scholarly journals Associating Molecular Markers with Virus Resistance to Classify Sweetpotato Genotypes

2005 ◽  
Vol 130 (3) ◽  
pp. 355-359 ◽  
Author(s):  
M. Mcharo ◽  
D. LaBonte ◽  
R.O.M. Mwanga ◽  
A. Kriegner
Keyword(s):  
Molecular Markers ◽  
Qtl Analysis ◽  
Ipomoea Batatas ◽  
Rapd Markers ◽  
Dna Marker ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Multivariate Techniques ◽  
Accuracy Rates

Molecular markers linked to resistance to sweetpotato chlorotic stunt closterovirus [SPCSV (genus Crinivirus, family Closteroviridae)] and sweetpotato feathery mottle virus [SPFMV (genus Potyvirus, family Potyviridae)] were selected using quantitative trait loci (QTL) analysis, discriminant analysis and logistic regression. Eighty-seven F1 sweetpotato [Ipomoea batatas (L.) Lam.] genotypes from a cross of `Tanzania' and `Wagabolige' landraces were used to generate DNA marker profiles for this study. Forty-five of the clones were resistant to SPCSV while 37 were resistant to SPFMV. A combination of 232 amplified fragment length polymorphism (AFLP) markers and 37 random amplified polymorphic DNA (RAPD) markers obtained were analyzed to determine the most informative markers. All three statistical procedures revealed that AFLP marker e41m33.a contributed the greatest variation in SPCSV resistance and RAPD marker S13.1130 accounted for most of the variation in SPFMV resistance. The power of discriminant and logistic analyses is that you do not need a parent-progeny population. An evaluation of these two models indicated a classification and prediction accuracy rates of 96% with as few as four markers in a model. Both multivariate techniques identified one important discriminatory marker (e44m41.j) for SPCSV and two markers (e41m37.a and e44m36.d) for SPFMV that were not identified by QTL analysis.

scholarly journals Keragaman Genetik Beberapa Genotipe Teh Berdasarkan Penanda RAPD (Random Amplified Polymorphic DNA)

2014 ◽  
Vol 1 (1) ◽  
pp. 1 ◽  
Author(s):  
Budi Martono ◽  
Laba Udarno
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Camellia Sinensis ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Dna Marker ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Plant Breeding Program ◽  
Marker Loci

<p>Informasi keragaman genetik dan ketersediaan plasma nutfah teh (Camellia sinensis) diperlukan dalam perakitan varietas unggul. Keragaman genetik berdasarkan penanda DNA dapat memberikan hasil yang lebih konsisten karena tidak dipengaruhi lingkungan. Dalam penelitian ini sebanyak 9 genotipe teh dianalisis keragamannya menggunakan enam penanda RAPD (OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, dan OPD 08). Penelitian dilakukan mulai bulan Maret sampai Mei 2013 di Laboratorium Terpadu Biotrop Bogor. Perhitungan koefisien kesamaan genetik dan analisis gerombol dilakukan dengan menggunakan perangkat lunak NTSYSpc versi 2.02. Sebanyak 54 lokus penanda RAPD berhasil diamplifikasi menggunakan enam primer dan 47 lokus di antaranya memiliki alel yang polimorfik (87,04%). Hasil analisis gerombol berdasarkan kesamaan genetiknya mengelompokkan 9 genotipe ke dalam enam kelompok. Empat kelompok (I, II, IV, V) masing-masing terdiri atas satu genotipe, sementara dua kelompok yang lain yaitu kelompok III dan VI masing-masing beranggotakan tiga dan dua genotipe.</p><p>Kata Kunci: Camellia sinensis, diversitas genetik, penanda RAPD</p><p>The availability of diverse tea (Camellia sinensis) germplasms as well as the information about their genetic diversity is required for plant breeding program. Genetic diversity analysis based on DNA marker is known to be more effective since the markers provide more consistent results. In this study, nine tea genotypes were evaluated for their genetic diversity using six Random Amplified Polymorphic DNA (RAPD) markers (OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, and OPD 08). The study was conducted from March to May 2013 in the Integrated Laboratory of Biotrop Bogor. The estimation of genetic similarity and the cluster analysis were done using NTSYSpc version 2.02. Of the six RAPD markers used in this study, a total of 54 RAPD marker loci have been successfully amplified. In which, 47 loci (87.04%) were polymorphic and subsequently used for the evaluation of tea genotypes. The results of cluster analysis showed that those tea genotypes were clustered into six groups. Each of four groups (I, II, IV, V) consisted of only one genotype. Meanwhile, the other two groups (III and VI) had three and two genotypes, respectively.</p>

scholarly journals Segregation for Resistance to Eastern Filbert Blight in Progeny of `Zimmerman' Hazelnut

2006 ◽  
Vol 131 (6) ◽  
pp. 731-737 ◽  
Author(s):  
China F. Lunde ◽  
Shawn A. Mehlenbacher ◽  
David C. Smith
Keyword(s):  
Rapd Markers ◽  
Chromosome Region ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Segregation Ratio ◽  
Enzyme Linked Immunosorbent Assay ◽  
Resistance Locus ◽  
Resistance Allele ◽  
Reciprocal Translocations ◽  
Eastern Filbert Blight

Eastern filbert blight (EFB), caused by the fungus Anisogramma anomala (Peck) E. Müller, is an important disease of european hazelnut (Corylus avellana L.) in the Pacific northwestern United States. In 1989, a chance seedling free of EFB was discovered adjacent to a severely diseased orchard near Troutdale, Ore. This selection, subsequently named `Zimmerman', was crossed with three susceptible selections. Based on morphological characters and incompatibility alleles, we speculated that `Zimmerman' (S1 S3) was a hybrid between `Barcelona' (S1 S2) and `Gasaway' (S3 S26). The three seedling populations were inoculated with spores of the pathogen in a greenhouse test and assayed by indirect enzyme-linked immunosorbent assay (ELISA) and by observation of canker incidence. The observed segregation fit a 3 resistant : 1 susceptible ratio in all three progenies, in contrast to the 1 : 1 ratio found when the resistant pollinizer `Gasaway' was crossed to susceptible genotypes. Random amplified polymorphic DNA (RAPD) marker UBC 152800 linked to the resistance gene in `Gasaway' co-segregated with the resistant phenotype in all three populations with 2%, 4%, and 6% recombination, respectively. Seed germination and transplanting records did not provide evidence of selection in favor of resistant seedlings. Pollen germination was 71% in `Gasaway', 29% in `Zimmerman', and 18% in `Barcelona', indicating possible selection at the gametophytic level. Subsequently 16 resistant seedlings of `Zimmerman' were crossed with the highly susceptible selection OSU 313.078. Segregation fit a 3 : 1 ratio in 14 of the 16 progenies, and showed a surplus of resistant seedlings in the other two. None showed a 1 : 1 segregation. Resistance co-segregated with two RAPD markers that flank the `Gasaway' resistance allele. To test allelism of resistance from `Gasaway' and `Zimmerman', VR 6-28 with resistance from `Gasaway' was crossed with `Zimmerman'. Eight resistant selections from this progeny were crossed with OSU 313.078. Five of the eight progenies segregated 3 : 1, two progenies segregated 1 : 1, and OSU 313.078 × OSU 720.056 gave only resistant offspring. The ratios indicate that OSU 720.056 is homozygous resistant and that `Zimmerman' and `Gasaway' share a common resistance allele. Reciprocal translocations have been reported in hazelnut cultivars, including `Barcelona', the leading cultivar in Oregon. `Zimmerman' appears to be a hybrid of `Barcelona' and `Gasaway', but because of cytogenetic abnormalities, `Zimmerman' may have inherited two copies of the chromosome region that contain the resistance locus and flanking RAPD markers. If the region containing the resistance were attached to two independent centromeres, a 3 : 1 segregation ratio for disease response and flanking markers would be expected, and we propose this as the most likely explanation. Resistance from `Gasaway' and `Zimmerman' has been called “immunity” or “complete resistance.” However, we noted a few seedlings with small cankers, nearly all of which lacked sporulating stromata. Flanking RAPD markers indicate that the resistance allele is present in these seedlings. Although not “immune” or “completely resistant,” `Gasaway' and `Zimmerman' transmit a very high level of resistance.

Identification of restriction fragment length polymorphism and random amplified polymorphic DNA markers linked to downy mildew resistance genes in lettuce, using near-isogenic lines

Genome ◽  
1991 ◽  
Vol 34 (6) ◽  
pp. 1021-1027 ◽  
Author(s):  
Ilan Paran ◽  
Richard Kesseli ◽  
Richard Michelmore
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Rapd Markers ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Near Isogenic Lines ◽  
Isogenic Lines ◽  
Restriction Fragment Length

Near-isogenic lines were used to identify restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers linked to genes for resistance to downy mildew (Dm) in lettuce. Two pairs of near-isogenic lines that differed for Dm1 plus Dm3 and one pair of near-isogenic lines that differed for Dm11 were used as sources of DNA. Over 500 cDNAs and 212 arbitrary 10-mer oligonucleotide primers were screened for their ability to detect polymorphism between the near-isogenic lines. Four RFLP markers and four RAPD markers were identified as linked to the Dm1 and Dm3 region. Dm1 and Dm3 are members of a cluster of seven Dm genes. Marker CL922 was absolutely linked to Dm15 and Dm16, which are part of this cluster. Six RAPD markers were identified as linked to the Dm11 region. The use of RAPD markers allowed us to increase the density of markers in the two Dm regions in a short time. These regions were previously only sparsely populated with RFLP markers. The rapid screening and identification of tightly linked markers to the target genes demonstrated the potential of RAPD markers for saturating genetic maps.Key words: lettuce, downy mildew, near-isogenic lines, disease resistance, restriction fragment length polymorphism, random amplified polymorphic DNA.

Segregation of random amplified polymorphic DNA markers and strategies for molecular mapping in tetraploid alfalfa

Genome ◽  
1993 ◽  
Vol 36 (5) ◽  
pp. 844-851 ◽  
Author(s):  
K. F. Yu ◽  
K. P. Pauls
Keyword(s):  
Chromosome Segregation ◽  
Dna Markers ◽  
Rapd Markers ◽  
Molecular Mapping ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Female Parent ◽  
Linkage Groups ◽  
Double Reduction ◽  
Chromatid Segregation

An F1 population was used to analyze the inheritance of random amplified polymorphic DNA (RAPD) markers in tetraploid alfalfa. Of the 32 RAPD markers that were used for a segregation analysis in this study, 27 gave ratios that are consistent with random chromosome and random chromatid segregation at meiosis. However, among all of the RAPD markers (121) that were screened in this study, only one example of a double reduction, that is typical of chromatid segregation, was observed. These results indicate that random chromosome segregation is likely the predominant but not the exclusive mode of inheritance for tetraploid alfalfa. χ2 analyses of cosegregation for RAPD marker pairs derived from the female parent revealed nine linkages that fell into four linkage groups. The recombination fractions among linked marker pairs ranged from 1 to 37%. These are the first molecular linkage groups reported in tetraploid alfalfa. In addition, various strategies for molecular mapping in the tetraploid alfalfa genome are proposed that should be of interest to plant breeders who are planning to use molecular markers for alfalfa or other tetraploid species.Key words: RAPD markers, tetraploid alfalfa, segregation, linkage groups.

scholarly journals Phenotype Instability in Botrytis cinerea in the Absence of Benzimidazole and Dicarboximide Fungicides

2001 ◽  
Vol 91 (3) ◽  
pp. 307-315 ◽  
Author(s):  
L. F. Yourman ◽  
S. N. Jeffers ◽  
R. A. Dean
Keyword(s):  
Botrytis Cinerea ◽  
High Frequency ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Potato Dextrose Agar ◽  
Multiple Generations ◽  
Rapd Fingerprints ◽  
Growth Room ◽  
Conidium Germination

Stability of phenotypes of isolates of Botrytis cinerea that were sensitive or resistant to benzimidazole and dicarboximide fungicides was examined in the absence of fungicides in laboratory and growth room experiments. Twelve greenhouse isolates of B. cinerea were subcultured on potato dextrose agar (PDA) for 20 generations and on geranium seedlings for 15 generations. Three isolates of each of the following four phenotypes were used: sensitive to the fungicides thiophanate-methy1 (a benzimidazole) and vinclozolin (a dicarboximide) (STSV), resistant to both fungicides (RTRV), resistant to thiophanate-methy1 and sensitive to vinclozolin (RTSV), and sensitive to thiophanate-methy1 and resistant to vinclozolin (STRV). In three trials on PDA, 36 populations were subcultured; 8 populations changed phenotypes by the end of 20 generations, as determined by conidium germination on fungicide-amended medium. Five of the eight initially were STRV; the resulting phenotypes were STSV, RTSV, and RTRV. Populations from eight other isolates exhibited temporary changes in phenotype during intermediate generations on PDA but reverted to initial phenotypes by the twentieth generation; five of these populations changed to phenotype RTRV. In two geranium seedling trials, each of the 12 greenhouse isolates was inoculated onto a set of three seedlings for each generation, and diseased tissue that developed was used to initiate the next generation. Therefore, a total of 72 populations of B. cinerea were subcultured in the two trials; 5 of these populations changed phenotype at the end of 15 generations. Three of the five initially were STRV; these changed to phenotypes STSV or RTRV. In each of the two trials on geranium seedlings, a population subcultured from one STSV isolate changed phenotype one to phenotype RTRV and one to phenotype RTSV. In all trials, no population resistant to thiophanate-methy1 changed to a thiophanate-methy1-sensitive phenotype, and no population changed to phenotype STRV. Random amplified polymorphic DNA (RAPD) fingerprints were generated with the 12 initial isolates and 49 isolates subcultured on PDA or geranium seedlings. Cluster analyses of RAPD markers showed that subcultured isolates exhibiting the same phenotype clustered together and that subcultured isolates derived from a common greenhouse isolate but with different phenotypes were in different clusters. Some populations that did not change phenotype exhibited considerable differences in RAPD marker patterns. The results of this study indicate that, in the absence of fungicides, sensitive populations of B. cinerea can develop resistance to thiophanate-methy1 and vinclozolin, and this resistance can be maintained in populations through multiple generations. Populations resistant only to vinclozolin (STRV) exhibited a high frequency of phenotype change, and populations resistant to both fungicides (RTRV) were stable.

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 Molecular Evaluation of Three Populations of Farafra Sheep in Comparison to Ossimi and Rahmani Sheep Breeds

2020 ◽  
Vol 68 (6) ◽  
pp. 929-936
Author(s):  
Talaat Bashandy ◽  
Ahmed Hussein ◽  
Mohamed Solma ◽  
Ayman Kassab ◽  
Hatem Hamdon
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Rapd Marker ◽  
Sheep Breeds ◽  
Main Cluster ◽  
Ideal Approach ◽  
Different Populations ◽  
The Mean ◽  
Molecular Evaluation

Molecular markers are the most ideal approach to study genetic diversity. Consequently, we utilized both ISSR and RAPD markers to assess genetic diversity and relationships among three different populations of Farafra, Ossimi and Rahmani Egyptian sheep breeds. Both ISSR and RAPD gave moderate polymorphism 41.3% and 48.51%, respectively. Besides, this value was consistent with the moderate value of the mean of polymorphism information content (0.16 and 0.20, respectively). Farafra-F and Farafra-D populations had the highest similarity which was 0.92 for ISSR and 0.90 for the RAPD marker. Furthermore, ISSR and RAPD constructed dendrogram separated all the studied sheep into two main clusters. All the three populations of Farafra breed combined into one main cluster, while the second cluster contained both Rahmani and Ossimi breeds. The used molecular markers were able to discriminate among evaluated sheep and displayed that Farafra breed more closely related to Ossimi than Rahmani breed.

scholarly journals 666 PB 110 RANDOM AMPLIFIED POLYMORPHIC DNA MARKERS ARE INADEQUATE FOR FINGERPRINTING GRAPE ROOTSTOCKS

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 528c-528
Author(s):  
Alan T. Bakalinsky ◽  
Hong Xu ◽  
Diane J. Wilson ◽  
S. Arulsekar
Keyword(s):  
Dna Markers ◽  
Rapd Markers ◽  
Restriction Site ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Base Length ◽  
Specific Primer ◽  
Annealing Temperatures ◽  
Individual Reaction ◽  
Length Variant

A total of eight random amplified polymorphic DNA (RAPD) markers were generated in a screen of 77 primers of 10-base length and were detected reproducibly among nine different grape (Vitis) rootstocks. Occasional failed amplifications could not be explained rationally nor easily corrected by systematic replacement of individual reaction components. In an effort to improve their reliability, the RAPD markers were cloned, their termini sequenced, and new sequence-specific primer pairs were synthesized based on addition of 10 to 14 bases to the 3' termini of the original 10-mers. Six pairs of the new primers were evaluated at their optimal and higher-than optimal annealing temperatures. One primer pair amplified a product the same size as the original RAPD marker in all rootstocks, resulting in loss of polymorphism. Post-amplification digestion with 7 different restriction endonucleases failed to reveal restriction site differences. Three primer pairs amplified an unexpected length variant in some accessions. Two other pairs of primers amplified a number of unexpected bands. Better approaches for exploiting the sequence differences that account for the RAPD phenomenon will be discussed.

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 Random Amplified Polymorphic DNA Analysis of Garlic (Allium sativum L.) Germplasm Collection

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 452F-452
Author(s):  
M.M. Jenderek ◽  
K.A. Schierenbeck ◽  
R.M. Hannan
Keyword(s):  
Rapd Markers ◽  
Allium Sativum ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Pcr Amplification ◽  
Germplasm Collection ◽  
Plant Introduction ◽  
Germplasm Collections ◽  
Dna Template

Maintenance of garlic (A. sativum L.) germplasm collections is based on year-to-year vegetative propagation of individual accessions. Several accessions are phenotypically similar, often originating from the same region of the world, but have been collected by different people at different times. These accessions are currently maintained as separate and unique samples, but may represent genetic duplication in the collection. In order to identify genetic duplication in the USDA collection, 45 garlic Plant Introduction accessions from the garlic USDA germplasm collection were analyzed for RAPD marker polymorphism. The samples originated from 20 countries worldwide. RAPD bands were generated by 20 decamer primers, using 100-ng DNA template, and 38 PCR amplification cycles. Polymorphism between accessions was defined as presence or absence of particular bands at given loci. However, a few distinguishing RAPD markers were established for selected accessions, identifying additional molecular markers to wholly assess the similarities or polymorphism of the garlic collection units is necessary.

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