Displaying publications 1 - 20 of 51 in total

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  1. García-Berro A, Talla V, Vila R, Wai HK, Shipilina D, Chan KG, et al.
    Mol Ecol, 2023 Feb;32(3):560-574.
    PMID: 36336800 DOI: 10.1111/mec.16770
    Migration is typically associated with risk and uncertainty at the population level, but little is known about its cost-benefit trade-offs at the species level. Migratory insects in particular often exhibit strong demographic fluctuations due to local bottlenecks and outbreaks. Here, we use genomic data to investigate levels of heterozygosity and long-term population size dynamics in migratory insects, as an alternative to classical local and short-term approaches such as regional field monitoring. We analyse whole-genome sequences from 97 Lepidoptera species and show that individuals of migratory species have significantly higher levels of genome-wide heterozygosity, a proxy for effective population size, than do nonmigratory species. Also, we contribute whole-genome data for one of the most emblematic insect migratory species, the painted lady butterfly (Vanessa cardui), sampled across its worldwide distributional range. This species exhibits one of the highest levels of genomic heterozygosity described in Lepidoptera (2.95 ± 0.15%). Coalescent modelling (PSMC) shows historical demographic stability in V. cardui, and high effective population size estimates of 2-20 million individuals 10,000 years ago. The study reveals that the high risks associated with migration and local environmental fluctuations do not seem to decrease overall genetic diversity and demographic stability in migratory Lepidoptera. We propose a "compensatory" demographic model for migratory r-strategist organisms in which local bottlenecks are counterbalanced by reproductive success elsewhere within their typically large distributional ranges. Our findings highlight that the boundaries of populations are substantially different for sedentary and migratory insects, and that, in the latter, local and even regional field monitoring results may not reflect whole population dynamics. Genomic diversity patterns may elucidate key aspects of an insect's migratory nature and population dynamics at large spatiotemporal scales.
    Matched MeSH terms: Genetic Variation/genetics
  2. Vankova OE, Brusnigina NF, Novikova NA
    Sovrem Tekhnologii Med, 2023;15(2):41-46.
    PMID: 37389021 DOI: 10.17691/stm2023.15.2.04
    Modern molecular genetic methods, massive parallel sequencing in particular, allow for genotyping of various pathogens with the aim of their epidemiological marking and improvement of molecular epidemiological surveillance of actual infections, including cytomegalovirus infection. The aim of the study is to evaluate the next-generation sequencing (NGS) technology for genotyping clinical isolates of cytomegalovirus (CMV).

    MATERIALS AND METHODS: The object of the study were samples of biological substrates (leukocyte mass, saliva, urine) taken from patients who underwent liver and kidney transplantation. Detection of CMV DNA was carried out by a real-time PCR using commercial diagnostic AmpliSense CMV-FL test systems (Central Research Institute for Epidemiology, Moscow, Russia). DNA extraction was performed using DNA-sorb AM and DNA-sorb V kits (Central Research Institute for Epidemiology) in accordance with manufacturer's manual. The quality of the prepared DNA library for sequencing was assessed by means of the QIAxcel Advanced System capillary gel electrophoresis system (QIAGEN, Germany). Alignment and assembly of nucleotide sequences were carried out using CLC Genomics Workbench 5.5 software (CLC bio, USA). The sequencing results were analyzed using BLAST of NCBI server.

    RESULTS: CMV DNA samples were selected for genotyping. The two variable genes, UL55(gB) and UL73(gN), were used for CMV genotype determination, which was performed using NGS technology MiSeq sequencer (Illumina, USA). Based on the exploratory studies and analysis of literature sources, primers for genotyping on the UL55(gB) and UL73(gN) genes have been selected and the optimal conditions for the PCR reaction have been defined. The results of sequencing the UL55(gB) and UL73(gN) gene fragments of CMV clinical isolates from recipients of solid organs made it possible to determine the virus genotypes, among which gB2, gN4c, and gN4b were dominant. In some cases, association of two and three CMV genotypes has been revealed.

    CONCLUSION: The application of the NGS technology for genotyping cytomegalovirus strains can become one of the main methods of CMV infection molecular epidemiology, as it allows for obtaining reliable results with a significant reduction in research time.

    Matched MeSH terms: Genetic Variation/genetics
  3. Noh A, Rafii MY, Saleh G, Kushairi A, Latif MA
    ScientificWorldJournal, 2012;2012:792601.
    PMID: 22701095 DOI: 10.1100/2012/792601
    The performance of 11 oil palm AVROS (Algemene Vereniging van Rubberplanters ter Oostkust van Sumatra) pisiferas was evaluated based on their 40 dura x pisifera (DxP) progenies tested on inland soils, predominantly of Serdang Series. Fresh fruit bunch (FFB) yield of each pisiferas ranged from 121.93 to 143.9 kg palm⁻¹ yr⁻¹ with trial mean of 131.62 kg palm⁻¹ yr⁻¹. Analysis of variance (ANOVA) showed low genetic variability among pisifera parents for most of the characters indicating uniformity of the pisifera population. This was anticipated as the AVROS pisiferas were derived from small population and were inbred materials. However, some of the pisiferas have shown good general combining ability (GCA) for certain important economic traits. Three pisiferas (P1 (0.174/247), P3 (0.174/498), P11 (0.182/308)) were identified of having good GCA for FFB yield while pisiferas P1 (0.174/247), P10 (0.182/348), and P11 (0.182/308) were good combiners for oil-to-bunch ratio (O/B). The narrow genetic base of these materials was the main obstacle in breeding and population improvement. However, efforts have been made to introgress this material with the vast oil palm germplasm collections of MPOB for rectifying the problem.
    Matched MeSH terms: Genetic Variation/genetics*
  4. Sohrabi M, Rafii MY, Hanafi MM, Siti Nor Akmar A, Latif MA
    ScientificWorldJournal, 2012;2012:416291.
    PMID: 22654604 DOI: 10.1100/2012/416291
    Genetic diversity is prerequisite for any crop improvement program as it helps in the development of superior recombinants. Fifty Malaysian upland rice accessions were evaluated for 12 growth traits, yield and yield components. All of the traits were significant and highly significant among the accessions. The higher magnitudes of genotypic and phenotypic coefficients of variation were recorded for flag leaf length-to-width ratio, spikelet fertility, and days to flowering. High heritability along with high genetic advance was registered for yield of plant, days to flowering, and flag leaf length-to-width ratio suggesting preponderance of additive gene action in the gene expression of these characters. Plant height showed highly significant positive correlation with most of the traits. According to UPGMA cluster analysis all accessions were clustered into six groups. Twelve morphological traits provided around 77% of total variation among the accessions.
    Matched MeSH terms: Genetic Variation/genetics*
  5. Redjeki ES, Ho WK, Shah N, Molosiwa OO, Ardiarini NR, Kuswanto, et al.
    Genome, 2020 Jun;63(6):319-327.
    PMID: 32097026 DOI: 10.1139/gen-2019-0137
    A total of 170 bambara groundnut (Vigna subterranea) accessions were evaluated using both simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers generated using genotyping-by-sequencing (GbS), of which 56 accessions were collected from West and East Java. Principal coordinate analysis (PCoA), population structure, and cluster analysis suggest that the East Java accessions could be a result of the introduction of selected West Java accessions. In addition, the current Indonesian accessions were likely introduced from Southern Africa, which would have produced a very marked founding effect such that these accessions present only a fraction of the genetic variability that exists within this species.
    Matched MeSH terms: Genetic Variation/genetics*
  6. Khan MMH, Rafii MY, Ramlee SI, Jusoh M, Al Mamun M, Kundu BC
    Mol Biol Rep, 2023 Sep;50(9):7619-7637.
    PMID: 37531035 DOI: 10.1007/s11033-023-08693-x
    BACKGROUND: A set of 44 selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions was sampled from 11 distinct populations of four geographical zones to assess the genetic drift, population structure, phylogenetic relationship, and genetic differentiation linked with ISSR primers.

    METHODS AND RESULTS: The amplification of genomic DNA with 32 ISSR markers detected an average of 97.64% polymorphism while 35.15% and 51.08% polymorphism per population and geographical zone, respectively. Analysis of molecular variance revealed significant variation within population 75% and between population 25% whereas within region 84% and between region 16%. The Bidillali exposed greater number of locally common band i.e., NLCB (≤ 25%) = 25 and NLCB (≤ 50%) = 115 were shown by Cancaraki while the lowest was recorded as NLCB (≤ 25%) = 6 and NLCB (≤ 50%) = 72 for Roko and Maibergo, accordingly. The highest PhiPT value was noted between Roko and Katawa (0.405*) whereas Nei's genetic distance was maximum between Roko and Karu (0.124). Based on Nei's genetic distance, a radial phylogenetic tree was constructed that assembled the entire accessions into 3 major clusters for further confirmation unrooted NJ vs NNet split tree analysis based on uncorrected P distance exposed the similar result. Principal coordinate analysis showed variation as PC1 (15.04%) > PC2 (5.81%).

    CONCLUSIONS: The current study leads to prompting the genetic improvement and future breeding program by maximum utilization and better conservation of existing accessions. The accessions under Cancaraki and Jatau are population documented for future breeding program due to their higher genetic divergence and homozygosity.

    Matched MeSH terms: Genetic Variation/genetics
  7. Oladosu Y, Rafii MY, Abdullah N, Abdul Malek M, Rahim HA, Hussin G, et al.
    ScientificWorldJournal, 2014;2014:190531.
    PMID: 25431777 DOI: 10.1155/2014/190531
    Genetic based knowledge of different vegetative and yield traits play a major role in varietal improvement of rice. Genetic variation gives room for recombinants which are essential for the development of a new variety in any crop. Based on this background, this work was carried out to evaluate genetic diversity of derived mutant lines and establish relationships between their yield and yield components using multivariate analysis. To achieve this objective, two field trials were carried out on 45 mutant rice genotypes to evaluate their growth and yield traits. Data were taken on vegetative traits and yield and its components, while genotypic and phenotypic coefficients, variance components, expected genetic advance, and heritability were calculated. All the genotypes showed variations for vegetative traits and yield and its components. Also, there was positive relationship between the quantitative traits and the final yield with the exception of number of tillers. Finally, the evaluated genotypes were grouped into five major clusters based on the assessed traits with the aid of UPGMA dendrogram. So hybridization of group I with group V or group VI could be used to attain higher heterosis or vigour among the genotypes. Also, this evaluation could be useful in developing reliable selection indices for important agronomic traits in rice.
    Matched MeSH terms: Genetic Variation/genetics*
  8. Joy N, Prasanth VP, Soniya EV
    Genetica, 2011 Aug;139(8):1033-43.
    PMID: 21874534 DOI: 10.1007/s10709-011-9605-x
    The genotypes of black pepper are morphologically and genotypically highly diverse and carry all the cumulative variations inherited and maintained through generations. The present study describes the Simple Sequence Repeat (SSR) or microsatellite based assessment of genetic diversity among forty popular genotypes and four different species of black pepper in Southern region of India. For isolation of SSR primers, our earlier attempts with enrichment strategies like 'Triplex affinity capture' did not extract a single SSR primer due to close proximity of restriction sites to the SSR motif. Hence we developed a 'Sequential Reverse Genome Walking (SRGW)' strategy with better enrichment efficiency of 72% that generated seven new SSR primers. Genotyping precisely discriminated majority of genotypes which indicated that the SSR primers are very informative. A total of 62 alleles with an average of 15.5 alleles over 4 loci were identified. All the SSR primers showed an average Polymorphism Information Content (PIC) value of 0.85. The estimated average Shared Allele Frequency ranged between 1.57 and 20.12%. The PCA plot revealed four closely related individual groups and identified Karimunda, Wild pepper and a local landrace 'local b' as the most divergent genotypes. Cluster analysis exposed the genetic relatedness between hybrids and selections with other known cultivars. The introduction of black pepper from South India to Malaysia was emphasized from the observation of genetic similarity of Malaysian cultivar 'Kuching' with other indigenous popular cultivars. The study was first to portray the precise genetic relatedness among the major indigenous genotypes of black pepper.
    Matched MeSH terms: Genetic Variation/genetics*
  9. Mohd Nawawi N, Selveindran NM, Rasat R, Chow YP, Abdul Latiff Z, Syed Zakaria SZ, et al.
    Clin Chim Acta, 2018 Sep;484:141-147.
    PMID: 29807018 DOI: 10.1016/j.cca.2018.05.048
    BACKGROUND: Osteogenesis imperfecta (OI) is a rare genetic bone disease characterized by bone fragility and low bone mass. OI was mainly caused by genetic mutations in collagen genes, COL1A1 and COL1A2. Nevertheless, new genes have been identified to be causally linked to OI. The clinical features between each OI groups share great similarities and it is sometimes difficult for clinicians to diagnose the disease accurately. Here, we identify the genetic mutations of OI patients from Malaysia and correlate the genetic mutations with the clinical features.

    METHOD: Targeted sequencing of fourteen genes panel was performed to identify the mutations in 29 OI patients with type I, III, IV and V disease. The mutations were determined using Ion Torrent Suite software version 5 and variant annotation was conducted using ANNOVAR. The identified mutations were confirmed using Sanger sequencing and in silico analysis was performed to evaluate the effects of the candidate mutations at protein level.

    RESULTS: Majority of patients had mutations in collagen genes, 48% (n = 14) in COL1A1 and 14% (n = 4) in COL1A2. Type I OI was caused by quantitative mutations in COL1A1 whereas most of type III and IV were due to qualitative mutations in both of the collagen genes. Those with quantitative mutations had milder clinical severity compared to qualitative mutations in terms of dentinogenesis imperfecta (DI), bone deformity and the ability to walk with aid. Furthermore, a few patients (28%, n = 8) had mutations in IFITM5, BMP1, P3H1 and SERPINF1.

    CONCLUSION: Majority of our OI patients have mutations in collagen genes, similar to other OI populations worldwide. Genotype-phenotype analysis revealed that qualitative mutations had more severe clinical characteristics compared to quantitative mutations. It is crucial to identify the causative mutations and the clinical severity of OI patients may be predicted based on the types of mutations.

    Matched MeSH terms: Genetic Variation/genetics
  10. Yaacob JS, Loh HS, Mat Taha R
    ScientificWorldJournal, 2013;2013:613635.
    PMID: 23844406 DOI: 10.1155/2013/613635
    Mantled fruits as a result of somaclonal variation are often observed from the oil palm plantlets regenerated via tissue culture. The mantling of fruits with finger-like and thick outer coating phenotypes significantly reduces the seed size and oil content, posing a threat to oil palm planters, and may jeopardize the economic growth of countries that depend particularly on oil palm plantation. The molecular aspects of the occurrence of somaclonal variations are yet to be known, possibly due to gene repression such as DNA methylation, histone methylation and histone deacetylation. Histone deacetylases (HDACs), involved in eukaryotic gene regulation by catalyzing the acetyl groups are removal from lysine residues on histone, hence transcriptionally repress gene expression. This paper described the total protein polymorphism profiles of somaclonal variants of oil palm and the effects of histone deacetylation on this phenomenon. Parallel to the different phenotypes, the protein polymorphism profiles of the mantled samples (leaves, fruits, and florets) and the phenotypically normal samples were proven to be different. Higher HDAC activity was found in mantled leaf samples than in the phenotypically normal leaf samples, leading to a preliminary conclusion that histone deacetylation suppressed gene expression and contributed to the development of somaclonal variants.
    Matched MeSH terms: Genetic Variation/genetics*
  11. Yaacob JS, Taha RM, Khorasani Esmaeili A
    ScientificWorldJournal, 2013;2013:686752.
    PMID: 23766703 DOI: 10.1155/2013/686752
    The present study deals with the cytological investigations on the meristematic root cells of carnation (Dianthus caryophyllus Linn.) grown in vivo and in vitro. Cellular parameters including the mitotic index (MI), chromosome count, ploidy level (nuclear DNA content), mean cell and nuclear areas, and cell doubling time (Cdt) were determined from the 2 mm root tip segments of this species. The MI value decreased when cells were transferred from in vivo to in vitro conditions, perhaps due to early adaptations of the cells to the in vitro environment. The mean chromosome number was generally stable (2n = 2x = 30) throughout the 6-month culture period, indicating no occurrence of early somaclonal variation. Following the transfer to the in vitro environment, a significant increase was recorded for mean cell and nuclear areas, from 26.59 ± 0.09  μm² to 35.66 ± 0.10  μm² and 142.90 ± 0.59  μm² to 165.05 ± 0.58  μm², respectively. However, the mean cell and nuclear areas of in vitro grown D. caryophyllus were unstable and fluctuated throughout the tissue culture period, possibly due to organogenesis or rhizogenesis. Ploidy level analysis revealed that D. caryophyllus root cells contained high percentage of polyploid cells when grown in vivo and maintained high throughout the 6-month culture period.
    Matched MeSH terms: Genetic Variation/genetics*
  12. Fix AG
    Am J Hum Biol, 2004 Jul-Aug;16(4):387-94.
    PMID: 15214057
    Migration among local populations classically has been seen as the principal process retarding genetic microdifferentiation. However, as Sewall Wright pointed out long ago, migration may also act as a random differentiating force. In fact, when migrants comprise a biological kin group, migration may be considered a component of genetic drift. The causes of kin-structured migration (KSM) lie in the common, if not universal, tendency for kin to associate and cooperate. However, similar to genetic drift, KSM has its greatest effect in smaller populations and is most apparent in low-density fission-fusion societies such as the Yanomamo of South America and the Semai of Malaysia, and less salient in higher density, low-mobility populations such as those of the New Guinea Highlands. The evolutionary consequences of KSM begin with increased genetic variation among populations. Such intergroup variation provides a basis for group selection. The origin of larger-scale geographic differentiation can arise from kin-structured migrant groups colonizing new regions. Waves of colonizing kin-structured founder groups may produce gene frequency clines, mimicking demic diffusion and natural selection. Finally, because kin structuring reduces the effective size of a population, it may be speculated that the extremely small effective size inferred for ancestral populations of Homo sapiens may be an artifact of kin-structured demographically larger populations.
    Matched MeSH terms: Genetic Variation/genetics*
  13. Benavente ED, Gomes AR, De Silva JR, Grigg M, Walker H, Barber BE, et al.
    Sci Rep, 2019 07 08;9(1):9873.
    PMID: 31285495 DOI: 10.1038/s41598-019-46398-z
    The zoonotic Plasmodium knowlesi parasite is the most common cause of human malaria in Malaysia. Genetic analysis has shown that the parasites are divided into three subpopulations according to their geographic origin (Peninsular or Borneo) and, in Borneo, their macaque host (Macaca fascicularis or M. nemestrina). Whilst evidence suggests that genetic exchange events have occurred between the two Borneo subpopulations, the picture is unclear in less studied Peninsular strains. One difficulty is that P. knowlesi infected individuals tend to present with low parasitaemia leading to samples with insufficient DNA for whole genome sequencing. Here, using a parasite selective whole genome amplification approach on unprocessed blood samples, we were able to analyse recent genomes sourced from both Peninsular Malaysia and Borneo. The analysis provides evidence that recombination events are present in the Peninsular Malaysia parasite subpopulation, which have acquired fragments of the M. nemestrina associated subpopulation genotype, including the DBPβ and NBPXa erythrocyte invasion genes. The NBPXb invasion gene has also been exchanged within the macaque host-associated subpopulations of Malaysian Borneo. Our work provides strong evidence that exchange events are far more ubiquitous than expected and should be taken into consideration when studying the highly complex P. knowlesi population structure.
    Matched MeSH terms: Genetic Variation/genetics*
  14. Leonhard SE, Mandarakas MR, Gondim FAA, Bateman K, Ferreira MLB, Cornblath DR, et al.
    Nat Rev Neurol, 2019 11;15(11):671-683.
    PMID: 31541214 DOI: 10.1038/s41582-019-0250-9
    Guillain-Barré syndrome (GBS) is a rare, but potentially fatal, immune-mediated disease of the peripheral nerves and nerve roots that is usually triggered by infections. The incidence of GBS can therefore increase during outbreaks of infectious diseases, as was seen during the Zika virus epidemics in 2013 in French Polynesia and 2015 in Latin America. Diagnosis and management of GBS can be complicated as its clinical presentation and disease course are heterogeneous, and no international clinical guidelines are currently available. To support clinicians, especially in the context of an outbreak, we have developed a globally applicable guideline for the diagnosis and management of GBS. The guideline is based on current literature and expert consensus, and has a ten-step structure to facilitate its use in clinical practice. We first provide an introduction to the diagnostic criteria, clinical variants and differential diagnoses of GBS. The ten steps then cover early recognition and diagnosis of GBS, admission to the intensive care unit, treatment indication and selection, monitoring and treatment of disease progression, prediction of clinical course and outcome, and management of complications and sequelae.
    Matched MeSH terms: Genetic Variation/genetics
  15. Hu J, Chan LF, Souza RP, Tampakeras M, Kennedy JL, Zai C, et al.
    Neurosci Lett, 2014 Jan 24;559:39-43.
    PMID: 24275212 DOI: 10.1016/j.neulet.2013.11.025
    Evidence has shown that attempted suicide in psychiatric disorders is a complex interplay of genes and environment. Noradrenergic dysfunction due to abnormalities in the tyrosine hydroxylase (TH) gene has been implicated in the pathogenesis of suicidal behavior in mood disorders. However, suicide is a leading cause of mortality in schizophrenia too. Recent evidence suggests that TH gene variants may also increase the risk of suicide attempts in schizophrenia patients, although the interaction with established clinical risk factors is unclear. This study aimed to identify TH gene variants conferring risk for suicide attempt in schizophrenia while accounting for the interaction between this gene and clinical risk factors. We performed analysis on four TH SNPs (rs11564717, rs11042950, rs2070762, rs689) and the common TCAT repeat (UniSTS:240639) for 234 schizophrenia patients (51 suicide attempters and 183 non-attempters). Clinical risk factors and ethnic stratification were included as covariates. Single marker analysis identified the SNP rs11564717 (p=0.042) and the TCAT(6) (p=0.004) as risk variants for suicide attempt. We also identified the haplotype A-A-A-G as a risk factor for suicide attempt (p=0.0025). In conclusion, our findings suggest that TH polymorphisms may contribute to the risk of attempted suicide in schizophrenia even after accounting for established clinical risk factors and ethnic stratification. Further larger scale studies are needed to confirm these findings and to understand the mechanisms underlying the role of TH gene variants in suicide attempt in schizophrenia.
    Matched MeSH terms: Genetic Variation/genetics*
  16. Yew CW, Lu D, Deng L, Wong LP, Ong RT, Lu Y, et al.
    Hum Genet, 2018 Feb;137(2):161-173.
    PMID: 29383489 DOI: 10.1007/s00439-018-1869-0
    Southeast Asia (SEA) is enriched with a complex history of peopling. Malaysia, which is located at the crossroads of SEA, has been recognized as one of the hubs for early human migration. To unravel the genomic complexity of the native inhabitants of Malaysia, we sequenced 12 samples from 3 indigenous populations from Peninsular Malaysia and 4 native populations from North Borneo to a high coverage of 28-37×. We showed that the Negritos from Peninsular Malaysia shared a common ancestor with the East Asians, but exhibited some level of gene flow from South Asia, while the North Borneo populations exhibited closer genetic affinity towards East Asians than the Malays. The analysis of time of divergence suggested that ancestors of Negrito were the earliest settlers in the Malay Peninsula, whom first separated from the Papuans ~ 50-33 thousand years ago (kya), followed by East Asian (~ 40-15 kya), while the divergence time frame between North Borneo and East Asia populations predates the Austronesian expansion period implies a possible pre-Neolithic colonization. Substantial Neanderthal ancestry was confirmed in our genomes, as was observed in other East Asians. However, no significant difference was observed, in terms of the proportion of Denisovan gene flow into these native inhabitants from Malaysia. Judging from the similar amount of introgression in the Southeast Asians and East Asians, our findings suggest that the Denisovan gene flow may have occurred before the divergence of these populations and that the shared similarities are likely an ancestral component.
    Matched MeSH terms: Genetic Variation/genetics*
  17. Ting NC, Zaki NM, Rosli R, Low ET, Ithnin M, Cheah SC, et al.
    J Genet, 2010 Aug;89(2):135-45.
    PMID: 20861564
    This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) markers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique sequences, of which 629 ESTs were found to contain 722 SSRs with a variety of motifs. Dinucleotide repeats formed the largest group (45.6%) consisting of 66.9% AG/CT, 21.9% AT/AT, 10.9% AC/GT and 0.3% CG/CG motifs. This was followed by trinucleotide repeats, which is the second most abundant repeat types (34.5%) consisting of AAG/CTT (23.3%), AGG/CCT (13.7%), CCG/CGG (11.2%), AAT/ATT (10.8%), AGC/GCT (10.0%), ACT/AGT (8.8%), ACG/CGT (7.6%), ACC/GGT (7.2%), AAC/GTT (3.6%) and AGT/ACT (3.6%) motifs. Primer pairs were designed for 405 unique EST-SSRs and 15 of these were used to genotype 105 E. guineensis and 30 E. oleifera accessions. Fourteen SSRs were polymorphic in at least one germplasm revealing a total of 101 alleles. The high percentage (78.0%) of alleles found to be specific for either E. guineensis or E. oleifera has increased the power for discriminating the two species. The estimates of genetic differentiation detected by EST-SSRs were compared to those reported previously. The transferability across palm taxa to two Cocos nucifera and six exotic palms is also presented. The polymerase chain reaction (PCR) products of three primer-pairs detected in E. guineensis, E. oleifera, C. nucifera and Jessinia bataua were cloned and sequenced. Sequence alignments showed mutations within the SSR site and the flanking regions. Phenetic analysis based on the sequence data revealed that C. nucifera is closer to oil palm compared to J. bataua; consistent with the taxanomic classification.
    Matched MeSH terms: Genetic Variation/genetics*
  18. 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: Genetic Variation/genetics*
  19. Hu T, Qiu W, He B, Zhang Y, Yu J, Liang X, et al.
    BMC Microbiol, 2014;14:293.
    PMID: 25433675 DOI: 10.1186/s12866-014-0293-4
    In recent years novel human respiratory disease agents have been described for Southeast Asia and Australia. The causative pathogens were classified as pteropine orthoreoviruses with a strong phylogenetic relationship to orthoreoviruses of bat origin.
    Matched MeSH terms: Genetic Variation/genetics
  20. Chong PP, Lee YL, Tan BC, Ng KP
    J Med Microbiol, 2003 Aug;52(Pt 8):657-66.
    PMID: 12867559
    The aims of this study were to compare the genetic relatedness of: (i) sequential and single isolates of Candida strains from women with recurrent vaginal candidiasis (RVC); and (ii) Candida strains from women who had only one episode of infection within a 1-year period. In total, 87 isolates from 71 patients were cultured, speciated and genotyped by random amplification of polymorphic DNA (RAPD) analysis. Patients were categorized into three groups, namely those with: (i) a history of RVC from whom two or more yeast isolates were obtained (group A); (ii) a history of RVC from whom only a single isolate was obtained (group B); and (iii) a single episode of vaginal candidiasis within a 1-year period (group C). Six yeast species were detected: Candida albicans, Candida glabrata, Candida lusitaniae, Candida famata, Candida krusei and Candida parapsilosis. Interestingly, the prevalence of non-albicans species was higher in group A patients (50 %) than in patients in groups B (36 %) or C (18.9 %). Eighty RAPD profiles were observed, with a total of 61 polymorphic PCR fragments of distinct sizes. Clustering analysis showed that, overall, the majority of patients in group A had recurrent infections caused by highly similar, but not identical, sequential strains [mean pairwise similarity coefficient (S(AB)) = 0.721 +/- 0.308]. The range of mean S(AB) values for intergroup comparisons for C. albicans isolates alone was 0.50-0.56, suggesting that there was no significant relatedness between strains from different groups. Genetic similarity of C. albicans isolates from patients in group A was lower than that of C. albicans isolates from patients in group C (mean S(AB) = 0.532 +/- 0.249 and 0.636 +/- 0.206, respectively); this difference was statistically significant (P = 0.036). These results demonstrate that the cause of recurrent infections varies among individuals and ranges between strain maintenance, strain microevolution and strain replacement; the major scenario is strain maintenance with microevolution. They also show that C. albicans strains that cause recurrent infections are less similar to each other than strains that cause one-off infections, suggesting that the former may represent more virulent subtypes.
    Matched MeSH terms: Genetic Variation/genetics*
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