scholarly journals Genetic diversity analysis in cashew (Anacardium occidentale L.) germplasm using RAPD marker

2019 ◽  
Vol 17 (4) ◽  
pp. 461-465
Author(s):  
T Bhadra ◽  
AZM Obaidullah ◽  
Mst Sabiha Sultana ◽  
M Ahmed ◽  
MM Islam
Keyword(s):  
Genetic Distance ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Climatic Conditions ◽  
Anacardium Occidentale ◽  
Cashew Nut ◽  
Major Cluster ◽  
The Family ◽  
Wide Potential

Anacardium occidentale L., commonly known as cashew nut, belongs to the family Anacardiaceae.  It is regarded as a high valued fruit nut crop world-wide. Potential of this economically important nut  is under-utilized in Bangladesh in spite of having all favorable agro-climatic conditions. The objective of the present investigation was to characterize six cashew accessions using Random Amplified Polymorphic DNA (RAPD) markers. Four random primers viz. OPE-02, OPE-18, OPK-03 and OPB-15 were used to amplify DNA segments. A total of 33 reproducible bands were obtained, out of which 11 were monomorphic and 22 were polymorphic. On average 74.12% polymorphism was observed. . Primers OPB-15 and OPK-03 yielded 100% polymorphism and OPE 02 and OPE 18 produced 33.33% and 63.16 % polymorphism, respectively. Cluster analysis revealed two main distinct groups, first group included GP-1 and the second consisted of five genotypes viz. GP-2, GP-3, GP-4, GP-5and GP-6 The major cluster- II was further subdivided into two minor clusters i.e. minor cluster- III and IV. Minor cluster- III contained only one genotype GP-4. Minor cluster- IV consists of four rest genotypes. The genetic distance between the groups was found low and varied from 0.002 to 0.0308. Maximum genetic distance was observed between GP-1 and GP-2cashew germplasm and minimum between GP-5 and GP-6. The low genetic distance which is unusual for this out crossing long-lived tree species, indicates the probability of having common ancestry among the germplasm or may be due to the use of a narrow range of populations for the investigation. J Bangladesh Agril Univ 17(4): 461–465, 2019

Genetic Variability and Relationships among Seventeen Trichoderma Isolates to Control Dry Root Rot Disease Using RAPD Markers

2008 ◽  
Vol 63 (9-10) ◽  
pp. 740-746 ◽  
Author(s):  
Kuruba Gopal ◽  
Yasodam Sreenivasulu ◽  
Venati Gopi ◽  
Gundala Prasadbabu ◽  
Teruvai Bharat Kumar ◽  
...  
Keyword(s):  
Root Rot ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Trichoderma Spp ◽  
Major Cluster ◽  
Rot Disease ◽  
And Cluster Analysis ◽  
The Relationship ◽  
Potential Antagonist

Trichoderma spp. has been identified as potential antagonist of Fusarium solani, which is causing dry root rot of Citrus. A random amplified polymorphic DNA (RAPD) marker was used to estimate the genetic variation among 17 isolates of Trichoderma. These isolates were characterized using 20 random primers of the OPM series, out of which 16 primers gave a total of 145 DNA fragments, showing 91.8% polymorphism. The genetic distance between each isolate was calculated, and cluster analysis was used to generate a dendrogram showing the relationship among them. The isolates grouped into two major clusters, the first major cluster consisted of TCT14, TCT17, TCT13, TCT12 and TCT16. The remaining isolates in the second major cluster separated in two sub-clusters; the first cluster consisted of TCT4, TCT10, TCT2, TCT3, TCT8, TCT6, TCT9, and the second sub-cluster consisted of TCT1 TCT15 TCT5, TCT11, and TCT7. The similarity matrix indicated that TCT6 and TCT13 were genetically distinct as they showed only 22.6% similarity followed by TCT5 and TCT16; TCT6 and TCT16 (25%), while the isolates TCT4 and TCT10 were found to be genetically similar, as 66.7% similarity was observed between the isolates followed by 61.3% similarity between the TCT2 and TCT4 isolates.

scholarly journals Assessment of Genetic Diversity of Chili Cultivars Using RAPD Markers

2013 ◽  
Vol 22 (2) ◽  
pp. 127-136
Author(s):  
MM Uddin ◽  
MI Khalil ◽  
MS Haque ◽  
MB Meah
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Plant Tissue ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Polymorphic Locus ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Genetic Identity ◽  
Cluster 2

Random amplified polymorphic DNA (RAPD) assay was performed to estimate genetic polymorphisim in ten chili cultivars. Out of 12 primers four (OPA11, OPB03, OPB04 and OPB17) showed amplification of genomic DNA and generated 21 distinct score able bands of which 17 (80.95%) were polymorphic. The highest percentage (85.71) polymorphic locus was found in OPB03 while the lowest (66.67) in OPA11. The highest genetic distance was computed between Jamalpur Balujuri and Matal marich with the lowest genetic identity as against the lowest genetic distance between Hajari marich and Balujuri marich. The UPGMA dendogram indicated segregation of ten chili varieties and genotypes into two main clusters. Variety Bogra marich and Matal marich formed cluster 1 and Balujuri marich, Deshi marich, Jamalpuri balujuri, Bindu marich, Syloti, Hajari, Biroli city, and the genotype Ausadhebrara grouped in cluster 2. The result indicates the genetic diversity among the chili cultivars and RAPD marker could be used for improvement of chili varieties. DOI: http://dx.doi.org/10.3329/ptcb.v22i2.14201 Plant Tissue Cult. & Biotech. 22(2): 127-136, 2012 (December)

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.

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.

Molecular Diversity Analysis of Lentil (Lens culinaris Medik.) through RAPD Markers

2012 ◽  
Vol 22 (1) ◽  
pp. 51-58 ◽  
Author(s):  
M.E. Hoque ◽  
M.M. Hasan
Keyword(s):  
Genetic Distance ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Group Method ◽  
Diversity Analysis ◽  
Pair Group ◽  
Molecular Genetic Diversity

Random Amplified Polymorphic DNA (RAPD) markers were used to study the molecular genetic diversity analysis among six BARI released lentil varieties viz. BARI masur-1, BARI masur-2, BARI masur-3, BARI masur-4, BARI masur-5 and BARI masur-6. PCR amplified products were visualized on 1.0% agarose gel and the band for each primer were scored. Ten RAPD markers were used in this study. Out of them 7 primers showed amplification of 53 DNA fragments with 60.37% of them being polymorphic. The highest number of polymorphic loci was noticed in the variety BARI masur-3. The same variety also showed maximum Nei’s gene diversity value (0.0552). The highest Nei’s genetic distance (0.5002) was observed in BARI masur-1 vs. BARI masur-5 whereas, the lowest genetic distance (0.0692) was found in BARI masur-1 vs. BARI masur-2. The unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Nei’s genetic distance grouped the six cultivars into two main clusters. BARI masur-1, BARI masur-2 and BARI masur-3 were in cluster I and BARI masur-4, BARI masur-5 and BARI masur-6 were in cluster II. The cultivar BARI masur-4 was closest to the cultivar BARI masur-6 with the lowest genetic distance (0.0972) and the highest genetic distance (0.5002) was found between BARI masur-1 and BARI masur-5. The RAPD markers were found to be useful in molecular characterization of lentil varieties which could be utilized by the breeders for the improvement of lentil cultivars. DOI: http://dx.doi.org/10.3329/ptcb.v22i1.11260 Plant Tissue Cult. & Biotech. 22(1): 51-58, 2012 (June)

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.

Rapd variation of late-maturing sorghum [ Sorghum bicolor (L.) Moench] landraces from Ethiopia

2007 ◽  
Vol 55 (3) ◽  
pp. 375-382 ◽  
Author(s):  
S. Mamo ◽  
A. Ayana ◽  
T. Tesso
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Sorghum Bicolor ◽  
Rapd Markers ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
The Mean ◽  
Polymorphic Bands ◽  
High Degree ◽  
Sorghum Bicolor L

A study on the extent and pattern of genetic variability in late-maturing sorghum [ Sorghum bicolor (L.) Moench] landraces collected from the Wello and Hararge areas of Ethiopia was conducted using random amplified polymorphic DNA (RAPD) markers for 70 individuals representing 14 populations. Four oligonucleotide primers generated a total of 55 polymorphic bands with 13–19 bands per primer and a mean of 16 bands across the 70 individuals. The value of the Shannon diversity index among the populations (0.26) and between the two regions (0.24) was low to moderate, despite the high degree of polymorphic bands per primer. The mean genetic distance (0.25) between the populations was found to be low. The low genetic variation may be due to the reduced population size of late-maturing sorghum landraces in the two regions of Ethiopia because of farmers’ decisions in the process of planting, managing, harvesting and processing their crops. Partitioning of the genetic variation into variation between and within the population revealed that 92.9% and 7.10% of the variation was found to be between and within the populations, respectively. Cluster analysis of genetic distance estimates further confirmed a low level of differentiation in late-maturing sorghum populations both between and within the regions. The implications of the results for genetic conservation purposes are discussed.

scholarly journals Vegetation Types, Climatic Conditions and Trigona sp. Honey Quality in Onewila Village, Ranomeeto District South Konawe Regency

2020 ◽  
Vol 9 (1) ◽  
pp. 57-63
Author(s):  
Aminuddin Mane Kandari ◽  
Zakiah Uslinawaty ◽  
Muh. Ilton
Keyword(s):  
Air Temperature ◽  
Coffea Arabica ◽  
Cocos Nucifera ◽  
Climatic Conditions ◽  
Anacardium Occidentale ◽  
National Standard ◽  
Vegetation Types ◽  
Cashew Nut ◽  
Areca Catechu

Kandari AM, Uslinawaty Z, Ilton M. 2020. Vegetation types, climatic conditions and Trigona sp. honey quality in Onewila Village, Ranomeeto district South Konawe Regency. Jurnal Lahan Suboptimal: Journal of Suboptimal Lands 9(1):57-63.Forests in Indonesia have considerable potential because besides being used in the form of wood for various purposes, it also has the potential of non-timber products that can be used for various things, one of which is as a vegetation for honey bees, especially bees Trigona sp.This study aims to identification of vegetation types, climatic conditions and honey quality of Trigona sp. in the Onewila village, Ranomeeto District South Konawe Regency. The observed variables were vegetation, temperature, rainfall, and honey quality based on SNI 2013 standards. The results found the vegetation types at the cultivation location was Caliandra (Caliandra calothyrsus =10), coconut (Cocos nucifera = 12), teak (Tectona grandis= 20), peat (Syzygium polycephalum Merr = 7), mango (Mangifera indica =5), langsat (Lansium domesticum =15), kedondong (Spondias dulcis =3), guava (Psidium guajava =4), areca (Areca catechu = 10), coffee (Coffea Arabica = 15), cashew nut (Anacardium occidentale =15), areca nut (Areca catechu), coffee (Coffea arabica), cashew nut (Spondias dulcis), Cashew nut (Anacardium occidentale = 15), Sirsak ((Annona muricata = 2), and asoka flowers (Saraca asoka= 5). The air temperature and rainfall conditions in the location is very supportive of Trigona cultivation because the average of air temperature ranges from 29oC, and the average monthly rainfall at Ranomeeto station is highest in January (135 mm) and lowest in August (16.8 mm). The honey quality of Trigona sp, from several variables such as water content, acidity, HMF levels, and reducing sugar levels are 16.98%, 33.94 mg/kg, 17.3 mg/kg, 69.31 % b/b. This means that the honey quality of Trigona sp found in Onewila village meets the Indonesian National Standard (SNI 01-3545-2013 2013).

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 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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