Displaying publications 121 - 140 of 443 in total

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  1. Genotype associations among seven apolipoprotein B polymorphisms in a population of Orang Asli of western Malaysia
    Gajra B, Candlish JK, Heng CK, Mak JW, Saha N
    Hum Biol, 1997 Oct;69(5):629-40.
    PMID: 9299883
    Associations among seven apolipoprotein B (APOB) gene polymorphisms [C-T promoter site; Leu-Ala-Leu signal peptide (SP) insertion/deletion; AG C,G site at codon 71; AG A1,D site at codon 591; XbaI site at codon 2488; AG H,I site at codon 3611; and AG T,Z site at codon 4154] were investigated in 195 members of an Orang Asli (aborigine) population from western Malaysia. Frequencies of the rare alleles for all these polymorphisms turned out to be low when compared with European but not Asian populations. The AG H,I site was not polymorphic. The highly polymorphic sites are in linkage disequilibrium among themselves, as shown by their delta values: SP 24,27 and AG C,G, 0.68; SP 24,27 and AG A1,D, 0.71; XbaI and AG C,G, 0.64; XbaI and AG A1,D, 0.57; SP 24,27 and XbaI, 0.48; and AG C,G and AG A1,D, 0.68. Ten unequivocal haplotypes on the basis of six sites (excluding the promoter polymorphism) were observed, and they represent 80% of the sample. The frequency of haplotype SP27,G,A1,X-,I,T, defined by the common homozygotes at all the sites for the APOB gene was 0.7, compared with 0.22 in Europeans. The ancestral haplotype SP27,G,D,X-,I,T was present at low frequency (0.01) in both the Orang Asli and Europeans. A cladogram constructed on the basis of haplotypes in the Orang Asli shows two different lines of evolution and that other haplotypes evolved by subsequent mutations on the ancestral haplotype.
    Matched MeSH terms: Polymorphism, Genetic*
  2. Recent Advances in the Genetics of Hypertension
    Wei LK, Au A, Teh LK, Lye HS
    Adv Exp Med Biol, 2017;956:561-581.
    PMID: 27957710 DOI: 10.1007/5584_2016_75
    Hypertension is a silent killer worldwide, caused by both genetic and environmental factors. Until now, genetic and genomic association studies of hypertension are reporting different degree of association on hypertension. Hence, it is essential to gather all the available information on the reported genetic loci and to determine if any biomarker(s) is/are significantly associated with hypertension. Current review concluded the potential biomarkers for hypertension, with regards to electrolyte and fluid transports, as well as sodium/potassium ions homeostasis, which are supported by the results of case-controls and meta-analyses.
    Matched MeSH terms: Polymorphism, Genetic*
  3. Genetic polymorphisms of CYP3A4: CYP3A4*18 allele is found in five healthy Malaysian subjects
    Ruzilawati AB, Suhaimi AW, Gan SH
    Clin Chim Acta, 2007 Aug;383(1-2):158-62.
    PMID: 17601520 DOI: 10.1016/j.cca.2007.05.004
    BACKGROUND: Cytochrome P450 3A4 (CYP3A4) is the major cytochrome involved in metabolizing of >60% of all drugs used in humans. A number of allelic variations in CYP3A4 gene are known to affect catalytic activity including CYP3A4*4, CYP3A4*5 and CYP3A4*18. We investigated the frequencies of CYP3A4*4, CYP3A4*5 and CYP3A4*18 alleles in a Malaysian population. This will impact treatment of patients receiving drugs metabolized by these alleles.

    METHODS: The study was conducted in 121 healthy Malaysian volunteers. DNA was extracted from leucocytes and the 3 alleles were determined by PCR-RFLP. The PCR product was later digested with restriction enzymes BstMA I, BshV I and Hpa II.

    RESULTS: No mutations were detected for CYP3A4*4 and CYP3A4*5 alleles. The frequency of the CYP3A4*18 allele in the Malaysian population is 2.1%. All 5 subjects with CYP3A4*18 mutations were found to be heterozygous.

    CONCLUSION: The present study describes polymorphisms of CYP3A4 among Malaysian subjects. Clinical relevance of these genetic variants in these healthy volunteers is under investigation.
    Matched MeSH terms: Polymorphism, Genetic*
  4. A simple method for the detection of CYP2C9 polymorphisms: nested allele-specific multiplex polymerase chain reaction
    Zainuddin Z, Teh LK, Suhaimi AW, Salleh MZ, Ismail R
    Clin Chim Acta, 2003 Oct;336(1-2):97-102.
    PMID: 14500040 DOI: 10.1016/s0009-8981(03)00319-x
    BACKGROUND: Cytochrome P4502C9 (CYP2C9), a principle drug-metabolizing enzyme is polymorphic in humans and is responsible for important pharmacokinetic and pharmacodynamic variations of CYP2C9 substrates. We developed an allele-specific multiplex polymerase chain reaction (PCR) method for the detection of common CYP2C9 alleles.
    METHOD: Genomic DNA was extracted from blood obtained from 40 unrelated healthy Malaysian Indian volunteers. The DNA was subjected to a first PCR that was used to amplify both exons 3 and 7 simultaneously in one reaction tube and a second PCR that was used to detect the polymorphic sites of CYP2C9 alleles using allele-specific primers. Sequencing was performed to validate the test results.
    RESULTS: We were successful in amplifying the fragments of interest from the DNA samples. The method was also reproducible and specific. The amplified sequences showed 100% homology to CYP2C9 sequence.
    CONCLUSION: This is the first nested allele-specific multiplex PCR method reported to allow for the simultaneously detection of five CYP2C9 alleles.
    Matched MeSH terms: Polymorphism, Genetic/genetics
  5. Moving into a new era of periodontal genetic studies: relevance of large case-control samples using severe phenotypes for genome-wide association studies
    Vaithilingam RD, Safii SH, Baharuddin NA, Ng CC, Cheong SC, Bartold PM, et al.
    J Periodontal Res, 2014 Dec;49(6):683-95.
    PMID: 24528298 DOI: 10.1111/jre.12167
    Studies to elucidate the role of genetics as a risk factor for periodontal disease have gone through various phases. In the majority of cases, the initial 'hypothesis-dependent' candidate-gene polymorphism studies did not report valid genetic risk loci. Following a large-scale replication study, these initially positive results are believed to be caused by type 1 errors. However, susceptibility genes, such as CDKN2BAS (Cyclin Dependend KiNase 2B AntiSense RNA; alias ANRIL [ANtisense Rna In the Ink locus]), glycosyltransferase 6 domain containing 1 (GLT6D1) and cyclooxygenase 2 (COX2), have been reported as conclusive risk loci of periodontitis. The search for genetic risk factors accelerated with the advent of 'hypothesis-free' genome-wide association studies (GWAS). However, despite many different GWAS being performed for almost all human diseases, only three GWAS on periodontitis have been published - one reported genome-wide association of GLT6D1 with aggressive periodontitis (a severe phenotype of periodontitis), whereas the remaining two, which were performed on patients with chronic periodontitis, were not able to find significant associations. This review discusses the problems faced and the lessons learned from the search for genetic risk variants of periodontitis. Current and future strategies for identifying genetic variance in periodontitis, and the importance of planning a well-designed genetic study with large and sufficiently powered case-control samples of severe phenotypes, are also discussed.
    Matched MeSH terms: Polymorphism, Genetic/genetics
  6. Fulltext CYP2C9 polymorphism: prevalence in healthy and warfarin-treated Malay and Chinese in Malaysia
    Ngow HA, Wan Khairina WM, Teh LK, Lee WL, Harun R, Ismail R, et al.
    Singapore Med J, 2009 May;50(5):490-3.
    PMID: 19495518
    Genetic polymorphisms of CYP2C9 among different populations in different geographical regions could be different. CYP2C9 has been reported to be the enzyme responsible for the metabolism of many drugs, including warfarin and other drugs with a narrow therapeutic index. Realising the importance of inter-individual differences in the genetic profile in determining the outcome of a drug therapy, this study was conducted to explore the types and frequencies of CYP2C9 alleles in healthy and warfarin-treated Malays and Chinese, the two major ethnic groups in Malaysia. We aimed to evaluate the prevalence of the types and frequencies of common CYP2C9 alleles (*1, *2, *3 and *4) among the healthy unrelated individuals and diseased patients prescribed with warfarin.
    Matched MeSH terms: Polymorphism, Genetic*
  7. Fulltext Metabolic and genetic screening of electromagnetic hypersensitive subjects as a feasible tool for diagnostics and intervention
    De Luca C, Thai JC, Raskovic D, Cesareo E, Caccamo D, Trukhanov A, et al.
    Mediators Inflamm, 2014;2014:924184.
    PMID: 24812443 DOI: 10.1155/2014/924184
    Growing numbers of "electromagnetic hypersensitive" (EHS) people worldwide self-report severely disabling, multiorgan, non-specific symptoms when exposed to low-dose electromagnetic radiations, often associated with symptoms of multiple chemical sensitivity (MCS) and/or other environmental "sensitivity-related illnesses" (SRI). This cluster of chronic inflammatory disorders still lacks validated pathogenetic mechanism, diagnostic biomarkers, and management guidelines. We hypothesized that SRI, not being merely psychogenic, may share organic determinants of impaired detoxification of common physic-chemical stressors. Based on our previous MCS studies, we tested a panel of 12 metabolic blood redox-related parameters and of selected drug-metabolizing-enzyme gene polymorphisms, on 153 EHS, 147 MCS, and 132 control Italians, confirming MCS altered (P < 0.05-0.0001) glutathione-(GSH), GSH-peroxidase/S-transferase, and catalase erythrocyte activities. We first described comparable-though milder-metabolic pro-oxidant/proinflammatory alterations in EHS with distinctively increased plasma coenzyme-Q10 oxidation ratio. Severe depletion of erythrocyte membrane polyunsaturated fatty acids with increased ω 6/ ω 3 ratio was confirmed in MCS, but not in EHS. We also identified significantly (P = 0.003) altered distribution-versus-control of the CYP2C19∗1/∗2 SNP variants in EHS, and a 9.7-fold increased risk (OR: 95% C.I. = 1.3-74.5) of developing EHS for the haplotype (null)GSTT1 + (null)GSTM1 variants. Altogether, results on MCS and EHS strengthen our proposal to adopt this blood metabolic/genetic biomarkers' panel as suitable diagnostic tool for SRI.
    Matched MeSH terms: Polymorphism, Genetic/genetics
  8. Genetic polymorphisms as potential pharmacogenetic biomarkers for platinum-based chemotherapy in non-small cell lung cancer
    Sito H, Tan SC
    Mol Biol Rep, 2024 Jan 13;51(1):102.
    PMID: 38217759 DOI: 10.1007/s11033-023-08915-2
    Platinum-based chemotherapy (PBC) is a widely used treatment for various solid tumors, including non-small cell lung cancer (NSCLC). However, its efficacy is often compromised by the emergence of drug resistance in patients. There is growing evidence that genetic variations may influence the susceptibility of NSCLC patients to develop resistance to PBC. Here, we provide a comprehensive overview of the mechanisms underlying platinum drug resistance and highlight the important role that genetic polymorphisms play in this process. This paper discussed the genetic variants that regulate DNA repair, cellular movement, drug transport, metabolic processing, and immune response, with a focus on their effects on response to PBC. The potential applications of these genetic polymorphisms as predictive indicators in clinical practice are explored, as are the challenges associated with their implementation.
    Matched MeSH terms: Polymorphism, Genetic/genetics
  9. Allozyme polymorphisms and heavy metal levels in the green-lipped mussel Perna viridis (Linnaeus) collected from contaminated and uncontaminated sites in Malaysia
    Yap CK, Tan SG, Ismail A, Omar H
    Environ Int, 2004 Mar;30(1):39-46.
    PMID: 14664863
    It has been widely reported that heavy metal contamination in coastal waters can modify the allozyme profiles of marine organisms. Previous studies have recorded elevated metal concentrations in sediments and mussel tissues off Peninsular Malaysia. In the present study, horizontal starch gel electrophoresis was carried out to estimate the levels of allelic variation of the green-lipped mussel, Perna viridis, collected from one contaminated and three relatively uncontaminated sites off Peninsular Malaysia. Fourteen polymorphic loci were observed. In addition, the concentrations of cadmium, copper, lead, mercury and zinc were determined in the sediments and in the soft tissues of the mussels. Mussels from contaminated site, evidenced by high metal pollution indices (MPI) of the sediment and the mussel tissues, showed the highest percentage of polymorphic loci (78.6%), while those collected from the uncontaminated sites had lower MPI of the sediment and mussel tissue, and exhibited lower percentages of polymorphic loci (35.7-57.1%). The population from the contaminated site showed the highest excess of heterozygosity (0.289) when compared to that of the populations from the three uncontaminated sites (0.108-0.149). Allozyme frequencies at the phosphoglucomutase (PGM; E.C. 2.7.5.1) locus also differed between the contaminated and uncontaminated populations. Previous studies have shown that exposure to heavy metals can select or counter-select for particular alleles at this locus. The present results suggest that allozyme polymorphism in P. viridis is a potential biomonitoring tool for heavy metal contamination but further validation is required.
    Matched MeSH terms: Polymorphism, Genetic*
  10. Fulltext DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system
    Khan MMH, Rafii MY, Ramlee SI, Jusoh M, Al Mamun M, Halidu J
    Sci Rep, 2021 Jul 15;11(1):14527.
    PMID: 34267249 DOI: 10.1038/s41598-021-93867-5
    As a new crop in Malaysia, forty-four Bambara groundnut (Vigna subterranea L. verdc.) genotypes were sampled from eleven distinct populations of different origins to explore the genetic structure, genetic inconsistency, and fixation index. The Bambara groundnut, an African underutilized legume, has the capacity to boost food and nutrition security while simultaneously addressing environmental sustainability, food availability, and economic inequalities. A set of 32 ISSRs were screened out of 96 primers based on very sharp, clear, and reproducible bands which detected a total of 510 loci with an average of 97.64% polymorphism. The average calculated value of PIC = 0.243, RP = 5.30, H = 0.285, and MI = 0.675 representing the efficiency of primer set for genetic differentiation among the genotypes. The ISSR primers revealed the number of alleles (Na = 1.97), the effective number of alleles (Ne = 1.38), Nei's genetic diversity (h = 0.248), and a moderate level of gene flow (Nm = 2.26) across the genotypes studied. The estimated Shannon's information index (I = 0.395) indicates a high level of genetic variation exists among the accessions. Based on Nei's genetic dissimilarity a UPMGA phylogenetic tree was constructed and grouped the entire genotypes into 3 major clusters and 6 subclusters. PCA analysis revealed that first principal component extracted maximum variation (PC1 = 13.92%) than second principal component (PC2 = 12.59%). Bayesian model-based STRUCTURE analysis assembled the genotypes into 3 (best ΔK = 3) genetic groups. The fixation-index (Fst) analysis narrated a very great genetic diversity (Fst = 0.19 to 0.40) exists within the accessions of these 3 clusters. This investigation specifies the effectiveness of the ISSR primers system for the molecular portrayal of V. subterranea genotypes that could be used for genetic diversity valuation, detection, and tagging of potential genotypes with quick, precise, and authentic measures for this crop improvement through effective breeding schemes.
    Matched MeSH terms: Polymorphism, Genetic*
  11. Fulltext Homogeneous Nature of Malaysian Marine Fish Epinephelus fuscoguttatus (Perciformes; Serranidae): Evidence Based on Molecular Markers, Morphology and Fourier Transform Infrared Analysis
    Nurdalila AA, Bunawan H, Kumar SV, Rodrigues KF, Baharum SN
    Int J Mol Sci, 2015 Jul 02;16(7):14884-900.
    PMID: 26147421 DOI: 10.3390/ijms160714884
    Taxonomic confusion exists within the genus Epinephelus due to the lack of morphological specializations and the overwhelming number of species reported in several studies. The homogenous nature of the morphology has created confusion in the Malaysian Marine fish species Epinephelus fuscoguttatus and Epinephelus hexagonatus. In this study, the partial DNA sequence of the 16S gene and mitochondrial nucleotide sequences of two gene regions, Cytochrome Oxidase Subunit I and III were used to investigate the phylogenetic relationship between them. In the phylogenetic trees, E. fuscoguttatus was monophyletic with E. hexagonatus species and morphology examination shows that no significant differences were found in the morphometric features between these two taxa. This suggests that E. fuscoguttatus is not distinguishable from E. hexagonatus species, and that E. fuscoguttatus have been identified to be E. hexagonatus species is likely attributed to differences in environment and ability to camouflage themselves under certain conditions. Interestingly, this finding was also supported by Principal Component Analysis on Attenuated Total Reflectance-Fourier-transform Infrared (ATR-FTIR) data analysis. Molecular, morphological and meristic characteristics were combined with ATR-FTIR analysis used in this study offer new perspectives in fish species identification. To our knowledge, this is the first report of an extensive genetic population study of E. fuscoguttatus in Malaysia and this understanding will play an important role in informing genetic stock-specific strategies for the management and conservation of this highly valued fish.
    Matched MeSH terms: Polymorphism, Genetic*
  12. Fulltext Sequence polymorphism and PCR-restriction fragment length polymorphism analysis of the flagellin gene of Burkholderia pseudomallei
    Tay ST, Cheah PC, Puthucheary SD
    J Clin Microbiol, 2010 Apr;48(4):1465-7.
    PMID: 20089759 DOI: 10.1128/JCM.01131-09
    Four flagellin allelic types (I to IV) of Burkholderia pseudomallei were identified based on their sequence variation and restriction fragment length polymorphism (RFLP) analysis of the amplified flagellin gene. Flagellin allelic type I was the most predominantly (75.0%) found among the 100 clinical isolates of B. pseudomallei investigated in this study.
    Matched MeSH terms: Polymorphism, Genetic*
  13. Fulltext Selections, frameshift mutations, and copy number variation detected on the surf4.1gene in the western Kenyan Plasmodium falciparum population
    Gitaka JN, Takeda M, Kimura M, Idris ZM, Chan CW, Kongere J, et al.
    Malar J, 2017 03 02;16(1):98.
    PMID: 28253868 DOI: 10.1186/s12936-017-1743-x
    BACKGROUND: Plasmodium falciparum SURFIN4.1is a putative ligand expressed on the merozoite and likely on the infected red blood cell, whose gene was suggested to be under directional selection in the eastern Kenyan population, but under balancing selection in the Thai population. To understand this difference, surf4.1sequences of western Kenyan P. falciparum isolates were analysed. Frameshift mutations and copy number variation (CNV) were also examined for the parasites from western Kenya and Thailand.

    RESULTS: Positively significant departures from neutral expectations were detected on the surf4.1region encoding C-terminus of the variable region 2 (Var2) by 3 population-based tests in the western Kenyan population as similar in the Thai population, which was not covered by the previous analysis for eastern Kenyan population. Significant excess of non-synonymous substitutions per nonsynonymous site over synonymous substitutions per synonymous site was also detected in the Var2 region. Negatively significant departures from neutral expectations was detected on the region encoding Var1 C-terminus consistent to the previous observation in the eastern Kenyan population. Parasites possessing a frameshift mutation resulting a product without intracellular Trp-rich (WR) domains were 22/23 in western Kenya and 22/36 in Thailand. More than one copy of surf4.1gene was detected in western Kenya (4/24), but no CNV was found in Thailand (0/36).

    CONCLUSIONS: The authors infer that the high polymorphism of SURFIN4.1Var2 C-terminus in both Kenyan and Thai populations were shaped-up by diversifying selection and maintained by balancing selection. These phenomena were most likely driven by immunological pressure. Whereas the SURFIN4.1Var1 C-terminus is suggested to be under directional selection consistent to the previous report for the eastern Kenyan population. Most western Kenyan isolates possess a frameshift mutation that would limit the expression of SURFIN4.1on the merozoite, but only 60% of Thai isolates possess this frameshift, which would affect the level and type of the selection pressure against this protein as seen in the two extremities of Tajima's D values for Var1 C-terminus between Kenyan and Thai populations. CNV observed in Kenyan isolates may be a consequence of this frameshift mutation to increase benefits on the merozoite surface.

    Matched MeSH terms: Polymorphism, Genetic*
  14. Influence of genetic polymorphisms on pharmacokinetics and treatment response of mycophenolic acid: a scoping review
    Yow HY, Ikawati M, Siswanto S, Hermawan A, Rahmat AK, Tan JS, et al.
    Pharmacogenomics, 2024;25(5-6):259-288.
    PMID: 38884938 DOI: 10.1080/14622416.2024.2344430
    This scoping review explores the impact of genetic polymorphisms on the pharmacokinetics and treatment responses of mycophenolic acid (MPA), an immunosuppressant. The study includes 83 articles from 1226 original studies, focusing on transplantation (n = 80) and autoimmune disorders (n = 3). Genetic variants in uridine 5'-diphospho-glucuronosyltransferase (UGT1A9, UGT1A8 and UGT2B7) and transmembrane transporters (ABCC2, SLCO1B1, SLCO1B3 and ABCB1) significantly affected MPA's pharmacokinetics and susceptibility to its adverse effect. Whereas variants in several genes including UGT1A9, UGT2B7, IMPDH1 and IMPDH2 have been associated with a higher risk of transplant rejection. However, there is a lack of studies on MPA's impact on autoimmune disorders and limited research on the Asian population. The findings underscore the need for further research on MPA's impact across different populations and diseases, particularly among other Asian ethnic groups, to advance personalized medicine in MPA therapy.
    Matched MeSH terms: Polymorphism, Genetic/genetics
  15. CYP2A6 polymorphisms in Malays, Chinese and Indians
    Nurfadhlina M, Foong K, Teh LK, Tan SC, Mohd Zaki S, Ismail R
    Xenobiotica, 2006 Aug;36(8):684-92.
    PMID: 16891249
    The genetically polymorphic cytochrome P450 (CYP) 2A6 is the major nicotine-oxidase in humans that may contribute to nicotine dependence and cancer susceptibility. The authors investigated the types and frequencies of CYP2A6 alleles in the three major ethnic groups in Malaysia and CYP2A6*1A, CYP2A6*1B, CYP2A6*1x2, CYP2A6*2, CYP2A6*3, CYP2A6*4, CYP2A6*5, CYP2A6*7, CYP2A6*8 and CYP2A6*10 were determined by allele-specific polymerase chain reaction (PCR) in 270 Malays, 172 Chinese and 174 Indians. Except for CYP2A6*2 and *3 that were not detected in the Malays and Chinese, all the other alleles were detected. Frequencies for the CYP2A6*4 allele were 7, 5 and 2%, respectively, in Malays, Chinese and Indians. A statistically significant high frequency of the duplicated CYP2A6*1x2 allele occurred among Chinese. Among Malays and Chinese, the most common allele was CYP2A6*1B, but it was CYP2A6*1A among Indians. These ethnic difference in frequencies suggested that further studies are required to investigate the implications on diseases such as cancer and smoking behaviour among these major ethnic groups in Malaysia.
    Matched MeSH terms: Polymorphism, Genetic*
  16. Fulltext Amplification of Bcl I region of the factor VIII gene by PCR
    Ishak R, Khim LC
    Southeast Asian J Trop Med Public Health, 1996 Jun;27(2):364-6.
    PMID: 9280004
    A study was initiated to amplify by polymerase chain reaction (PCR), a short factor VIII gene fragment containing the Bcl I restriction site from hemophilia patients using published primer sequences. Preliminary findings indicated that the resulting fragment is 142 bp long. This fragment, when digested with Bcl I restriction enzyme produced two fragments, 99 bp and 43 bp in length. Polymorphism in the Bcl I region can be used to detect carrier state in the family members of the hemophiliacs.
    Matched MeSH terms: Polymorphism, Genetic/genetics*
  17. Enzyme polymorphism of the malaria vector, An. balabacensis (Diptera: Culicidae) revisited--why sample natural populations?
    Hii JL, Chew M, Vun YS, Nasir M, Chang MS
    Southeast Asian J Trop Med Public Health, 1988 Dec;19(4):689-701.
    PMID: 3238482
    Two separate observations from recent electrophoretic studies of the systematics and population genetics of laboratory-reared populations which had a long history of colonization in various laboratories, were found to be inconsistent with the present study which used wild-caught populations from East Malaysia. Reanalysis of the two data sets generally indicated a low amount of genetic variation in laboratory colonies. The latter is characterized by higher frequency of monomorphic loci, low average heterozygosity values and, in one extreme case, no variability at two loci. However, natural populations of An. balabacensis and An. leucosphyrus showed more protein variability by the use of polyacrylamide gel electrophoresis. Since laboratory-maintained mosquitoes are genetically and phenotypically different from those in the field, results of laboratory studies on the systematics and population genetics of Anopheles species complexes may be biased.
    Matched MeSH terms: Polymorphism, Genetic*
  18. Genetic diversity analysis among collected purslane (Portulaca oleracea L.) accessions using ISSR markers
    Alam MA, Juraimi AS, Rafii MY, Hamid AA, Arolu IW, Abdul Latif M
    C. R. Biol., 2015 Jan;338(1):1-11.
    PMID: 25468001 DOI: 10.1016/j.crvi.2014.10.007
    Genetic diversity and relationships among 45 collected purslane accessions were evaluated using ISSR markers. The 28 primers gave a total of 167 bands, among which 163 were polymorphic (97.6%). The genetic diversity as estimated by Shannon's information index was 0.513, revealing a quite high level of genetic diversity in the germplasm. The average number of observed allele, effective allele, expected heterozygosity, polymorphic information content (PIC) and Nei's index were 5.96, 1.59, 0.43, 0.35 and 0.35, respectively. The UPGMA dendrogram based on Nei's genetic distance grouped the whole germplasm into 7 distinct clusters. The analysis of molecular variance (AMOVA) revealed that 89% of total variation occurred within population, while 11% were found among populations. Based on the constructed dendrogram using ISSR markers those accessions that are far from each other by virtue of genetic origin and diversity index (like Ac1 and Ac42; Ac19 and Ac45; Ac9 and Ac23; Ac18 and A25; Ac24 and Ac18) are strongly recommended to select as parent for future breeding program to develop high yielding and stress tolerant purslane variety in contribution to global food security.
    Matched MeSH terms: Polymorphism, Genetic
  19. Fulltext Assessing the genetic relationships of Curcuma alismatifolia varieties using simple sequence repeat markers
    Taheri S, Abdullah TL, Abdullah NA, Ahmad Z, Karimi E, Shabanimofrad MR
    Genet. Mol. Res., 2014;13(3):7339-46.
    PMID: 25222232 DOI: 10.4238/2014.September.5.12
    The genus Curcuma is a member of the ginger family (Zingiberaceae) that has recently become popular for use as flowering pot plants, both indoors and as patio and landscape plants. We used PCR-based molecular markers (SSRs) to elucidate genetic variation and relationships between five varieties of Curcuma (Curcuma alismatifolia) cultivated in Malaysia. Of the primers tested, 8 (of 17) SSR primers were selected for their reproducibility and high rates of polymorphism. The number of presumed alleles revealed by the SSR analysis ranged from two to six alleles, with a mean value of 3.25 alleles per locus. The values of HO and HE ranged from 0 to 0.8 (mean value of 0.2) and 0.1837 to 0.7755 (mean value of 0.5102), respectively. Eight SSR primers yielded 26 total amplified fragments and revealed high rates of polymorphism among the varieties studied. The polymorphic information content varied from 0.26 to 0.73. Dice's similarity coefficient was calculated for all pairwise comparisons and used to construct an unweighted pair group method with arithmetic average (UPGMA) dendrogram. Similarity coefficient values from 0.2105 to 0.6667 (with an average of 0.4386) were found among the five varieties examined. A cluster analysis of data using a UPGMA algorithm divided the five varieties/hybrids into 2 groups.
    Matched MeSH terms: Polymorphism, Genetic
  20. Genetic relationships among five varieties of Curcuma alismatifolia (Zingiberaceae) based on ISSR markers
    Taheri S, Abdullah TL, Abdullah NA, Ahmad Z
    Genet. Mol. Res., 2012;11(3):3069-76.
    PMID: 23007984
    The genus Curcuma is a member of the ginger family (Zingiberaceae) that has recently become popular for use as flowering pot plants, both indoors and as patio and landscape plants. We used PCR-based molecular markers (ISSRs) to assess genetic variation and relationships between five varieties of curcuma (Curcuma alismatifolia) cultivated in Malaysia. Sixteen ISSR primers generated 139 amplified fragments, of which 77% had high polymorphism among these varieties. These markers were used to estimate genetic similarity among the varieties using Jaccard's similarity coefficient. The similarity matrix was used to construct a dendrogram, and a principal component plot was developed to examine genetic relationships among varieties. Similarity coefficient values ranged from 0.40 to 0.58 (with a mean of 0.5) among the five varieties. The mean value of number of observed alleles, number of effective alleles, mean Nei's gene diversity, and Shannon's information index were 8.69, 1.48, 0.29, and 0.43, respectively.
    Matched MeSH terms: Polymorphism, Genetic
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