Displaying publications 1 - 20 of 81 in total

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  1. Fulltext Development of species-specific SCAR markers for identification and authentication of three rare Peninsular Malaysian endemic Coelogyne (Orchidaceae) orchids
    Kok Hon Y, Yong CS, Abdullah JO, Go R
    F1000Res, 2020;9:1161.
    PMID: 33299554 DOI: 10.12688/f1000research.26170.2
    Background:Coelogyne kaliana, Coelogyne stenochila and Coelogyne tiomanensis are three valuable rare orchid species endemic to Peninsular Malaysia, currently rampantly traded illegally via the internet and through local nurseries, which label them as hybrids to avoid enforcement detection. Drastic measures to ensure the continued existence of their populations in the wild should be introduced as they are rapidly diminishing into extinction, including the development of rapid and accurate species-specific identification tools. These three orchid species are highly similar morphologically and currently it is impossible to distinguish among them without their reproductive structures. Methods:  RAPD-based species-specific SCAR markers were developed to distinguish and authenticate the identity of these three endemic Peninsular Malaysian Coelogyne species. Results: Three SCAR markers were successfully developed in this study. SCAR marker primer pair , CKL_f / CKL_r was specific to C. kaliana as it produced a unique single band of 271 bp but not in C. stenochila and C. tiomanensis.  SCAR marker primer pair CST_f / CST_r amplified a single band of 854 bp in C. stenochila and two bands of different sizes (372 bp and 858 bp) in C. tiomanensis, but no amplification in C. kaliana. The third SCAR marker primer pair, CTI_f / CTI_r produced a single band (about 500 bp) for both C. stenochila and C. tiomanensis, but showed no amplification in C. kaliana. Conclusions: Although not all these SCAR markers were species amplification specific, they could be used to discriminate among the three Coelogyne species effectively.  Accurate species identification is one of the most important steps to allow a proper management plan to be established in the effort to conserve these three endangered orchid species of Peninsular Malaysia. Besides, it could effectively put a stop to the illegal trading of these rare endangered orchid species worldwide.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
  2. Fulltext Genetic relationship among Labisia pumila (Myrsinaceae) species based on ISSR-PCR
    Karimi E, Jaafar HZ, Aziz MA, Taheri S, AzadiGonbad R
    Genet. Mol. Res., 2014;13(2):3301-9.
    PMID: 24841662 DOI: 10.4238/2014.April.29.8
    The genus Labisia (Myrsinaceae) is a popular medicinal plant in Malaysia. We examined the genetic relationship among three varieties of L. pumila var. pumila, L. pumila var. alata, L. pumila var. lanceolata and Labisia paucifolia using an ISSR assay. Fifty-eight primers were tested, among which 18 gave reliable polymorphic banding patterns; these yielded 264 polymorphic markers. A similarity matrix was used to construct a dendrogram, and a principal component plot was developed to examine genetic relationships among varieties. Jaccard's similarity coefficient among species ranged from 0.09 to 0.14. At a similarity of 0.117%, species were divided into two main clusters. The mean value of the observed number of alleles, the effective number of alleles, mean Nei's gene diversity, and Shannon's information index were 1.98, 1.64, 0.38, and 0.57, respectively.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique*
  3. Fulltext Antibodies against citrullinated proteins in relation to periodontitis with or without rheumatoid arthritis: a cross-sectional study
    Lew PH, Rahman MT, Safii SH, Baharuddin NA, Bartold PM, Sockalingam S, et al.
    BMC Oral Health, 2021 07 20;21(1):360.
    PMID: 34284769 DOI: 10.1186/s12903-021-01712-y
    BACKGROUND: Previous studies have reported conflicting findings between serum anti-citrullinated protein antibodies (ACPA) levels in rheumatoid arthritis (RA) participants with and without periodontitis (Pd). This study aimed to analyse possible correlations between serum ACPA levels and clinical parameters in Pd and RA participants.

    METHODS: Full mouth periodontal examination (probing pocket depth, clinical attachment levels, gingival bleeding index, visual plaque index) was conducted and serum samples obtained from 80 participants comprising RA, Pd, both RA and Pd (RAPd) and healthy individuals (HC). Erythrocyte sedimentation rates (ESR) and periodontal inflamed surface area (PISA) were obtained. Serum samples were analysed for ACPA quantification using enzyme-linked immunosorbent assay (ELISA).

    RESULTS: Median levels (IU/mL) of ACPA (interquartile range, IQR) in RAPd, RA, Pd and HC groups were 118.58(274.51), 102.02(252.89), 78.48(132.6) and 51.67(91.31) respectively. ACPA levels were significantly higher in RAPd and RA as compared to HC group (p  RA > Pd > HC. However, lack of any significant correlation between the serum ACPA levels with the clinical Pd and RA parameters warrants further studies to investigate the causal link between RA and Pd for such a trend. Further studies involving more inflammatory biomarkers might be useful to establish the causal link between Pd in the development and progression of RA or vice versa.

    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
  4. Fulltext Antibiotic susceptibility and genotyping by RAPD of Campylobacter jejuni isolated from retailed ready-to-eat sushi
    Tan, Y.F., Haresh, K.K., Chai, L.C., Son R.
    International Food Research Journal, 2009;16(1):31-38.
    MyJurnal
    A study to determine the antibiotic sensitivity pattern and genotyping using RAPD-PCR was performed on 50 C. jejuni isolated from sushi retailed in different supermarkets. With less than half of the isolates susceptible to the antibiotics tested, resistant to two or more antibiotics were observed in most of the isolates. The banding patterns obtained from RAPD-PCR revealed that no predominant clone exists and the bacterial population is rather diverse. Hence, the resistance of the C. jejuni to different classes of antibiotic as well as their diverse genotypes suggests that these C. jejuni isolates were generated from different sources in the contaminated supermarkets where sushi were retailed. Our data showed that C. jejuni can be an important reservoir for resistance genes and that study with comprehensive collections of samples are urgently required to establish better measures to reduce or eliminate the risk from antibiotic resistant and pathogenic bacteria originating from minimally processed ready-to-eat food.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
  5. SCAR markers and multiplex PCR-based identification of isomorphic species in the Anopheles dirus complex in Southeast Asia
    Manguin S, Kengne P, Sonnier L, Harbach RE, Baimai V, Trung HD, et al.
    Med Vet Entomol, 2002 Mar;16(1):46-54.
    PMID: 11963981
    The Anopheles dirus Peyton & Harrison complex of mosquitoes (Diptera: Culicidae) comprises seven known species, including important malaria vectors in Southeast Asia. Specific identification of each species of the complex, which cannot be distinguished using morphological characters, is crucial for understanding vector ecology and implementing effective control measures. Derived from individual random amplified polymorphic DNA (RAPD) markers, sequence characterized amplified regions (SCAR) were analysed for the design of specific paired-primers. Combination of six SCAR primers resulted in the development of a simple, robust, single multiplex PCR able to identify three important malaria vectors among the four most common species (A, B, C, D) of the complex: species A from several Southeast Asian countries, species B from Perlis, Malaysia, and species C and D from Thailand.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique/methods; Random Amplified Polymorphic DNA Technique/veterinary*
  6. Fulltext Genetic diversity of Sabah rice cultivars using random amplified polymorphic dna (rapd) markers
    Alvina Simon, Vijay Kumar Subbiah, Chee, Fong Tyng, Noor Hydayaty Md Yusuf
    Borneo International Journal of Biotechnology, 2020;1(1):35-43.
    MyJurnal
    Rice is the most important staple crop in Malaysia and is cultivated all over the country, including the state of Sabah. The uniqueness of rice cultivation in Sabah lies in the type of rice itself, deriving mainly from local or non-commercial cultivars but with distinctive characteristics including long grains, aromatic properties, and drought tolerance. However, despite having these important agricultural traits, information on the genetic diversity of Sabah rice remains limited. Hence, the purpose of this study was to determine the genetic polymorphisms of Sabah rice using random amplification of polymorphic DNA (RAPD) markers. A total of 101 alleles were profiled, from which 94% were identified as polymorphic. Phylogenetic analysis grouped the rice samples into three clusters, with two clusters classifying the ability of rice to grow under different planting conditions, suitable for growth irrigate and upland condition. The first cluster was dominated by cultivars that could survive in wet (irrigated) areas, while the other featured those that were found in dry (upland) areas. Furthermore, two alleles, OPA-05-B2 and OPA-01-B11, were found to be unique to cultivars within the upland cluster and were thus proposed to be involved in dry environmental adaptation. The results of the present study provide an insight into the genetic relationships and diversity of Sabah rice.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
  7. Fulltext Random amplified polymorphic DNA-PCR and ERIC PCR analysis on Vibrio parahaemolyticus isolated from cockles in Padang, Indonesia
    Zulkifli, Y., Alitheen, N.B., Son, R., Raha, A.R., Samuel, L., Yeap, S.K., et al.
    International Food Research Journal, 2009;16(2):141-150.
    MyJurnal
    In this study, RAPD-PCR and ERIC-PCR were used to study the epidemiology of V. parahaemolyticus isolated from cockles in Padang, Indonesia. The Gold Oligo OPAR3 primer produced bands ranged from 1-8 with sizes from 0.2 – 5.0 kb and the Gold Oligo OPAR8 primer produced 1-7 bands with sizes 0.7 – 1.5 kb. Both primers produced twenty five RAPD patterns with a few isolates failed to produce any products. Based on phylogenetic dendrogram, all the isolates can be divided into 6 major clusters with similarity between 0 to 52%. For the ERIC primer, it produced bands ranged from 3-15 with sizes from 0.1 – 5.0 kb and twenty seven different ERIC patterns. Construction of the phylogenetic dendogram showed the isolates can be divided into 4 major clusters with similarity between 56 to 86%. The high diversity of both processes may be due to the multiple contamination sources of V. parahaemolyticus.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
  8. Fulltext Characterization of enterobacter cloacae isolated from street foods
    Haryani, Y., Tunung, R., Chai, L.C., Lee, H.Y., Tang, S.Y., Son, R.
    International Food Research Journal, 2008;15(1):57-64.
    MyJurnal
    A total of 78 samples comprising different types of street foods, sold in different locations in Malaysia, were examined for the presence of Enterobacter cloacae. E. cloacae contamination was recorded in 9% of the samples examined. Tests for susceptibility to 12 different antibiotics showed that all were resistant to six or more antibiotics, but susceptible to chloramphenicol and gentamicin. Plasmids of four different sizes were detected from the three plasmid positive isolates. RAPD analysis using four primers yielded completely different banding patterns for all E. cloacae studied. In Malaysia, no published information on street foods in the epidemiological investigation of E.cloacae related disease is available. However, their occurrences have provided compelling evidence that the risk of disease transmission caused by E. cloacae through street foods is moderate.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
  9. Fulltext Assessment of the genetic variability and fibre composition of Gamma Ray induced mutant lines of Ginger (Zingiber Officinale Roscoe)
    Nor Yusliza Kamaruddin, Shamsiah Abdullah
    Pertanika Journal of Science & Technology, 2017;25(103):325-334.
    MyJurnal
    This study looked at mutagenic effectiveness of gamma rays d on two varieties of Zingiber officinale Roscoe: Bentong and Tanjung Sepat. The rhizomes were exposed to different doses (0, 5, 7, 9, 11, 13 and 15 Gy) using Caesium-137 as source of the gamma rays. The effect of different gamma doses on the crude fibre composition of irradiated ginger was studied and genetic variability was assessed using molecular marker technique, RAPD. Findings showed different doses of gamma rays could induce variability in these two ginger varieties and the effect was found to be variety-dependent. Bentong variety irradiated with 9 Gy recorded 8.53% of crude fibre composition while Tanjung Sepat irradiated ginger with 5 Gy recorded 8.70% of crude fibre which gave the lowest composition compared with other irradiated ginger. A total of nine different arbitrary decamers were used as primers to amplify DNA from mutant plant material to assess their polymorphism level of ginger mutant lines. Polymorphism of all mutant lines was 97.62% indicating that there were significant changes in genetic sequences in irradiated ginger genotypes.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
  10. Fulltext Molecular confirmation and characterization of Vibrio parahaemolyticus from retailed fish
    Vincent, M., Chan, C. S. W., Apun, K.
    International Food Research Journal, 2015;22(4):1705-1710.
    MyJurnal
    The present study was conducted to assess the rapid molecular identification and characterization of 45 Vibrio parahaemolyticus isolates from 15 samples of 3 different types of fish (Kembung, Bawal and Sangeh) in the Kuching-Samarahan district. Polymerase chain reaction (PCR) based confirmation was done targeting the 450 bp fragment of the thermolabile (tl) gene, while DNA fingerprinting was performed using Randomly Amplified Polymorphic DNA (RAPD) PCR with the primer GEN15008. All the 45 V. parahaemolyticus isolates were positive for the tl gene, however, only 34 were typable via RAPD-PCR with bands sizes ranging from slightly over 250 bp to 2.5 kbp. The degree of diversity was then determined via the Simpson Index which showed a value of 0.891, indicating high diversity among the isolates. Data from the RAPD-PCR fingerprints were later used to construct a dendrogram for clustal analysis. From the dendrogram, the 34 isolates were grouped into 2 major clusters containing 26 and 8 isolates, respectively. Further analyses of the dendrogram also indicated that the 34 isolated were clustered according to the period of sampling. This is an interesting observation as it shows the high discriminatory capability of RAPD-PCR to be used as molecular epidemiological tool to study the temporal distribution of V. parahaemolyticus.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
  11. Evaluation of genetic diversity of Clinacanthus nutans (Acanthaceaea) using RAPD, ISSR and RAMP markers
    Ismail NZ, Arsad H, Samian MR, Ab Majid AH, Hamdan MR
    Physiol Mol Biol Plants, 2016 Oct;22(4):523-534.
    PMID: 27924125
    Three polymerase chain reaction (PCR) techniques were compared to analyse the genetic diversity of Clinacanthus nutans eight populations in the northern region of Peninsular Malaysia. The PCR techniques were random amplified polymorphic deoxyribonucleic acids (RAPD), inter-simple sequence repeats (ISSR) and random amplified microsatellite polymorphisms (RAMP). Leaf genomic DNA was PCR amplified using 17 RAPD, 8 ISSR and 136 RAMP primers . However, only 10 RAPD primers, 5 ISSR primers and 37 RAMP primers produced reproducible bands. The results were evaluated for polymorphic information content (PIC), marker index (MI) and resolving power (RP). The RAMP marker was the most useful marker compared to RAPD and ISSR markers because it showed the highest average value of PIC (0.25), MI (11.36) and RP (2.86). The genetic diversity showed a high percentage of polymorphism at the species level compared to the population level. Furthermore, analysis of molecular variance revealed that the genetic diversity was higher within populations, as compared to among populations of C. nutans. From the results, the RAMP technique was recommended for the analysis of genetic diversity of C. nutans.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
  12. Fulltext Genotyping of Salmonella strains isolated from ducks, their rearing and processing environments in Penang, Malaysia, using RAPD
    Adzitey F, Ali GR, Huda N, Ahmad R
    3 Biotech, 2013 Dec;3(6):521-527.
    PMID: 28324423 DOI: 10.1007/s13205-013-0115-7
    Salmonella species are important foodborne pathogens that can cause illness and death in humans. The objective of this study was to determine the genetic relatedness of 115 Salmonella strains isolated from ducks and their environment using random amplified polymorphic deoxyribonucleic acid (RAPD). The analysis of Salmonella strains by RAPD produced DNA fingerprints of different sizes for differentiation purposes, and cluster analysis at a coefficient of 0.85 grouped the Salmonella strains into various clusters and singletons. S. Typhimurium were grouped into nine clusters and ten singletons, S. Hadar were grouped into seven clusters and nine singletons, S. Enteritidis were grouped into four clusters and five singletons, S. Braenderup were grouped into five clusters and four singletons, S. Albany were grouped into two clusters and seven singletons, and S. Derby were grouped into two clusters and four singletons at a coefficient of 0.85 with discriminatory index (D) ranging from 0.879 to 0.957. With the exception of S. Typhimurium strains which were grouped into three major groups (genotypes) by RAPD analysis, the rest were grouped into two major genotypes. RAPD was a useful genotyping tool for determining the genetic relatedness of the duck Salmonella strains. Comparison of the genetic relatedness among foodborne pathogens and their sources of isolation are important to trace their source and possibly the source of human infection.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
  13. Fulltext Studies on the genetic variation of the green unicellular alga Haematococcus pluvialis (Chlorophyceae) obtained from different geographical locations using ISSR and RAPD molecular marker
    Mostafa N, Omar H, Tan SG, Napis S
    Molecules, 2011 Mar 22;16(3):2599-608.
    PMID: 21441863 DOI: 10.3390/molecules16032599
    Haematococcus pluvialis (Flotow) is a unicellular green alga, which is considered to be the best astaxanthin-producing organism. Molecular markers are suitable tools for the purpose of finding out genetic variations in organisms; however there have been no studies conducted on ISSR or RAPD molecular markers for this organism. The DNA of 10 different strains of H. pluvialis (four strains from Iran, two strains from Finland, one strain from Switzerland and three strains from the USA) was extracted. A genetic similarity study was carried out using 14 ISSR and 12 RAPD primers. Moreover, the molecular weights of the bands produced ranged from 0.14 to 3.4 Kb. The PCA and dendrogram clustered the H. pluvialis strains into various groups according to their geographical origin. The lowest genetic similarity was between the Iran2 and USA2 strains (0.08) and the highest genetic similarity was between Finland1 and Finland2 (0.64). The maximum numbers of bands produced by the ISSR and RAPD primers were 35 and 6 bands, respectively. The results showed that ISSR and RAPD markers are useful for genetic diversity studies of Haematococcus as they showed geographical discrimination.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
  14. Identification and characterization of RAPD-SCAR markers linked to glyphosate-susceptible and -resistant biotypes of Eleusine indica (L.) Gaertn
    Cha TS, Anne-Marie K, Chuah TS
    Mol Biol Rep, 2014 Feb;41(2):823-31.
    PMID: 24374894 DOI: 10.1007/s11033-013-2922-7
    Eleusine indica is one of the most common weed species found in agricultural land worldwide. Although herbicide-glyphosate provides good control of the weed, its frequent uses has led to abundant reported cases of resistance. Hence, the development of genetic markers for quick detection of glyphosate-resistance in E. indica population is imperative for the control and management of the weed. In this study, a total of 14 specific random amplified polymorphic DNA (RAPD) markers were identified and two of the markers, namely S4R727 and S26R6976 were further sequence characterized. Sequence alignment revealed that marker S4R727 showing a 12-bp nucleotides deletion in resistant biotypes, while marker S26R6976 contained a 167-bp nucleotides insertion in the resistant biotypes. Based on these sequence differences, three pairs of new sequence characterized amplified region (SCAR) primers were developed. The specificity of these primer pairs were further validated with genomic DNA extracted from ten individual plants of one glyphosate-susceptible and five glyphosate-resistant (R2, R4, R6, R8 and R11) populations. The resulting RAPD-SCAR markers provided the basis for assessing genetic diversity between glyphosate-susceptible and -resistant E. indica biotypes, as well for the identification of genetic locus link to glyphosate-resistance event in the species.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique/methods*
  15. Fulltext Genetic dissection of new genotypes of drumstick tree (Moringa oleifera Lam.) using random amplified polymorphic DNA marker
    Rufai S, Hanafi MM, Rafii MY, Ahmad S, Arolu IW, Ferdous J
    Biomed Res Int, 2013;2013:604598.
    PMID: 23862149 DOI: 10.1155/2013/604598
    The knowledge of genetic diversity of tree crop is very important for breeding and improvement program for the purpose of improving the yield and quality of its produce. Genetic diversity study and analysis of genetic relationship among 20 Moringa oleifera were carried out with the aid of twelve primers from, random amplified polymorphic DNA marker. The seeds of twenty M. oleifera genotypes from various origins were collected and germinated and raised in nursery before transplanting to the field at University Agricultural Park (TPU). Genetic diversity parameter, such as Shannon's information index and expected heterozygosity, revealed the presence of high genetic divergence with value of 1.80 and 0.13 for Malaysian population and 0.30 and 0.19 for the international population, respectively. Mean of Nei's gene diversity index for the two populations was estimated to be 0.20. In addition, a dendrogram constructed, using UPGMA cluster analysis based on Nei's genetic distance, grouped the twenty M. oleifera into five distinct clusters. The study revealed a great extent of variation which is essential for successful breeding and improvement program. From this study, M. oleifera genotypes of wide genetic origin, such as T-01, T-06, M-01, and M-02, are recommended to be used as parent in future breeding program.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique/methods*
  16. Comparing interfertility data with random amplified microsatellites DNA (RAMS) studies in Ganoderma Karst. Taxonomy
    Nudin NF, S S
    Mol Biol Rep, 2012 Mar;39(3):2861-6.
    PMID: 21938434 DOI: 10.1007/s11033-011-1045-2
    The taxonomy of the causal pathogen of basal stem rot of oil palms, Ganoderma is somewhat problematic at present. In order to determine the genetic distance relationship between G. boninense isolates and non-boninense isolates, a random amplified microsatellites DNA (RAMS) technique was carried out. The result was then compared with interfertility data of G. boninense that had been determined in previous mating studies to confirm the species of G. boninense. Dendrogram from cluster analysis based on UPGMA of RAMS data showed that two major clusters, I and II which separated at a genetic distance of 0.7935 were generated. Cluster I consisted of all the biological species G. boninense isolates namely CNLB, GSDK 3, PER 71, WD 814, GBL 3, GBL 6, OC, GH 02, 170 SL and 348781 while all non-boninense isolates namely G. ASAM, WRR, TFRI 129, G. RES, GJ, and CNLM were grouped together in cluster II. Although the RAMS markers showed polymorphisms in all the isolates tested, the results obtained were in agreement with the interfertility data. Therefore, the RAMS data could support the interfertility data for the identification of Ganoderma isolates.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique/methods*
  17. Fulltext Food assimilated by two sympatric populations of the brown planthopper Nilaparvata lugens (Delphacidae) feeding on different host plants contaminates insect DNA detected by RAPD-PCR analysis
    Latif MA, Omar MY, Tan SG, Siraj SS, Ali ME, Rafii MY
    Genet. Mol. Res., 2012;11(1):30-41.
    PMID: 22290463 DOI: 10.4238/2012.January.9.4
    Contamination of insect DNA for RAPD-PCR analysis can be a problem because many primers are non-specific and DNA from parasites or gut contents may be simultaneously extracted along with that of the insect. We measured the quantity of food ingested and assimilated by two sympatric populations of brown planthopper (BPH), Nilaparvata lugens, one from rice and the other from Leersia hexandra (Poaceae), a wetland forage grass, and we also investigated whether host plant DNA contaminates that of herbivore insects in extractions of whole insects. Ingestion and assimilation of food were reduced significantly when individuals derived from one host plant were caged on the other species. The bands, OPA3 (1.25), OPD3 (1.10), OPD3 (0.80), OPD3 (0.60), pUC/M13F (0.35), pUC/M13F (0.20), BOXAIR (0.50), peh#3 (0.50), and peh#3 (0.17) were found in both rice-infesting populations of brown planthopper and its host plant (rice). Similarly, the bands, OPA4 (1.00), OPB10 (0.70), OPD3 (0.90), OPD3 (0.80), OPD3 (0.60), pUC/ M13F (0.35), pUC/M13F (0.20), and BOXAIR (0.50) were found in both Leersia-infesting populations of brown planthopper and the host plant. So, it is clear that the DNA bands amplified in the host plants were also found in the extracts from the insects feeding on them.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique/methods
  18. Identification and characterization of Malaysian river catfish, Mystus nemurus (C&V): RAPD and AFLP analysis
    Chong LK, Tan SG, Yusoff K, Siraj SS
    Biochem Genet, 2000 Apr;38(3-4):63-76.
    PMID: 11100266
    This work represents the first application of the amplified fragment length polymorphism (AFLP) technique and the random amplified polymorphic DNA (RAPD) technique in the study of genetic variation within and among five geographical populations of M. nemurus. Four AFLP primer combinations and nine RAPD primers detected a total of 158 and 42 polymorphic markers, respectively. The results of AFLP and RAPD analysis provide similar conclusions as far as the population clustering analysis is concerned. The Sarawak population, which is located on Borneo Island, clustered by itself and was thus isolated from the rest of the populations located in Peninsular Malaysia. Both marker systems revealed high genetic variability within the Universiti Putra Malaysia (UPM) and Sarawak populations. Three subgroups each from the Kedah, Perak, and Sarawak populations were detected by AFLP but not by RAPD. Unique AFLP fingerprints were also observed in some unusual genotypes sampled in Sarawak. This indicates that AFLP may be a more efficient marker system than RAPD for identifying genotypes within populations.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique*
  19. Random amplified polymorphic DNA analysis of genetically modified organisms
    Yoke-Kqueen C, Radu S
    J Biotechnol, 2006 Dec 15;127(1):161-6.
    PMID: 16860900
    Randomly amplified polymorphic DNA (RAPD) was used to analyzed 78 samples comprises of certified reference materials (soya and maize powder), raw seeds (soybean and maize), processed food and animal feed. Combination assay of two arbitrary primers in the RAPD analysis enable to distinguish genetically modified organism (GMO) reference materials from the samples tested. Dendrogram analysis revealed 13 clusters at 45% similarity from the RAPD. RAPD analysis showed that the maize and soybean samples were clustered differently besides the GMO and non-GMO products.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique*
  20. Fulltext Genetic Diversity and Differentiation of Colletotrichum spp. Isolates Associated with Leguminosae Using Multigene Loci, RAPD and ISSR
    Mahmodi F, Kadir JB, Puteh A, Pourdad SS, Nasehi A, Soleimani N
    Plant Pathol J, 2014 Mar;30(1):10-24.
    PMID: 25288981 DOI: 10.5423/PPJ.OA.05.2013.0054
    Genetic diversity and differentiation of 50 Colletotrichum spp. isolates from legume crops studied through multigene loci, RAPD and ISSR analysis. DNA sequence comparisons by six genes (ITS, ACT, Tub2, CHS-1, GAPDH, and HIS3) verified species identity of C. truncatum, C. dematium and C. gloeosporiodes and identity C. capsici as a synonym of C. truncatum. Based on the matrix distance analysis of multigene sequences, the Colletotrichum species showed diverse degrees of intera and interspecific divergence (0.0 to 1.4%) and (15.5-19.9), respectively. A multilocus molecular phylogenetic analysis clustered Colletotrichum spp. isolates into 3 well-defined clades, representing three distinct species; C. truncatum, C. dematium and C. gloeosporioides. The ISSR and RAPD and cluster analysis exhibited a high degree of variability among different isolates and permitted the grouping of isolates of Colletotrichum spp. into three distinct clusters. Distinct populations of Colletotrichum spp. isolates were genetically in accordance with host specificity and inconsistent with geographical origins. The large population of C. truncatum showed greater amounts of genetic diversity than smaller populations of C. dematium and C. gloeosporioides species. Results of ISSR and RAPD markers were congruent, but the effective maker ratio and the number of private alleles were greater in ISSR markers.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
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