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Fulltext Development of novel microsatellite markers using RAD sequencing technology for diversity assessment of rambutan (Nephelium lappaceum L.) germplasm

Ab Razak S, Mad Radzuan S, Mohamed N, Nor Azman NHE, Abd Majid AM, Ismail SN, et al.

Heliyon, 2020 Sep;6(9):e05077.
PMID: 33024864 DOI: 10.1016/j.heliyon.2020.e05077

The trend of microsatellite marker discovery and development revolved as a result of the advancement of next generation sequencing (NGS) technology as it has developed numerous microsatellites within a short period of time at a low cost. This study generated microsatellite markers using RAD sequencing technologies for the understudied Nephelium lappaceum. A total of 1403 microsatellite markers were successfully designed, which consisted of 853 di-, 525 tri-, 17 tetra-, 5 penta-, and 3 hexanucleotide microsatellite markers. Subsequently, selection of 39 microsatellites was made for the evaluation of genetic diversity of the selected 22 rambutan varieties. Twelve microsatellites, which exhibited high call rates across the samples, were used to assess the diversity of the aforementioned rambutan varieties. The analysis of 12 microsatellites revealed the presence of 72 alleles and six alleles per locus in average. Furthermore, the polymorphic information content (PIC) value ranged from 0.326 (NlaSSR20) to 0.832 (NlaSSR32), which included an average of 0.629 per locus, while the generated Neighbour Joining dendrogram showed two major clusters. The pairwise genetic distance of shared alleles exhibited a range of values from 0.046 (R134↔R170) to 0.818 (R5↔R170), which suggested highest dissimilarity detected between R5 and R170. Notably, these research findings would useful for varietal identification, proper management and conservation of the genetic resources, and exploitation and utilization in future breeding programs.

Matched MeSH terms: Genetic Variation
Population genetic analysis of oceanic paddle crab (varuna litterata) in Thailand

Uthamas Suppapan, Jamjun Pechsiri, Sompong O-thong, Arunrat Vanichanon, Pradit Sangthong, Verakiat Supmee

Sains Malaysiana, 2017;46:2251-2261.

Population genetic structure of Varuna litterata living along the coast of Thailand were examined in this study. The samples were collected from 3 coastal regions: The Andaman sea (Satun, Trang, Phang Nga), the lower Gulf of Thailand (Pattani, Songkhla, Nakhon Si Thammarat) and the upper Gulf of Thailand (Petchburi, Samut Songkram, Rayong, Trat). Intraspecific variation was determined based on partial sequences of the cytochrome oxidase subunits I gene. A total of 182 samples were collected but only 32 haplotypes were obtained from these samples. An excess of rare haplotypes indicated that the female effective population size of V. litterata living along the coast of Thailand is large. Estimated values of haplotype diversity and nucleotide diversity were 0.790 and 0.003, respectively. The AMOVA (analysis of molecular variance) and phylogenetic analysis results showed that based on genetic variation, the population of this organism was found to have 2 genetically different populations: The Andaman sea population and the Gulf of Thailand population. Genetic exchange of V. litterata among populations inhabiting along the coast of Thailand could be described by the stepping stone model. The results of neutrality tests, both Tajima's D and Fu's Fs statistics, yielded negative values (-1.992 and -26.877, respectively) and statistically significant deviation from the neutrality, indicating that the V. litterata living along the Thailand coast had experienced population expansion. Mismatch distribution analysis indicated that a possible expansion occurred 211,428 years ago during the Pleistocene glaciations period.

Matched MeSH terms: Genetic Variation
Comment on Seri Masran and Ab Majid 2017

Tseng SP, Yang CS

J Med Entomol, 2017 09 01;54(5):1107-1108.
PMID: 28874021 DOI: 10.1093/jme/tjx136
Matched MeSH terms: Genetic Variation
Fulltext Hidden genetic diversity in snakeskin gourami, Trichopodus pectoralis (Perciformes, Osphronemidae), inferred from the mitochondrial DNA CO1 gene

Tan MP, Amornsakun T, Siti Azizah MN, Habib A, Sung YY, Danish-Daniel M

Mitochondrial DNA B Resour, 2019 Sep 12;4(2):2966-2969.
PMID: 33365813 DOI: 10.1080/23802359.2019.1662741

Eighty-four specimens collected from 13 populations from Malaysia, Thailand, and Vietnam were analysed, revealing 21 putative haplotypes with overall estimated haplotype and nucleotide diversities of 0.79 and 0.0079, respectively. High levels of diversity and an absence of founder effects were observed among populations in peninsular Malaysia. In contrast, populations from Sarawak exhibited low genetic diversity, which is a typical sign of colonies introduced from a single source. Historical translocation of Trichopodus pectoralis from Thailand to Malaysia, as well as to the Philippines, Indonesia, and Myanmar was apparent. Historical introduction of T. pectoralis from Vietnam was also detected in peninsular Malaysia.

Matched MeSH terms: Genetic Variation
International stroke genetics consortium recommendations for studies of genetics of stroke outcome and recovery

Lindgren AG, Braun RG, Juhl Majersik J, Clatworthy P, Mainali S, Derdeyn CP, et al.

Int J Stroke, 2021 Apr 26.
PMID: 33739214 DOI: 10.1177/17474930211007288

Numerous biological mechanisms contribute to outcome after stroke, including brain injury, inflammation, and repair mechanisms. Clinical genetic studies have the potential to discover biological mechanisms affecting stroke recovery in humans and identify intervention targets. Large sample sizes are needed to detect commonly occurring genetic variations related to stroke brain injury and recovery. However, this usually requires combining data from multiple studies where consistent terminology, methodology, and data collection timelines are essential. Our group of expert stroke and rehabilitation clinicians and researchers with knowledge in genetics of stroke recovery here present recommendations for harmonizing phenotype data with focus on measures suitable for multicenter genetic studies of ischemic stroke brain injury and recovery. Our recommendations have been endorsed by the International Stroke Genetics Consortium.

Matched MeSH terms: Genetic Variation
25S rDNA genotyping and multi-locus sequence typing of Candida albicans of pathogenic and commensal origins in the Klang Valley, Malaysia

Illyaaseen Z, Ngeow YF, Yap SF, Ng HF

Malays J Pathol, 2021 Apr;43(1):55-61.
PMID: 33903306

Candida albicans is an important opportunistic fungal pathogen capable of causing fatal systemic infections in humans. Presently in Malaysia, there is little information available on the genetic diversity of this organism and trends in behavioural characteristics. In this project, three genotyping methods: 25S rDNA genotyping, Alternative Lengthening of Telomerase (ALT) sequence typing and Multi-Locus Sequence Typing (MLST) were applied to study the genetic diversity of strains from infected hospital in-patients and asymptomatic individuals in the community. The results showed that, with the 25S rDNA genotyping, as in other parts of the world, the most common genotype was type A which accounted for approximately 70% of the 111 isolates tested. Further typing with the ALT sequence showed type 3 to be the most common in the isolates tested. MLST analysis revealed many possibly novel sequence types, as well as a statistically significant association between pathogenicity and a group of closely related isolates, most of which were from hospital samples. Further work on genotypes associated with enhanced virulence will help to clarify the value of genotyping for clinical and epidemiological investigations.

Matched MeSH terms: Genetic Variation
Fulltext Markers for genetic change

Forcina G, Camacho-Sanchez M, Tuh FYY, Moreno S, Leonard JA

Heliyon, 2021 Jan;7(1):e05583.
PMID: 33437884 DOI: 10.1016/j.heliyon.2020.e05583

Background and aims: Wildlife conservation has focused primarily on species for the last decades. Recently, popular perception and laws have begun to recognize the central importance of genetic diversity in the conservation of biodiversity. How to incorporate genetic diversity in ongoing monitoring and management of wildlife is still an open question.
Methods: We tested a panel of multiplexed, high-throughput sequenced introns in the small mammal communities of two UNESCO World Heritage Sites on different continents to assess their viability for large-scale monitoring of genetic variability in a spectrum of diverse species. To enhance applicability across other systems, the bioinformatic pipeline for primer design was outlined.
Results: The number of loci amplified and amplification evenness decreased as phylogenetic distance increased from the reference taxa, yet several loci were still variable across multiple mammal orders.
Conclusions: Genetic variability found is informative for population genetic analyses and for addressing phylogeographic and phylogenetic questions, illustrated by small mammal examples here.

Matched MeSH terms: Genetic Variation
Fulltext Phylogenetic Relatedness of Several Agarwood-Producing Taxa (Thymelaeaceae) from Indonesia

Lee SY, Turjaman M, Mohamed R

Trop Life Sci Res, 2018 Jul;29(2):13-28.
PMID: 30112138 MyJurnal DOI: 10.21315/tlsr2018.29.2.2

Indonesia is home to several tree taxa that are harvested for agarwood. This highly valuable oleoresin ironically was the cause for some species to become vulnerable due to gluttonous human activity. However, information on the genetic diversity of these endangered trees is limited. In this study, 28 specimens representing eight species from two genera, Aquilaria and Gyrinops, were collected from ex-situ and in-situ populations in Indonesia. Phylogenetic analysis conducted on DNA sequences of the nuclear ribosomal internal transcribed spacer (ITS) and the trnL-trnF intergenic spacer regions, revealed that Aquilaria and Gyrinops are paraphyletic when Aquilaria cumingiana is excluded. The phylogenetic analysis for ITS and trnL-trnF showed capability to categorise agarwood-producing species based on their regions: East Indonesia and West Indonesia, using Wallace's Line as the divider. In addition, we discuss challenges in species identification and taxonomy of agarwood-producing genera, and their conservation efforts in Indonesia.

Matched MeSH terms: Genetic Variation
Fulltext Gamma irradiation effects on oil palm (elaies guinensis jacq.) pollen viability, fruits and bunch formations

Aida Nazlyn Nazari, Azhar Mohamad, Shuhaimi Shamsudin

Jurnal Sains Nuklear Malaysia, 2014;26(2):1-8.
MyJurnal

Assessing performance and genetic diversity of the wild material of oil palm is important for
under- standing genetic structure of natural oil palm populations towards improvement of the
crops. This in-formation is important for oil palm breeding programs, and also for continued exsitu
conservation of the germplasm and breeding program in Malaysia. Mutation induction is one
of the approaches in creating variants for selection in the breeding program. In this study, the
effect of irradiated pollen towards pollen viability, bunches formation and number of
parthenocarpic fruits were evaluated. Elaies guineensis Jacq. pollens were exposed to series of
acute gamma radiation at dose 0, 10, 20, 40, 50, 100, 200, 300, 500, 100 and 2000 Gy . Pollen
viability and pollen tube formation were disrupted in which unable the pollen to reach the ovule.
At this stage, embryo was aborted towards formation of parthenocarpic fruits and rotten bunches.
The study suggested that at low levels of irradiation i.e. < 200 Gy, generative nucleus partially
damage and it is still maintaining capacity of fertilizing the egg cells for hybridization. It is
important for breeders in understanding this finding towards novel variants of oil palm via
mutation induction

Matched MeSH terms: Genetic Variation
Human platelet antigen allelic diversity in Peninsular Malaysia

Syafawati WU, Zefarina Z, Zafarina Z, Hassan MN, Norazmi MN, Panneerchelvam S, et al.

Immunohematology, 2016 Dec;32(4):143-160.
PMID: 28257229
Matched MeSH terms: Genetic Variation
Fulltext Genomic diversity of cholera outbreak strains in East Malaysia

Bilung, Lesley Maurice, Yong, Sy Fuh, Linang, Velnetti, Benjamin, Adam, Vincent, Micky, Apun, Kasing, et al.

Malaysian Journal of Medicine and Health Sciences, 2014;10(2):19-26.
MyJurnal

Thirty one Vibrio cholera isolates recovered from cholera outbreak in Bintulu, Sarawak (Malaysia) were detected with the presence of ctx gene by using specific PCR. These isolates were further characterized and differentiated by using the Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR) and BOX-PCR to determine their genomic fingerprints. The specific PCR result confirmed the identities of 27 isolates out of 31 as pathogenic V. cholerae. The ERIC-PCR generated several genetic profiles consisting of 4-6 bands with sizes in the range of 100 to 600 bp, while the BOX-PCR produced profiles numbering 2-7 bands in the sizes between 200 to 1000 bp. Based on the dendrogram generated from the DNA fingerprinting profiles (ERIC-PCR and BOX-PCR), all of the isolates can be divided into 2 main clusters that is further divided into 2 sub-clusters. The low genetic diversity of the isolates indicated the outbreak of V. cholerae in the study area was due to the contamination from a single or few sources of V. cholerae.

Matched MeSH terms: Genetic Variation
Fulltext Seed morphology variation of rice landraces from Tuaran and Kota Belud districts of Sabah, Malaysia

CHEE, F. T., SIAMBUN, M. M., MARIAM A. L.

Buletin Persatuan Genetik Malaysia, 2011;18(1):10-16.
MyJurnal

There is a need to set up a germplasm resource centre or gene bank in Sabah to keep the collections of varieties of locally cultivated crops, especially rice. This is necessary to prevent genetic loss caused by the infrastructure development in the state of Sabah especially when Sabah is known for her rich genetic resources for food and agriculture. This gene bank will play an important role in the conservation of genetic resources especially for future rice crop improvement and development. These collections are known to carry useful gene(s) for crop improvement such as aroma, taste, resistance to insect pests and diseases, and tolerance to abiotic stress. Decades ago, a set of local landrace rice collection were made and conserved at International Rice Research Institute (IRRI) and Malaysia Agriculture Research and Development Institute (MARDI). Besides IRRI and MARDI, local farmers also play an important role as conservationist. Therefore, this study has been carried out to re ne the status of the current genetic diversity in local rice farming. From January 2009 to February 2010, 108 samples were collected from Tuaran and Kota Belud districts. Preliminary observation of 19 samples found that
there is a high genetic diversity based on seed morphology alone. Variations in the characteristics were detected in awn, apiculus, lemma and palea, sterile lemma and seed coat. Length and width of seeds were measured and calculated for ratio to estimate the shapes of the seeds. The weight of 100 grains ranged from 1.42 to 3.19 g. However, further studies on morphology evaluation, disease screening, and molecular evaluation are needed to be compared with the existing data. In addition, genetic erosion, migration, and drift also need to be studied due to high seed exchanges among the local farmers.

Matched MeSH terms: Genetic Variation
Supernumerary chromosomes in the black rat (Rattus rattus) and their distribution in three geographic variants

Yosida TH

Cytogenet. Cell Genet., 1977;18(3):149-59.
PMID: 862437

Supernumerary chromosomes have been examined in 352 black rats, covering three geographic variants, by use of conventional and C-band staining techniques. Metacentric supernumerary chromosomes, one to three in number, were found in Malayan black rats (Rattus rattus diardii), with 2n=42, in Indian black rats (R. rattus rufescens), with 2n=38, and in Ceylonese black rats (R. rattus kandianus), with 2n=40. The supernumeraries had similar morphology and stained heavily along their entire length by C-band staining. These findings suggested that the supernumeraries had originally developed in the Asian-type black rats and then were sequentially transmitted to the Ceylonese and Oceanian-type black rats, probably in southwestern Asia. A subtelocentric supernumerary chromosome found in one Japanese black rat seemed to have developed independently from the above metacentric supernumeraries.

Matched MeSH terms: Genetic Variation
Fulltext A review on induced mutagenesis of Stevia rebaudiana Bertoni

Chiew, Miao Si, Lai, Kok Song, Sobri Hussein, Janna Ong Abdullah

The Pertanika Journal of Scholarly Research Reviews, 2016;2(3):77-85.
MyJurnal

Stevia rebaudiana Bertoni in the Asteraceae family is commercially valuable and cultivated throughout the world due to the great demand for its steviol glycosides (SGs) contents particularly rebaudioside A. Previous studies confirmed that maximal content of SGs in stevia was achieved at or just before flowering, and delayed flowering with long days provide longer duration for steviol glycosides accumulation. However, there is no suitable stevia variety to be cultivated in Malaysia due to her short day length. Mutation induction, including gamma irradiation, had been shown to be useful for generating genetic variations as well as developing new plant varieties from which desired mutants were successfully selected. The use of mutagens, both physical and chemical, has helped in creating mutants that expressed the selected desirable traits. This paper presents some selected essential data available in extant scientific studies on stevia with the focus on application of gamma irradiation on stevia. Both established achievements and recent publications of gamma radiation on stevia were reviewed. Emphasis is on the exceptional potential of stevia through induced mutation approach especially by using gamma rays.

Matched MeSH terms: Genetic Variation
Fulltext Reading between the vines: Hosts as islands for extreme holoparasitic plants

Barkman TJ, Klooster MR, Gaddis KD, Franzone B, Calhoun S, Manickam S, et al.

Am J Bot, 2017 09;104(9):1382-1389.
PMID: 29885244 DOI: 10.3732/ajb.1700117

PREMISE OF THE STUDY: Partitioning of population genetic variation in plants may be affected by numerous factors including life history and dispersal characteristics. In parasitic plants, interactions with host populations may be an additional factor influencing partitioning. To test for hierarchical population genetic patterns related to obligate endoparasitism, we studied three species of Rafflesiaceae, which grow as extremely reduced endophytes infecting Tetrastigma vines in Southeast Asia.
METHODS: Microsatellite markers were developed and multilocus genotypes were determined for Rafflesia cantleyi, Rafflesia tuan-mudae, and Sapria himalayana and each of their Tetrastigma hosts. Relatedness among parasite individuals was estimated, and AMOVAs were used to determine levels of population genetic subdivision.
KEY RESULTS: Microsatellite genotypes for 340 paired parasite and host samples revealed that host vines were infected by numerous Rafflesiaceae individuals that may spread for up to 14 m within stem tissues. Surprisingly, Rafflesiaceae parasites within a given host are significantly more closely related to each other than individuals of the same species in other host individuals. The pattern of hierarchical population genetic subdivision we detected across species is likely due to limited seed dispersal with reinfection of natal host vines.
CONCLUSIONS: These findings demonstrate common population genetic patterns between animal and plant parasites, potentially indicating advantages of close relatives infecting hosts. This study also has important conservation implications for Rafflesiaceae since our data suggest that destruction of a single infected host vine could result in large genetic losses.

Matched MeSH terms: Genetic Variation
New scenario for speciation in the benthic dinoflagellate genus Coolia (Dinophyceae)

Leaw CP, Tan TH, Lim HC, Teng ST, Yong HL, Smith KF, et al.

Harmful Algae, 2016 05;55:137-149.
PMID: 28073527 DOI: 10.1016/j.hal.2016.02.010

In this study, inter- and intraspecific genetic diversity within the marine harmful dinoflagellate genus Coolia Meunier was evaluated using isolates obtained from the tropics to subtropics in both Pacific and Atlantic Ocean basins. The aim was to assess the phylogeographic history of the genus and to clarify the validity of established species including Coolia malayensis. Phylogenetic analysis of the D1-D2 LSU rDNA sequences identified six major lineages (L1-L6) corresponding to the morphospecies Coolia malayensis (L1), C. monotis (L2), C. santacroce (L3), C. palmyrensis (L4), C. tropicalis (L5), and C. canariensis (L6). A median joining network (MJN) of C. malayensis ITS2 rDNA sequences revealed a total of 16 haplotypes; however, no spatial genetic differentiation among populations was observed. These MJN results in conjunction with CBC analysis, rDNA phylogenies and geographical distribution analyses confirm C. malayensis as a distinct species which is globally distributed in the tropical to warm-temperate regions. A molecular clock analysis using ITS2 rDNA revealed the evolutionary history of Coolia dated back to the Mesozoic, and supports the hypothesis that historical vicariant events in the early Cenozoic drove the allopatric differentiation of C. malayensis and C. monotis.

Matched MeSH terms: Genetic Variation
Genetic diversity and virulence characteristics of Helicobacter pylori isolates in different human ethnic groups

Hanafiah A, Lopes BS

Infect Genet Evol, 2020 Mar;78:104135.
PMID: 31837482 DOI: 10.1016/j.meegid.2019.104135

Helicobacter pylori is the most predominant bacterium in almost 50% of the world's population and colonization causes a persistent inflammatory response leading to chronic gastritis. It shows high genetic diversity and individuals generally harbour a distinct bacterial population. With the advancement of whole-genome sequencing technology, new H. pylori subpopulations have been identified that show admixture between various H. pylori strains. Genotypic variation of H. pylori may be related to the presence of virulence factors among strains and is associated with different outcomes of infection in different individuals. This review summarizes the genetic diversity in H. pylori strain populations and its virulence characteristics responsible for variable outcomes in different ethnic groups.

Matched MeSH terms: Genetic Variation
Development and characterization of elaeis oleifera microsatellite markers

Noorhariza Mohd Zaki, Rozana Rosli, Ting NC, Singh R, Ismanizan Ismail

Sains Malaysiana, 2010;39.

Ten Elaeis oleifera microsatellite markers were developed and characterised from 1500 sequences of the E. oleifera genomic library. The markers were utilised to assess the genetic diversity of E. oleifera germplasm collections from four South American countries (Colombia, Costa Rica, Panama and Honduras). The number of alleles per-locus varied from 2 to 11 and the observed and expected heterozygosity ranged from 0.0685 to 0.9853 and 0.1393 to 0.8216 respectively. Majority of the markers showed transferability to Elaeis guineensis while two markers showed transferability across Arecaceae taxa. These E. oleifera microsatellite markers are expected to become useful tools to determine the population structure and conservation of E. oleifera populations.

Matched MeSH terms: Genetic Variation
Combining Understanding of Immunological Mechanisms and Genetic Variants Toward Development of Personalized Medicine for Psoriasis Patients

Gunter NV, Yap BJM, Chua CLL, Yap WH

Front Genet, 2019;10:395.
PMID: 31130981 DOI: 10.3389/fgene.2019.00395

Psoriasis is multifactorial disease with complex genetic predisposition. Recent advances in genetics and genomics analyses have provided many insights into the relationship between specific genetic predisposition and the immunopathological mechanisms driving psoriasis manifestation. Novel approaches which utilize array-based genotyping technologies such as genome-wide association studies and bioinformatics tools for transcriptomics analysis have identified single nucleotide polymorphisms, genes and pathways that are associated with psoriasis. The discovery of these psoriasis-associated susceptibility loci, autoimmune targets and altered signaling pathways have provided opportunities to bridge the gap of knowledge from sequence to consequence, allowing new therapeutic strategies for the treatment of psoriasis to be developed. Here, we discuss recent advances in the field by highlighting how immune functions associated with psoriasis susceptibility loci may contribute to disease pathogenesis in different populations. Understanding the genetic variations in psoriasis and how these may influence the immunological pathways to cause disease will contribute to the efforts in developing novel and targeted personalized therapies for psoriasis patients.

Matched MeSH terms: Genetic Variation
Fulltext Genetic assessment of the internal transcribed spacer region (ITS1.2) in Mangifera indica L. landraces

Fazeli-Nasab B, Sayyed RZ, Farsi M, Ansari S, El-Enshasy HA

Physiol Mol Biol Plants, 2020 Jan;26(1):107-117.
PMID: 32158124 DOI: 10.1007/s12298-019-00732-x

Mango (Mangifera indica) is one of the most important tropical fruits in the world. Twenty-two genotypes of native mangoes from different regions of southern Iran (Hormozgan and Kerman) were collected and analyzed for the ribosomal genes. GC content was found to be 55.5%. Fu and Li's D* test statistic (0.437), Fu and Li's F* test statistic (0.500) and Tajima's D (1.801) were positive and nonsignificant. A total of 769 positions were identified (319 with insertion or deletion including 250 polymorphic and 69 monomorphic loci; 450 loci without any insertion or deletion including 35 Singletons and 22 haplotypes). Nucleotide diversity of 0.309 and a high genetic differentiation including Chi square of 79.8; P value of 0.3605 and df value of 76 was observed among mango genotypes studied. The numerical value of the ratio dN/dS (0.45) indicated a pure selection in the examined gene and the absence of any key changes. Cluster analysis differentiated the mango used in this research (M. indica L.) into two genotypes but could not differentiate their geographical locations. The results of this study indicated that a high genetic distance exists between HajiGholam (Manojan) and Arbabi (Rodan) genotypes and showed higher genetic diversity in mango of Rodan region. Results of present study suggested that for successful breeding, the genotypes of Rodan region mango especially Arbabi mango can be used as a gene donor and ITS can be a suitable tool for genetic evaluations of inter and intra species.

Matched MeSH terms: Genetic Variation

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