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A twins heritability study on alpha hemoglobin stabilizing protein (AHSP) expression variability

Lai MI, Garner C, Jiang J, Silver N, Best S, Menzel S, et al.

Twin Res Hum Genet, 2010 Dec;13(6):567-72.
PMID: 21142933 DOI: 10.1375/twin.13.6.567

Cytotoxic precipitation of free α-globin monomers and its production of reactive oxygen species cause red cell membrane damage that leads to anemia and eventually ineffective erythropoiesis in β-thalassemia. Alpha hemoglobin stabilizing protein (AHSP) was found to bind only to free α-globin monomers creating a stable and inert complex which remains soluble in the cytoplasm thus preventing harmful precipitations. Alpha hemoglobin stabilizing protein was shown to bind nascent α-globin monomers with transient strength before transferring α-globin to β-globin to form hemoglobin tetramer. A classical twin study would be beneficial to investigate the role of genetics and environment in the variation of alpha hemoglobin stabilizing protein expression as this knowledge will enable us to determine further investigations with regards to therapeutic interventions if alpha hemoglobin stabilizing protein is to be a therapeutic agent for β-thalassemia. This study investigates the heritability influence of alpha hemoglobin stabilizing protein expression and factors that may contribute to this. Results indicated that a major proportion of alpha hemoglobin stabilizing protein expression was influenced by genetic heritability (46%) with cis-acting factors accounting for 19% and trans-acting factors at 27%.

Matched MeSH terms: Microsatellite Repeats/genetics
Fulltext Accumulation of Mitochondrial DNA Microsatellite Instability in Malaysian Patients with Primary Central Nervous System Tumors

Radzak S, Khair Z, Ahmad F, Idris Z, Yusoff A

Turk Neurosurg, 2021;31(1):99-106.
PMID: 33491172 DOI: 10.5137/1019-5149.JTN.27893-20.4

AIM: To determine the mitochondrial microsatellite instability (mtMSI) status in a series of Malaysian patients with brain tumors. Furthermore, we analyzed whether the mtMSI status is associated with the clinicopathological features of the patients.
MATERIAL AND METHODS: Forty fresh frozen tumor tissues along with blood samples of brain tumor patients were analyzed for mtMSI by PCR amplification of genomic DNAs, and the amplicons were directly sequenced in both directions using Sanger sequencing.
RESULTS: Microsatellite analysis revealed that 20% (8 out of 40) of the tumors were mtMSI positive with a total of 8 mtMSI changes. All mtMSI markers were detected in D310 and D16184 of the D-loop region. Additionally, no significant association was observed between mtMSI status and clinicopathological features.
CONCLUSION: The variations, specifically the mtMSI, suggest that the mitochondrial DNA (mtDNA) can be targeted for genomic alteration in brain tumors. Therefore, the specific role of mtDNA alteration in brain tumor development and prognosis requires further investigation.

Matched MeSH terms: Microsatellite Repeats/genetics
Genetic Diversity of Pineapple (Ananas comosus) Germplasm in Malaysia Using Simple Sequence Repeat (SSR) Markers

Ismail SN, Ghani NSA, Ab Razak SF, Abidin RAZ, Mohd Yusof MF, Zubir MN, et al.

Trop Life Sci Res, 2020 Oct;31(3):15-27.
PMID: 33214853 DOI: 10.21315/tlsr2020.31.3.2

Assessments of genetic diversity have been claimed to be significantly efficient in utilising and managing resources of genetic for breeding programme. In this study, variations in genetic were observed in 65 pineapple accessions gathered from germplasm available at Malaysian Agriculture Research and Development Institute (MARDI) located in Pontian, Johor via 15 markers of simple sequence repeat (SSR). The results showed that 59 alleles appeared to range from 2.0 to 6.0 alleles with a mean of 3.9 alleles per locus, thus displaying polymorphism for all samples at a moderate level. Furthermore, the values of polymorphic information content (PIC) had been found to range between 0.104 (TsuAC035) and 0.697 (Acom_9.9), thus averaging at the value of 0.433. In addition, the expected and the observed heterozygosity of each locus seemed to vary within the ranges of 0.033 to 0.712, and from 0.033 to 0.885, along with the average values of 0.437 and 0.511, respectively. The population structure analysis via method of delta K (ΔK), along with mean of L (K) method, revealed that individuals from the germplasm could be divided into two major clusters based on genetics (K = 2), namely Group 1 and Group 2. As such, five accessions (Yankee, SRK Chalok, SCK Giant India, SC KEW5 India and SC1 Thailand) were clustered in Group 1, while the rest were clustered in Group 2. These outcomes were also supported by the dendrogram, which had been generated through the technique of unweighted pair group with arithmetic mean (UPGMA). These analyses appear to be helpful amongst breeders to maintain and to manage their collections of germplasm. Besides, the data gathered in this study can be useful for breeders to exploit the area of genetic diversity in estimating the level of heterosis.

Matched MeSH terms: Microsatellite Repeats
Genetic structure of the dengue vector Aedes albopictus (Skuse) from different developed settlements in Penang Island, Malaysia based on microsatellite markers

Muhammad NAF, Kassim NFA, Ab Majid AH, Wajidi MFF, Jamsari AFJ, Dieng H, et al.

Trop Biomed, 2018 Dec 01;35(4):1049-1063.
PMID: 33601852

The medically important mosquito, Aedes albopictus is native to Asia and has become a major health concern in most Asian countries including Malaysia. Being recognized as a dengue vector, a clearer understanding of how mosquito populations are geographically connected, may therefore represent a profound yet significant understanding of control strategies. There are no documented reports on the genetic structure of Ae. albopictus populations from different developed settlements inferred from microsatellite DNA markers in Malaysia, particularly in Penang Island (Northern Peninsular Malaysia). Here, we assessed the molecular population genetics of Ae. albopictus in terms of their allelic variation, genetic diversity and population structure. A total of 42 mosquitoes were sampled from Jelutong, Batu Maung and Balik Pulau which represented urban, suburban and rural areas in Penang Island respectively and analysed for polymorphism at six microsatellite loci. All of the microsatellite markers were successfully amplified and were polymorphic, showing low genetic structure among geographic populations (FST= 0.0362). It is supported with admixture individuals observed in STRUCTURE and FCA and this suggests that high gene flow has been experienced between populations. These findings implicate passive dispersal through human-aided transportation; as a factor shaping the genetic structure of Ae. albopictus populations in Penang Island.

Matched MeSH terms: Microsatellite Repeats
Fulltext Presence of allelic loss and PTEN mutations in malignant gliomas from Malay patients

Zainuddin N, Jaafar H, Isa MN, Abdullah JM

Med J Malaysia, 2004 Oct;59(4):468-79.
PMID: 15779579

Loss of heterozygosity (LOH) on several loci and mutations on PTEN tumor suppressor gene (10q23.3) occur frequently in sporadic gliomas. We have performed polymerase chain reaction (PCR)-LOH analysis using microsatellite markers and single-stranded conformational polymorphism (SSCP) analysis to determine the incidence of allelic losses on chromosome 10q, 9p, 17p and 13q and mutations of exons 5, 6 and 8 of the PTEN gene in malignant gliomas. Twelve of 23 (52.2%) malignant glioma cases showed allelic losses whereas 7 of 23, (30.4%) samples showed aberrant band patterns and mutations of the PTEN gene. Four of these cases showed LOH on 10q23 and mutations of the PTEN gene. The data on LOH indicated the involvement of different genes in gliomagenesis whereas mutations of the PTEN gene indicated the role of PTEN tumor suppressor gene in the progression of glioma in Malay population.

Matched MeSH terms: Microsatellite Repeats
Assessing donor chimerism using flow cytometry in paroxysmal nocturnal haemoglobinuria after stem cell transplantation--a case report

Azma RZ, Hamidah NH, Leong CF, Ainoon O, Cheong SK

Malays J Pathol, 2006 Dec;28(2):107-12.
PMID: 18376800

Paroxysmal nocturnal haemoglobinuria (PNH) is an acquired haemopoietic stem cell disorder arising from somatic mutation of the X-linked PIG-A gene which leads to deficiency of the glycosylphosphatidylinositol (GP1) membrane anchor proteins such as CD 59 (MIRL: membrane inhibitor of reactive lysis) and CD 55 (DAF: decay accelerating factor). Allogeneic peripheral blood stem cell transplant (PBSCT) is a curative mode of treatment in symptomatic PNH patients. Assessment of donor chimerism for PBSCT can be performed by various methods including short tandem repeat loci (STR) and variable number of tandem repeats (VNTR). Flow cytometry, which is much cheaper and faster, also can be used to assess engraftment in patients with PNH. Engrafted patients will show the presence of CD 55 and CD 59 on their red cells and white cells. We describe here the usefulness of flow cytometry in the assessment of donor chimerism following allogeneic PBSCT, in a case of PNH.

Matched MeSH terms: Microsatellite Repeats
Screening for microsatellite instability in colorectal carcinoma: Practical utility of immunohistochemistry and PCR with fragment analysis in a diagnostic histopathology setting

Cheah PL, Li J, Looi LM, Koh CC, Lau TP, Chang SW, et al.

Malays J Pathol, 2019 Aug;41(2):91-100.
PMID: 31427545

Since 2014, the National Comprehensive Cancer Network (NCCN) has recommended that colorectal carcinoma (CRC) be universally tested for high microsatellite instability (MSI-H) which is present in 15% of such cancers. Fidelity of resultant microsatellites during DNA replication is contingent upon an intact mismatch repair (MMR) system and lack of fidelity can result in tumourigenesis. Prior to commencing routine screening for MSI-H, we assessed two commonly used methods, immunohistochemical (IHC) determination of loss of MMR gene products viz MLH1, MSH2, MSH6 and PMS2 against PCR amplification and subsequent fragment analysis of microsatellite markers, BAT25, BAT26, D2S123, D5S346 and D17S250 (Bethesda markers) in 73 unselected primary CRC. 15.1% (11/73) were categorized as MSI-H while deficient MMR (dMMR) was detected in 16.4% (12/73). Of the dMMR, 66.7% (8/12) were classified MSI-H, while 33.3% (4/12) were microsatellite stable/low microsatellite instability (MSS/MSI-L). Of the proficient MMR (pMMR), 95.1% (58/61) were MSS/MSI-L and 4.9% (3/61) were MSI-H. The κ value of 0.639 (standard error =0.125; p = 0.000) indicated substantial agreement between detection of loss of DNA mismatch repair using immunohistochemistry and the detection of downstream microsatellite instability using PCR. After consideration of advantages and shortcomings of both methods, it is our opinion that the choice of preferred technique for MSI analysis would depend on the type of laboratory carrying out the testing.

Matched MeSH terms: Microsatellite Repeats
Fulltext Forensic DNA Profiling: Autosomal Short Tandem Repeat as a Prominent Marker in Crime Investigation

Nwawuba Stanley U, Mohammed Khadija A, Bukola AT, Omusi Precious I, Ayevbuomwan Davidson E

Malays J Med Sci, 2020 Jul;27(4):22-35.
PMID: 32863743 DOI: 10.21315/mjms2020.27.4.3

Short tandem repeat (STR) typing continues to be the primary workhorse in forensic DNA profiling. Therefore, the present review discusses the prominent role of STR marker in criminal justice system. All over the world, deoxyribonucleic acid (DNA) profiling provides evidence that may be used to convict criminals, as an irrefutable proof of wrongful convictions, invaluable links to the actual perpetrators of crimes, and could also deter some offenders from committing more serious offences. Clearly, DNA profiling tools have also aided forensic scientists to re-evaluate old cases that were considered closed as a result of inadequate evidence. In carrying out this review, a comprehensive electronic literature search using PubMed, ScienceDirect, Google Scholar and Google Search were used, and all works meeting the subject matter were considered, including reviews, retrospective studies, observational studies and original articles. Case reports presented here, further demonstrates the crucial role of forensic DNA profiling in mitigating and providing compelling evidence for the resolution of crimes. For case report 1, there was a 100% match between the DNA recovered from the items found in the crime scene, and the suspect's DNA sample collected via buccal swab following 15 STR loci examination. Case report 2 further highlights the indispensable contribution of DNA database in solving crime. Therefore, it has become very necessary for developing countries like Nigeria to develop a national DNA database and make policies and legislatures that will further expand and enable the practice of forensic genetics, particularly DNA profiling.

Matched MeSH terms: Microsatellite Repeats
Fulltext Electrophoretic Techniques for the Detection of Human Microsatellite D19S884

Mansor F, Zamri L, Hamzah SS

Malays J Med Sci, 2015 Mar-Apr;22(2):18-24.
PMID: 26023291 MyJurnal

The detection and analysis of microsatellites is very important for the mapping of genetic diseases because they are commonly used as genetic markers. Microsatellite marker D19S884 has been associated with polycystic ovary syndrome (PCOS), the most common reproductive endocrine disease of women in their childbearing years. It is responsible for an estimated 70% of cases of anovulatory infertility. In this work, we detected microsatellites in DNA extracted from the blood of PCOS patients.

Matched MeSH terms: Microsatellite Repeats
Genetic Structure and Diversity Among Historic and Modern Populations of the Sumatran Rhinoceros (Dicerorhinus sumatrensis)

Brandt JR, van Coeverden de Groot PJ, Witt KE, Engelbrektsson PK, Helgen KM, Malhi RS, et al.

J Hered, 2018 06 27;109(5):553-565.
PMID: 29684146 DOI: 10.1093/jhered/esy019

The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samples. Museum specimens from Laos and Myanmar had divergent mtDNA, consistent with the placement of western mainland rhinos into the distinct subspecies D. s. lasiotis (presumed extinct). Haplotypes from Bornean rhinos were highly diverse, but dissimilar from those of other regions, supporting the distinctiveness of the subspecies D. s. harrissoni. Rhinos from Sumatra and Peninsular Malaysia shared mtDNA haplotypes, consistent with their traditional placement into a single subspecies D. s sumatrensis. Modern samples of D. s. sumatrensis were genotyped at 18 microsatellite loci. Rhinos within Sumatra formed 2 sub-populations, likely separated by the Barisan Mountains, though with only modest genetic differentiation between them. There are so few remaining Sumatran rhinoceros that separate management strategies for subspecies or subpopulations may not be viable, while each surviving rhino pedigree is likely to retain alleles found in no other individuals. Given the low population size and low reproductive potential of Sumatran rhinos, rapid genetic erosion is inevitable, though an under-appreciated concern is the potential for fixation of harmful genetic variants. Both concerns underscore 2 overriding priorities for the species: 1) translocation of wild rhinos to ex situ facilities, and 2) collection and storage of gametes and cell lines from every surviving captive and wild individual.

Matched MeSH terms: Microsatellite Repeats
Genetic Diversity and Demographic History of an Upper Hill Dipterocarp (Shorea platyclados): Implications for Conservation

Ng CH, Lee SL, Tnah LH, Ng KKS, Lee CT, Diway B, et al.

J Hered, 2019 12 17;110(7):844-856.
PMID: 31554011 DOI: 10.1093/jhered/esz052

Southeast Asian rainforests at upper hill elevations are increasingly vulnerable to degradation because most lowland forest areas have been converted to different land uses. As such, understanding the genetics of upper hill species is becoming more crucial for their future management and conservation. Shorea platyclados is an important, widespread upper hill dipterocarp in Malaysia. To elucidate the genetic structure of S. platyclados and ultimately provide guidelines for a conservation strategy for this species, we carried out a comprehensive study of the genetic diversity and demographic history of S. platyclados. Twenty-seven populations of S. platyclados across its range in Malaysia were genotyped at 15 polymorphic microsatellite loci and sequenced at seven noncoding chloroplast DNA (cpDNA) regions. A total of 303 alleles were derived from the microsatellite loci, and 29 haplotypes were identified based on 2892 bp of concatenated cpDNA sequences. The populations showed moderately high genetic diversity (mean HE = 0.680 for microsatellite gene diversity and HT = 0.650 for total haplotype diversity) and low genetic differentiation (FST = 0.060). Bayesian clustering divided the studied populations into two groups corresponding to western and eastern Malaysia. Bottleneck analysis did not detect any recent bottleneck events. Extended Bayesian skyline analyses showed a model of constant size for the past population history of this species. Based on our findings, priority areas for in situ and ex situ conservation and a minimum population size are recommended for the sustainable utilization of S. platyclados.

Matched MeSH terms: Microsatellite Repeats
Fulltext Population Genetics of Identifiler System in Malaysia

Nakamura Y, Samejima M, Minaguchi K, Nambiar P

Bull. Tokyo Dent. Coll., 2016;57(4):233-239.
PMID: 28049971 DOI: 10.2209/tdcpublication.2016-1400

Short tandem repeat (STR) polymorphisms were investigated in 341 unrelated Malay individuals (218 males and 123 females) living in or around Kuala Lumpur by using a forensic analysts kit. The following STRs were targeted: D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA. The purpose of this study was to elucidate population genetics in Malaysia and calculate statistical parameters for forensic and anthropological research. Data on these STRs in the target population were obtained and subjected to statistical analysis. Accordance with the Hardy-Weinberg equilibrium was proven for all the loci targeted. The combined power of discrimination was greater than 0.9999999999, indicating that this multiplex system is an excellent tool for forensic casework. The allele frequency in the data were weighed against that in four other local populations (Chinese, Iranian, Belgian, and African). The average coefficient of correlation was strongest in the order of Africa (0.092522), Belgium (0.264822), Iran (0.404363), and China (0.706661). These results are consistent with what is known about the anthropological history of and prehistoric human migration in the Malay region. We believe that these data offer a valuable anthropological resource, being applicable to the statistical evaluation of DNA evidence in human identification, as well as the determination of ethnicity in healthy populations.

Matched MeSH terms: Microsatellite Repeats*
Fulltext Evaluation of two short tandem repeat multiplex systems for post-haematopoietic stem cell transplantation chimerism analysis

Ariffin H, Daud SS, Mohamed Z, Ibrahim K, Lee TF, Chong LA

Singapore Med J, 2007 Apr;48(4):333-7.
PMID: 17384881

The follow-up of chimerism status after allogeneic haematopoietic stem cell transplantation (HSCT) is essential to predict successful engraftment to assess the development of graft-versus-host disease, graft rejection and disease relapse. Analysis of short tandem repeats (STR) via polymerase chain reaction is frequently used for chimerism determination. However, most commercially-available kits have been designed for forensic purposes and may not be optimal for chimerism analysis. The present study aims to identify suitable STR markers for patient-donor pairs of predominantly Malay and Chinese ethnicity using two commercially-available forensic kits.

Matched MeSH terms: Microsatellite Repeats*
Fulltext Assessment of autosomal and male DNA extracted from casework samples using Casework Direct Kit, Custom and Maxwell 16 System DNA IQ Casework Pro Kit for autosomal-STR and Y-STR profiling

Hakim HM, Khan HO, Ismail SA, Ayob S, Lalung J, Kofi EA, et al.

Sci Rep, 2019 10 10;9(1):14558.
PMID: 31601905 DOI: 10.1038/s41598-019-51154-4

Short repetitive regions in autosomal and Y chromosomes known as short tandem repeats (STRs) are currently used for DNA profiling in crime investigations. However, DNA profiling requires a sufficient quality and quantity of DNA template, which is often not obtained from trace evidence or degraded biological samples collected at the scene of a crime. Here, we assessed autosomal and male DNA components extracted from crime scene and mock casework samples using the Casework Direct Kit, Custom and compared the results against those obtained by extraction of matching samples using well-established Maxwell 16 System DNA IQ Casework Pro Kit. The quantity and quality of extracted DNA obtained using both Casework Direct Kit, Custom and Maxwell 16 System DNA IQ Casework Pro Kit were analyzed using PowerQuant Systems followed by autosomal and Y-chromosome STR profiling using GlobalFiler Express PCR Amplification Kit and PowerPlex Y23 System, respectively. Our results showed that the Casework Direct Kit and Maxwell 16 DNA IQ Casework Pro Kit have more or less equal capacity to extract inhibitor free DNA, but that the latter produces slightly better quality and more DNA template and subsequently higher numbers of STR allele calls for autosomal and Y-STR analyses. Nonetheless, the Casework Direct Kit, Custom is the quicker and cheaper option for extraction of good, clean DNA from high content material and might best be used for extraction of reference samples. Such reference DNA samples typically come from buccal swabs or freshly drawn blood. So, in general, they can confidently be expected to have a high nucleic acid content and to be inhibitor-free.

Matched MeSH terms: Microsatellite Repeats*
Fulltext Low genetic diversity indicating the threatened status of Rhizophora apiculata (Rhizophoraceae) in Malaysia: declined evolution meets habitat destruction

Azman A, Ng KK, Ng CH, Lee CT, Tnah LH, Zakaria NF, et al.

Sci Rep, 2020 11 05;10(1):19112.
PMID: 33154411 DOI: 10.1038/s41598-020-76092-4

Worldwide, many mangrove species are experiencing significant population declines, including Rhizophora apiculata, which is one of the most widespread and economically important species in tropical Asia. In Malaysia, there has been an alarming decline in R. apiculata populations driven primarily by anthropogenic activities. However, the lack of genetic and demographic information on this species has hampered local efforts to conserve it. To address these gaps, we generated novel genetic information for R. apiculata, based on 1,120 samples collected from 39 natural populations in Peninsular Malaysia. We investigated its genetic diversity and genetic structure with 19 transcriptome and three nuclear microsatellite markers. Our analyses revealed a low genetic diversity (mean He: 0.352) with significant genetic differentiation (FST: 0.315) among populations of R. apiculata. Approximately two-third of the populations showed significant excess of homozygotes, indicating persistent inbreeding which might be due to the decrease in population size or fragmentation. From the cluster analyses, the populations investigated were divided into two distinct clusters, comprising the west and east coasts of Peninsular Malaysia. The western cluster was further divided into two sub-clusters with one of the sub-clusters showing strong admixture pattern that harbours high levels of genetic diversity, thus deserving high priority for conservation.

Matched MeSH terms: Microsatellite Repeats
Fulltext Molecular sexing and preliminary assessment of population sex ratio of the endangered Malayan tapir (Tapirus indicus) in Peninsular Malaysia

Lim QL, Tan YL, Ng WL, Yong CSY, Ismail A, Rovie-Ryan JJ, et al.

Sci Rep, 2020 03 04;10(1):3973.
PMID: 32132572 DOI: 10.1038/s41598-020-60552-y

A molecular sexing method by polymerase chain reaction (PCR) amplification of a portion of the sex-determining region Y (SRY) and the zinc finger (ZF) gene, as well as six equine Y-chromosome-specific microsatellite markers, were tested in the Malayan tapir (Tapirus indicus). While the microsatellite markers did not yield any male-specific amplicons for sex-typing, the SRY/ZF marker system produced reliable molecular sexing results by accurately sex-typing 31 reference Malayan tapirs, using whole blood, dried blood spot (DBS), or tissue samples as materials for DNA extraction. The marker system was also tested on 16 faecal samples, and the results were in general consistent with the pre-determined sexes of the animals, despite some amplification failures. A preliminary estimation of wild Malayan tapir population sex ratio was estimated from the Wildlife Genomic Resource Bank (WGRB) database of the Malaysian Department of Wildlife and National Parks (PERHILITAN), zoos, and the Sungai Dusun Wildlife Conservation Centre (WCC), as well as from the results of molecular sexing 12 samples of unknown sex. The overall sex ratio favoured females, but the deviation from parity was statistically not significant when tested using the binomial test (p > 0.05), which may be due to reduced statistical power caused by small sample sizes.

Matched MeSH terms: Microsatellite Repeats/genetics
Fulltext Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis

Chang W, Ee-Uli J, Ng WL, Rovie-Ryan JJ, Tan SG, Yong CSY

Sci Rep, 2019 06 11;9(1):8504.
PMID: 31186469 DOI: 10.1038/s41598-019-44870-4

Macaca fascicularis, also known as the cynomolgus macaque, is an important non-human primate animal model used in biomedical research. It is an Old-World primate widely distributed in Southeast Asia and is one of the most abundant macaque species in Malaysia. However, the genetic structure of wild cynomolgus macaque populations in Malaysia has not been thoroughly elucidated. In this study, we developed genic-simple sequence repeat (genic-SSR) markers from an in-house transcriptome dataset generated from the Malaysian cynomolgus macaque via RNA sequencing, and applied these markers on 26 cynomolgus macaque individuals. A collection of 14,751 genic-SSRs were identified, where 13,709 were perfect SSRs. Dinucleotide repeats were the most common repeat motifs with a frequency of 65.05%, followed by trinucleotide repeats (20.55%). Subsequently, we designed 300 pairs of primers based on perfect di- and trinucleotide SSRs, in which 105 SSRs were associated with functional genes. A subset of 30 SSR markers were randomly selected and validated, yielding 19 polymorphic markers with an average polymorphism information content value of 0.431. The development of genic-SSR markers in this study is indeed timely to provide useful markers for functional and population genetic studies of the cynomolgus macaque and other related non-human primate species.

Matched MeSH terms: Microsatellite Repeats
Fulltext Forensic characterization of 15 autosomal STRs in four populations from Xinjiang, China, and genetic relationships with neighboring populations

Zhan X, Adnan A, Zhou Y, Khan A, Kasim K, McNevin D

Sci Rep, 2018 03 16;8(1):4673.
PMID: 29549272 DOI: 10.1038/s41598-018-22975-6

The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors 47 ethnic groups including the Manchu (MCH: 0.11%), Mongols (MGL: 0.81%), Kyrgyz (KGZ: 0.86%) and Uzbek (UZK: 0.066%). To establish DNA databases for these populations, allele frequency distributions for 15 autosomal short tandem repeat (STR) loci were determined using the AmpFlSTR Identifiler PCR amplification kit. There was no evidence of departures from Hardy-Weinberg equilibrium (HWE) in any of the four populations and minimal departure from linkage equilibrium (LE) for a very small number of pairwise combinations of loci. The probabilities of identity for the different populations ranged from 1 in 1.51 × 1017 (MCH) to 1 in 9.94 × 1018 (MGL), the combined powers of discrimination ranged from 0.99999999999999999824 (UZK) to 0.9999999999999999848 (MCH) and the combined probabilities of paternal exclusion ranged from 0.9999979323 (UZK) to 0.9999994839 (MCH). Genetic distances, a phylogenetic tree and principal component analysis (PCA) revealed that the MCH, KGZ and UZK are genetically closer to the Han population of Liaoning and the Mongol population of Mongolia while the MGL are closer to Han, Japanese, Korean, Malaysian, Hong Kong Han and Russians living in China.

Matched MeSH terms: Microsatellite Repeats*
Fulltext Human profiling from STR and SNP analysis of tropical bed bug, Cimex hemipterus, for forensic science

Lim L, Ab Majid AH

Sci Rep, 2023 Jan 27;13(1):1506.
PMID: 36707655 DOI: 10.1038/s41598-023-28774-y

Tropical bed bugs, Cimex hemipterus, which commonly feeds on human blood, may be useful in forensic applications. However, unlike the common bed bug, Cimex lectularius, there is no information regarding tropical bed bug, C. hemipterus, being studied for its applications in forensics. Thus, in this study, lab-reared post-feeding tropical bed bugs were subjected to Short Tandem Repeat (STR) and Single Nucleotide Polymorphism (SNP) analyses to establish the usage of tropical bed bugs in forensics. Several post-feeding times (0, 5, 14, 30, and 45 days) were tested to determine when a complete human DNA profile could still be obtained after the bugs had taken the blood meal. The results showed that complete STR and SNP profiles could only be obtained from the D0 sample. The profile completeness decreased over time, and partial STR and SNP profiles could be obtained up to 45 days post-blood meal. The generated SNP profiles, complete or partial, were also viable for HIrisPlex-S phenotype prediction. In addition, field-collected bed bugs were also used to examine the viability of the tested STR markers, and the STR markers detected mixed profiles. The findings of this study established that the post-blood meal of tropical bed bugs is a suitable source of human DNA for forensic STR and SNP profiling. Human DNA recovered from bed bugs can be used to identify spatial and temporal relations of events.

Matched MeSH terms: Microsatellite Repeats/genetics
Fulltext De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing

Taheri S, Abdullah TL, Rafii MY, Harikrishna JA, Werbrouck SPO, Teo CH, et al.

Sci Rep, 2019 Feb 28;9(1):3047.
PMID: 30816255 DOI: 10.1038/s41598-019-39944-2

Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia. This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. For further genetic improvement, however, little genomic information and no specific molecular markers are available. The present study used Illumina sequencing and de novo transcriptome assembly of two C. alismatifolia cvs, 'Chiang Mai Pink' and 'UB Snow 701', to develop simple sequence repeat markers for genetic diversity studies. After de novo assembly, 62,105 unigenes were generated and 48,813 (78.60%) showed significant similarities versus six functional protein databases. In addition, 9,351 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified with a distribution frequency of 12.5% total unigenes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C. alismatifolia cultivars, one hybrid, three Curcuma, and two Zingiber species. Three different genetic groups within these species were revealed using EST-SSR markers, indicating that the markers developed in this study can be effectively applied to the population genetic analysis of Curcuma and Zingiber species. This report describes the first analysis of transcriptome data of an important ornamental ginger cultivars, also provides a valuable resource for gene discovery and marker development in the genus Curcuma.

Matched MeSH terms: Microsatellite Repeats/genetics*

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