Displaying publications 41 - 60 of 746 in total

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  1. Fulltext Cytochrome P450 2D6 (CYP2D6) and glucose-6-phosphate dehydrogenase (G6PD) genetic variations in Thai vivax malaria patients: Implications for 8-aminoquinoline radical cure
    Chamchoy K, Sudsumrit S, Thita T, Krudsood S, Patrapuvich R, Boonyuen U
    PLoS Negl Trop Dis, 2022 Dec;16(12):e0010986.
    PMID: 36508454 DOI: 10.1371/journal.pntd.0010986
    BACKGROUND: Primaquine and tafenoquine are the only licensed drugs that effectively kill the hypnozoite stage and are used to prevent Plasmodium vivax malaria relapse. However, both primaquine and tafenoquine can cause acute hemolysis in glucose-6-phosphate dehydrogenase (G6PD)-deficient people with varying degrees of severity depending on G6PD variants. Additionally, primaquine efficacy against malaria parasites was decreased in individuals with impaired cytochrome P450 2D6 (CYP2D6) activity due to genetic polymorphisms. This study aimed to characterize G6PD and CYP2D6 genetic variations in vivax malaria patients from Yala province, a malaria-endemic area along the Thai-Malaysian border, and determine the biochemical properties of identified G6PD variants.

    METHODOLOGY/PRINCIPLE FINDINGS: Multiplexed high-resolution melting assay and DNA sequencing detected five G6PD variants, including G6PD Kaiping, G6PD Vanua Lava, G6PD Coimbra, G6PD Mahidol, and G6PD Kerala-Kalyan. Biochemical and structural characterization revealed that G6PD Coimbra markedly reduced catalytic activity and structural stability, indicating a high susceptibility to drug-induced hemolysis. While Kerala-Kalyan had minor effects, it is possible to develop mild adverse effects when receiving radical treatment. CYP2D6 genotyping was performed using long-range PCR and DNA sequencing, and the phenotypes were predicted using the combination of allelic variants. Decreased and no-function alleles were detected at frequencies of 53.4% and 14.2%, respectively. The most common alleles were CYP2D6*36+*10 (25.6%), *10 (23.9%), and *1 (22.2%). Additionally, 51.1% of the intermediate metabolizers showed CYP2D6*10/*36+*10 as the predominant genotype (15.9%).

    CONCLUSIONS/SIGNIFICANCE: Our findings provide insights about genetic variations of G6PD and CYP2D6 in 88 vivax malaria patients from Yala, which may influence the safety and effectiveness of radical treatment. Optimization of 8-aminoquinoline administration may be required for safe and effective treatment in the studied population, which could be a significant challenge in achieving the goal of eliminating malaria.

    Matched MeSH terms: Genetic Variation
  2. Bovine anaplasmosis: A systematic review with meta-analysis on the global prevalence
    Trop Biomed, 2023 Dec 01;40(4):375-382.
    PMID: 38308823 DOI: 10.47665/tb.40.4.001
    Bovine anaplasmosis, caused by Anaplasma marginale, is a significant infectious disease affecting cattle populations globally. However, the prevalence and distribution of bovine anaplasmosis vary across regions, making it crucial to assess its global burden systematically. This study aims to provide a comprehensive understanding of the global prevalence of bovine anaplasmosis and synthesized data from diverse geographic regions. A literature search was conducted to identify all relevant published articles reporting the prevalence of bovine anaplasmosis and a total of 164 studies were found eligible for final systematic review and meta-analysis. Meta-analysis was conducted using meta package of R software and summary estimates of the prevalence were calculated. Meta-analysis of 129,851 samples from 42 countries was conducted and the overall estimated prevalence of bovine anaplasmosis was found to be 38% (100% CI = 33% - 42%). The prevalence was found to be higher in cattle (39.9%) in comparison to yaks (6.4%). Diagnosis using serology (40.2%) yielded a higher prevalence compared to molecular testing (38.3%) and blood smears (22.4%) methods. Additionally, there were significant differences in the prevalence of bovine anaplasmosis between different countries (p<0.05). This study will inform evidence-based strategies for control and prevention of bovine anaplasmosis on a global scale by discovering the true extent of the disease and identifying high-prevalence areas.
    Matched MeSH terms: Genetic Variation
  3. Co-occurrence of dual lineages within Simulium (Gomphostilbia) atratum De Meijere in the Indonesian Archipelago along Wallace's Line
    Hew YX, Ya'cob Z, Chen CD, Lau KW, Sofian-Azirun M, Muhammad-Rasul AH, et al.
    Acta Trop, 2024 Feb;250:107097.
    PMID: 38097150 DOI: 10.1016/j.actatropica.2023.107097
    Mitochondrial cytochrome c oxidase subunit I (COI) sequences were utilized to infer the population genetic structure of Simulium (Gomphostilbia) atratum De Meijere, an endemic simulid species to Indonesia. Both median-joining haplotype network and maximum-likelihood tree revealed two genetic lineages (A and B) within the species, with an overlap distribution in Lombok, which is situated along Wallace's line. Genetic differentiation and gene flow with varying frequencies (FST = 0.02-0.967; Nm = 0.01-10.58) were observed between populations of S. (G.) atratum, of which population pairs of different lineages showed high genetic differentiation. Notably, the high genetic distance of up to 5.92 % observed within S. (G.) atratum in Lombok was attributed to the existence of two genetically distinct lineages. The co-occurrence of distinct lineages in Lombok indicated that Wallace's line did not act as faunistic border for S. (G.) atratum in the present study. Moreover, both lineages also exhibited unimodal distributions and negative values of neutrality tests, suggesting a pattern of population expansion. The expansion and divergence time estimation suggested that the two lineages of S. (G.) atratum diverged and expanded during the Pleistocene era in Indonesia.
    Matched MeSH terms: Genetic Variation
  4. Fulltext Heritability and genetic advance among chili pepper genotypes for heat tolerance and morphophysiological characteristics
    Usman MG, Rafii MY, Ismail MR, Malek MA, Abdul Latif M
    ScientificWorldJournal, 2014;2014:308042.
    PMID: 25478590 DOI: 10.1155/2014/308042
    High temperature tolerance is an important component of adaptation to arid and semiarid cropping environment in chili pepper. Two experiments were carried out to study the genetic variability among chili pepper for heat tolerance and morphophysiological traits and to estimate heritability and genetic advance expected from selection. There was a highly significant variation among the genotypes in response to high temperature (CMT), photosynthesis rate, plant height, disease incidence, fruit length, fruit weight, number of fruits, and yield per plant. At 5% selection intensity, high genetic advance as percent of the mean (>20%) was observed for CMT, photosynthesis rate, fruit length, fruit weight, number of fruits, and yield per plant. Similarly, high heritability (>60%) was also observed indicating the substantial effect of additive gene more than the environmental effect. Yield per plant showed strong to moderately positive correlations (r = 0.23-0.56) at phenotypic level while at genotypic level correlation coefficient ranged from 0.16 to 0.72 for CMT, plant height, fruit length, and number of fruits. Cluster analysis revealed eight groups and Group VIII recorded the highest CMT and yield. Group IV recorded 13 genotypes while Groups II, VII, and VIII recorded one each. The results showed that the availability of genetic variance could be useful for exploitation through selection for further breeding purposes.
    Matched MeSH terms: Genetic Variation*
  5. Killer immunoglobulin-like receptor diversity in Malay subethnic groups of Peninsular Malaysia
    NurWaliyuddin HZ, Edinur HA, Norazmi MN, Sundararajulu P, Chambers GK, Zafarina Z
    Int. J. Immunogenet., 2014 Dec;41(6):472-9.
    PMID: 25367623 DOI: 10.1111/iji.12161
    The KIR system shows variation at both gene content and allelic level across individual genome and populations. This variation reflects its role in immunity and has become a significant tool for population comparisons. In this study, we investigate KIR gene content in 120 unrelated individuals from the four Malay subethnic groups (Kelantan, Jawa, Banjar and Pattani Malays). Genotyping using commercial polymerase chain reaction-sequence-specific primer (PCR-SSP) kits revealed a total of 34 different KIR genotypes; 17 for Kelantan, 15 for Banjar, 14 for Jawa and 13 for Pattani Malays. Two new variants observed in Banjar Malays have not previously been reported. Genotype AA and haplotype A were the most common in Jawa (0.47 and 0.65, respectively), Banjar (0.37 and 0.52, respectively) and Pattani (0.40 and 0.60, respectively) Malays. In contrast, Kelantan Malays were observed to have slightly higher frequency (0.43) of genotype BB as compared with the others. Based on the KIR genes distribution, Jawa, Pattani and Banjar subethnic groups showed greater similarity and are discrete from Kelantan Malays. A principal component plot carried out using KIR gene carrier frequency shows that the four Malay subethnic groups are clustered together with other South-East Asian populations. Overall, our observation on prevalence of KIR gene content demonstrates genetic affinities between the four Malay subethnic groups and supports the common origins of the Austronesian-speaking people.
    Matched MeSH terms: Genetic Variation*
  6. 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: Genetic Variation*
  7. Fulltext Genetic variability and selection criteria in rice mutant lines as revealed by quantitative traits
    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. 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: Genetic Variation*
  9. Fulltext Genetic diversity in Passiflora species assessed by morphological and its sequence analysis
    Ramaiya SD, Bujang JS, Zakaria MH
    ScientificWorldJournal, 2014;2014:598313.
    PMID: 25050402 DOI: 10.1155/2014/598313
    This study used morphological characterization and phylogenetic analysis of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA to investigate the phylogeny of Passiflora species. The samples were collected from various regions of East Malaysia, and discriminant function analysis based on linear combinations of morphological variables was used to classify the Passiflora species. The biplots generated five distinct groups discriminated by morphological variables. The group consisted of cultivars of P. edulis with high levels of genetic similarity; in contrast, P. foetida was highly divergent from other species in the morphological biplots. The final dataset of aligned sequences from nine studied Passiflora accessions and 30 other individuals obtained from GenBank database (NCBI) yielded one most parsimonious tree with two strongly supported clades. Maximum parsimony (MP) tree showed the phylogenetic relationships within this subgenus Passiflora support the classification at the series level. The constructed phylogenic tree also confirmed the divergence of P. foetida from all other species and the closeness of wild and cultivated species. The phylogenetic relationships were consistent with results of morphological assessments. The results of this study indicate that ITS region analysis represents a useful tool for evaluating genetic diversity in Passiflora at the species level.
    Matched MeSH terms: Genetic Variation*
  10. DENVirDB: a web portal of dengue virus sequence information on Asian isolates
    Asnet MJ, Rubia AG, Ramya G, Nagalakshmi RN, Shenbagarathai R
    J Vector Borne Dis, 2014 Jun;51(2):82-5.
    PMID: 24947213
    DENVirDB is a web portal that provides the sequence information and computationally curated information of dengue viral proteins. The advent of genomic technology has increased the sequences available in the public databases. In order to create relevant concise information on Dengue Virus (DENV), the genomic sequences were collected, analysed with the bioinformatics tools and presented as DENVirDB. It provides the comprehensive information of complete genome sequences of dengue virus isolates of Southeast Asia, viz. India, Bangladesh, Sri Lanka, East Timor, Philippines, Malaysia, Papua New Guinea, Brunei and China. DENVirDB also includes the structural and non-structural protein sequences of DENV. It intends to provide the integrated information on the physicochemical properties, topology, secondary structure, domain and structural properties for each protein sequences. It contains over 99 entries in complete genome sequences and 990 entries in protein sequences, respectively. Therefore, DENVirDB could serve as a user friendly database for researchers in acquiring sequences and proteomic information in one platform.
    Matched MeSH terms: Genetic Variation*
  11. The mitochondrial 16 s rRNA reveals high anthropogenic influence on land snail diversity in a preliminary island survey
    Abu-Bakar SB, Razali NM, Naggs F, Wade C, Mohd-Nor SA, Aileen-Tan SH
    Mol Biol Rep, 2014 Mar;41(3):1799-805.
    PMID: 24443224 DOI: 10.1007/s11033-014-3029-5
    A total of 30 specimens belonging to five species, namely; Cryptozona siamensis, Sarika resplendens and Sarika sp. from the family Ariophantidae as well as Quantula striata and Quantula sp. from the family Dyakiidae were collected from the Langkawi Island in Northern Peninsular Malaysia. All specimens were identified through comparisons of shell morphology and amplification of a 500 bp segment of the 16S rRNA mtDNA gene. To assess phylogenetic insights, the sequences were aligned using ClustalW and phylogenetic trees were constructed. The analyses showed two major lineages in both Maximum Parsimony and Neighbour Joining phylogenetic trees. Each putative taxonomic group formed a monophyletic cluster. Our study revealed low species and intraspecies genetic diversities based on the 16S rRNA gene sequences. Thus, this study has provided an insight of land snail diversity in populations of an island highly influenced by anthropogenic activities through complementary use of shell morphological and molecular data.
    Matched MeSH terms: Genetic Variation*
  12. Fulltext Genetic structure and preliminary findings of cryptic diversity of the Malaysian Mahseer (Tor tambroides Valenciennes: Cyprinidae) inferred from mitochondrial DNA and microsatellite analyses
    Esa Y, Abdul Rahim KA
    Biomed Res Int, 2013;2013:170980.
    PMID: 24455674 DOI: 10.1155/2013/170980
    This study examines the population genetic structure of Tor tambroides, an important freshwater fish species in Malaysia, using fifteen polymorphic microsatellite loci and sequencing of 464 base pairs of the mitochondrial cytochrome c oxidase I (COI) gene. A total of 152 mahseer samples were collected from eight populations throughout the Malaysia river system. Microsatellites results found high levels of intrapopulation variations, but mitochondrial COI results found high levels of interpopulations differentiation. The possible reasons for their discrepancies might be the varying influence of genetic drift on each marker or the small sample sizes used in most of the populations. The Kelantan population showed very low levels of genetic variations using both mitochondrial and microsatellite analyses. Phylogenetic analysis of the COI gene found a unique haplotype (ER8∗), possibly representing a cryptic lineage of T. douronensis, from the Endau-Rompin population. Nevertheless, the inclusion of nuclear microsatellite analyses could not fully resolve the genetic identity of haplotype ER8∗ in the present study. Overall, the findings showed a serious need for more comprehensive and larger scale samplings, especially in remote river systems, in combination with molecular analyses using multiple markers, in order to discover more cryptic lineages or undescribed "genetic species" of mahseer.
    Matched MeSH terms: Genetic Variation*
  13. Analysis of the genetic diversity of physic nut, Jatropha curcas L. accessions using RAPD markers
    Rafii MY, Shabanimofrad M, Puteri Edaroyati MW, Latif MA
    Mol Biol Rep, 2012 Jun;39(6):6505-11.
    PMID: 22307785 DOI: 10.1007/s11033-012-1478-2
    A sum of 48 accessions of physic nut, Jatropha curcas L. were analyzed to determine the genetic diversity and association between geographical origin using RAPD-PCR markers. Eight primers generated a total of 92 fragments with an average of 11.5 amplicons per primer. Polymorphism percentages of J. curcas accessions for Selangor, Kelantan, and Terengganu states were 80.4, 50.0, and 58.7%, respectively, with an average of 63.04%. Jaccard's genetic similarity co-efficient indicated the high level of genetic variation among the accessions which ranged between 0.06 and 0.81. According to UPGMA dendrogram, 48 J. curcas accessions were grouped into four major clusters at coefficient level 0.3 and accessions from same and near states or regions were found to be grouped together according to their geographical origin. Coefficient of genetic differentiation (G(st)) value of J. curcas revealed that it is an outcrossing species.
    Matched MeSH terms: Genetic Variation*
  14. 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: Genetic Variation*
  15. Fulltext Morphometric and molecular analysis of mackerel (Rastrelliger spp) from the west coast of Peninsular Malaysia
    Darlina MN, Masazurah AR, Jayasankar P, Jamsari AF, Siti AM
    Genet. Mol. Res., 2011;10(3):2078-92.
    PMID: 21968625 DOI: 10.4238/vol10-3gmr1249
    Mackerel (Scombridae; Rastrelliger) are small commercially important pelagic fish found in tropical regions. They serve as a cheap source of animal protein and are commonly used as live bait. By using a truss morphometrics protocol and RAPD analysis, we examined morphological and genetic variation among 77 individual mackerel that were caught using long lines and gillnets at 11 locations along the west coast of Peninsular Malaysia. Nineteen morphometric traits were evaluated and genetic information was estimated using five 10-base RAPD random primers. Total DNA was extracted from muscle tissue. Morphometric discriminant function analysis revealed that two morphologically distinct groups of Rastrelliger kanagurta and a single group of R. brachysoma can be found along the west coast of Peninsular Malaysia. We also found that the head-related characters and those from the anterior part of the body of Rastrelliger spp significantly contribute to stock assessment of this population. RAPD analysis showed a trend similar to that of the morphometric analysis, suggesting a genetic component to the observed phenotypic differentiation. These data will be useful for developing conservation strategies for these species.
    Matched MeSH terms: Genetic Variation*
  16. Microsatellite based analysis of genetic diversity of popular black pepper genotypes in South India
    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*
  17. Initiating a Human Variome Project Country Node
    AlAama J, Smith TD, Lo A, Howard H, Kline AA, Lange M, et al.
    Hum Mutat, 2011 May;32(5):501-6.
    PMID: 21305654 DOI: 10.1002/humu.21463
    Genetic diseases are a pressing global health problem that requires comprehensive access to basic clinical and genetic data to counter. The creation of regional and international databases that can be easily accessed by clinicians and diagnostic labs will greatly improve our ability to accurately diagnose and treat patients with genetic disorders. The Human Variome Project is currently working in conjunction with human genetics societies to achieve this by establishing systems to collect every mutation reported by a diagnostic laboratory, clinic, or research laboratory in a country and store these within a national repository, or HVP Country Node. Nodes have already been initiated in Australia, Belgium, China, Egypt, Malaysia, and Kuwait. Each is examining how to systematically collect and share genetic, clinical, and biochemical information in a country-specific manner that is sensitive to local ethical and cultural issues. This article gathers cases of genetic data collection within countries and takes recommendations from the global community to develop a procedure for countries wishing to establish their own collection system as part of the Human Variome Project. We hope this may lead to standard practices to facilitate global collection of data and allow efficient use in clinical practice, research and therapy.
    Matched MeSH terms: Genetic Variation*
  18. Genetic differentiation of the Fejervarya limnocharis complex from Bangladesh and other Asian countries elucidated by allozyme analyses
    Islam MM, Khan MM, Tjong DH, Alam MS, Sumida M
    Zoolog Sci, 2008 Mar;25(3):261-72.
    PMID: 18393563 DOI: 10.2108/zsj.25.261
    The present study was conducted to elucidate the genetic divergence and the phylogenetic relationships in the F. limnocharis complex from Bangladesh and other Asian countries such as Sri Lanka, Thailand, Malaysia, Taiwan and Japan by allozyme analyses. We used a total of 95 frogs of the F. limnocharis complex from these countries and F. cancrivora from the Philippines as an outgroup. Based on body size, the F. limnocharis complex from Bangladesh was divided into three distinct groups: large, medium and small types. Allozyme analyses were carried out with 28 loci encoding 20 enzymes and two blood proteins by horizontal starch-gel electrophoresis. When genetic distance was calculated, distinct divergence was found among the three types: mean genetic distance was 0.782 between the small and medium types, 1.458 between the large and medium types, and 1.520 between the large and small types. Phylogenetic trees based on genetic distance showed that all populations of Bangladesh small type strongly formed a cluster and were found to be most closely related to the Sri Lanka population; that all populations of Bangladesh large type formed a very strong cluster and were grouped with several populations from Thailand, Malaysia, Japan, and Taiwan; and that the medium type was segregated from all other groups. This may imply that each of the three types is a different species, and that the medium type is possibly an undescribed taxon.
    Matched MeSH terms: Genetic Variation*
  19. Microsatellite variation among divergent populations of stalk-eyed flies, genus Cyrtodiopsis
    Wright TF, Johns PM, Walters JR, Lerner AP, Swallow JG, Wilkinson GS
    Genet. Res., 2004 Aug;84(1):27-40.
    PMID: 15663256
    Microsatellite primers are often developed in one species and used to assess neutral variability in related species. Such analyses may be confounded by ascertainment bias (i.e. a decline in amplification success and allelic variability with increasing genetic distance from the source of the microsatellites). In addition, other factors, such as the size of the microsatellite, whether it consists of perfect or interrupted tandem repeats, and whether it is autosomal or X-linked, can affect variation. To test the relative importance of these factors on microsatellite variation, we examine patterns of amplification and allelic diversity in 52 microsatellite loci amplified from five individuals in each of six populations of Cyrtodiopsis stalk-eyed flies that range from 2.2 % to 11.2% mitochondrial DNA sequence divergence from the population used for microsatellite development. We find that amplification success and most measures of allelic diversity declined with genetic distance from the source population, in some cases an order of magnitude faster than in birds or mammals. The median and range of the repeat array length did not decline with genetic distance. In addition, for loci on the X chromosome, we find evidence of lower observed heterozygosity compared with loci on autosomes. The differences in variability between X-linked and autosomal loci are not adequately explained by differences in effective population sizes of the chromosomes. We suggest, instead, that periodic selection events associated with X-chromosome meiotic drive, which is present in many of these populations, reduces X-linked variation.
    Matched MeSH terms: Genetic Variation*
  20. Genotyping of microsatellite markers to study genetic structure of the wild striped snakehead Channa striata in Malaysia
    Tan MP, Jamsari AF, Siti Azizah MN
    J Fish Biol, 2016 May;88(5):1932-48.
    PMID: 27027270 DOI: 10.1111/jfb.12956
    Genetic variability and differences in wild striped snakehead Channa striata from Malaysia were analysed by genotyping nine novel nuclear microsatellite loci. Analysis revealed moderate-to-high genetic diversity in most of the populations, indicative of large effective population sizes. The highly diversified populations are admixed populations and, therefore, can be recommended as potential candidates for selective breeding and conservation since they each contain most of the alleles found in their particular region. Three homogenous groups of the wild populations were identified, apparently separated by effective barriers, in accordance with contemporary drainage patterns. The highest population pairwise FST found between members of the same group reflects the ancient population connectivity; yet prolonged geographical isolation resulted in adaptation of alleles to local contemporary environmental change. A significant relationship between genetic distance and geographical isolation was observed (r = 0·644, P < 0·01). Anthropogenic perturbations indicated apparent genetic proximity between distant populations.
    Matched MeSH terms: Genetic Variation*
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