in asparagus.

scholarly journals Deteksi dan analisis sekuen gen inhibitor proteinase pada beberapa klon kakao harapan tahan penggerek buah kakao dari Sulawesi Selatan Detection and sequence analysis of proteinase inhibitor gene in cacao clones putatively cacao pod borer-tolerant from South Sulawesi

2016 ◽  
Vol 72 (1) ◽  
Author(s):  
Abdul Mollah S. JAYA ◽  
Hajrial ASWIDINNOOR ◽  
Djoko SANTOSO
Keyword(s):  
Sequence Analysis ◽  
Proteinase Inhibitor ◽  
Genomic Dna ◽  
Genetic Similarity ◽  
Sequence Analyses ◽  
South Sulawesi ◽  
Pod Borer ◽  
Special Programs ◽  
Pcr Products ◽  
Alignment Analysis

Summary Cacao is socially and economically an important commodity for Indonesia, in which the cacao plantations have been challenged with a threatening pest, cacao pod borer (CPB). This research aimed to identify and clone PIN (proteinase inhibitor), a gene carrying resistance of plant to some chewing pests like CPB. The methodology included several experiments. Detection of PIN in cacao was done by PCR using PIN-specific heterologous primers and cacao genomic DNA as templates. Cloning vector pGEM-T was utilized to clone the PCR products. Sequence analysis was conducted with BlastX and Blast Special programs from NCBI. Alignment analysis to determine genetic similarity was performed with ClustalW from EBI. Thirteen of the 18 clones tested were detected to have PIN homologs. Two DNA fragments from cacao clones putatively tolerant to CPB, MJ-1 and LW-1, were sequenced. One of them, MJ-1 was cloned. Sequence analyses of the fragments of both cacao clones, indicated that they have PIN homologs and a very closed genetic relation with 96% level of similarity. Ringkasan Kakao adalah komoditas yang secara sosial maupun ekonomi penting bagi Indonesia, dimana perkebunan kakao menghadapi masalah serius hamapenggerek buah kakao (PBK). Penelitian ini bertujuan mengidentifikasi dan mengklon PIN (inhibitor proteinase), gen yang membawa sifat ketahanan tanaman terhadap hama ulat seperti PBK. Metodologinya terdiri dari beberapa percobaan. Deteksi PIN di dalam kakao dikerjakan dengan PCR menggunakan primer heterologous yang spesifik terhadap PIN dan DNA genomik kakao sebagai templetnya. Vektor kloning pGEM-T digunakan untuk mengklon produk PCR. Analisis sekuen dilakukan dengan program BlastX dan Blast spesial dari NCBI. Analisis penjajaran (alignment) untuk menentukan kemiripan genetik menggunakan program ClustalW dari EBI. Tiga belas dari 18 klon kakao yang diuji  menunjukkan adanya  homolog  PIN. Dua DNA fragmen dari klon harapan tahan, MJ-1 dan LW-1, telah ditentukan sekuen nukleotidanya. Satu diantara-nya, MJ-1 berhasil diklon. Analisis sekuen  kedua klon tersebut menunjukkan identitas sebagai homolog PIN dan keduanya memiliki kemiripan genetik yang tinggi.

scholarly journals 469 PB 336 INTER- AND INTRA-LINE GENOTYPIC VARIATION OF U. S. COLLARD CULTIVARS AND LANDRACES DETERMINED BY RAPD ANALYSIS

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 498d-498
Author(s):  
Mark W. Farnham
Keyword(s):  
Genetic Variation ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Genotypic Variation ◽  
Land Race ◽  
Commercial Cultivars ◽  
Polymorphic Bands ◽  
Line Analysis ◽  
Brassica Oleracea L

Collard (Brassica oleracea L. var. acephala) is an important vegetable the southeastern U. S. There are few (about 10) commercial cultivars, half being open-pollinating (OP) lines, the remainder more recent F1 hybrids. There is a potential untapped B. oleracea germplasm pool in the form of collard landraces perpetuated by southeastern gardeners and farmers. To determine the amount of genetic variation among cultivars and also whether landraces represent unique genotypes, ten cultivars and eight lines or landraces were evaluated using RAPD analysis. Decamer primers were used to amplify total genomic DNA and to differentiate collard lines and other B. oleracea crop cultivars. Additionally, individuals of an OP collard cultivar and a land-race were analyzed to evaluate intra-line variation. Virtually all primers detected polymorphic bands among lines although some identified considerably more variants. Intra-line analysis indicated that OP lines are genetically broad-based populations. Many unique RAPD markers were identified in landraces indicating that the lines represent unique genotypes and that further line collection is warranted.

scholarly journals Genetic Diversity in Muscadine and Bunch Grapes Based on RAPD Analysis

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 877A-877
Author(s):  
Jiang Lu ◽  
Xianping Qu ◽  
Olusola Lamikanra
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Cluster Analysis ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
The United States ◽  
Separate Study ◽  
Random Primers ◽  
And Cluster Analysis ◽  
Grape Cultivars

Two morphologically very distinct grapevines belonging to the subgenera Euvitis and Muscadinia of the genus Vitis are cultivated in the United States. The former is commonly called “bunch” grape, while the latter is usually called “muscadine.” Genetic diversity among these grapes was investigated based on random amplified polymorphic DNAs (RAPDs). Sixteen grape cultivars, with their parentage including V. rotundifolia, V. vinifera, and several American Vitis species, were used for the RAPD analysis. More than 200 RAPDs were produced from 20 random primers. More than 90% of which were polymorphic between the muscadine and the bunch grapes, while polymorphism was considerably low within the muscadine and the bunch grapes. The relationships of grapes between these two subgenera were estimated based on bandsharing and cluster analysis. The result based on the DNA analysis agrees with the isozyme data obtained from a separate study, which demonstrated that the muscadine grape shares very low common alleles with the American bunch grapes and the European grapes.

scholarly journals DNA Stability Contrasts with Chromosome Variability in Allium Fistulosum Calli

2014 ◽  
Vol 56 (1) ◽  
pp. 66-72 ◽  
Author(s):  
Patryk Mizia ◽  
Dagmara Kwolek ◽  
Tomasz Ilnicki
Keyword(s):  
Genetic Similarity ◽  
Chromosomal Instability ◽  
Selection Pressure ◽  
Dna Polymorphism ◽  
Rapd Analysis ◽  
Polymorphic Band ◽  
Genetic Changes ◽  
Band Frequency ◽  
Callus Lines

Abstract RAPD analysis was applied to assess the degree of DNA polymorphism in A. fistulosum calli of high chromosomal instability. Nineteen of 24 randomly selected RAPD primers revealed scorable polymorphism between calli and seeds (reference material). Polymorphic band frequency was 55/237 in seeds and 36/233 in calli; variability on the DNA level was thus lower in calli than in seeds (15.4% vs. 23.2% of band positions). UPGMA analysis of Jaccard's coefficients confirmed the genetic similarity of the analyzed cultures. The most distinctive DNA changes in calli involved coincident loss of original bands or the appearance of novel bands. Seven such changes (4 losses, 3 gains) were observed. Our results suggest that changes on the chromosomal level and on the DNA level occurred independently of each other and that different callus lines underwent similar genetic changes during culture, presumably due to strong selection pressure effected by standard in vitro conditions.

scholarly journals Analysis of intra-population variability of bald cypress (Taxodium distichum L. Rich.) in seed stand near Backa Palanka using RAPD markers

Genetika ◽  
2015 ◽  
Vol 47 (2) ◽  
pp. 571-580
Author(s):  
Vladan Popovic ◽  
Aleksandar Lucic ◽  
Danijela Ristic ◽  
Ljubinko Rakonjac ◽  
Sabahudin Hadrovic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Dna Markers ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Genetic Distances ◽  
Similarity Coefficients ◽  
Bald Cypress ◽  
Seed Stand

The analysis of Bald cypress genetic variability at the level of test trees was performed using RAPD (Random Amlified Polymorphic DNA) markers. RAPD analysis was performed on 20 test trees with 13 primers. A total of ten primers gave a clear picture while three primers amplified weakly. 60 is a total number of detected bands obtained by RAPD analysis with 10 selected primers, and the average number of bands is 6. Based on presence/absence of RAPD fragments among all 20 Bald cypress test trees were calculated similarity coefficients by Dice and they range from 0.73 to 1. Based on similarity coefficients was performed the cluster analysis and results were presented as a dendrogram. All 20 test trees were grouped into two sub-clusters. Test trees 1, 4 and 11 were grouped in the first sub-cluster while other test trees were grouped in the second sub-cluster. By analysis of relations within every sub-cluster and sub-sub-cluster the existence of genetic distances between observed test trees can be noticed. The greatest similarity is between test trees 2, 12, 15 and 18. The results of genetic similarity and distance between observed test trees indicate the overwhelming presence of genetic diversity.

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