Displaying publications 1 - 20 of 55 in total

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  1. Yahya P, Sulong S, Harun A, Wangkumhang P, Wilantho A, Ngamphiw C, et al.
    Int J Legal Med, 2020 Jan;134(1):123-134.
    PMID: 31760471 DOI: 10.1007/s00414-019-02184-0
    Ancestry-informative markers (AIMs) can be used to infer the ancestry of an individual to minimize the inaccuracy of self-reported ethnicity in biomedical research. In this study, we describe three methods for selecting AIM SNPs for the Malay population (Malay AIM panel) using different approaches based on pairwise FST, informativeness for assignment (In), and PCA-correlated SNPs (PCAIMs). These Malay AIM panels were extracted from genotype data stored in SNP arrays hosted by the Malaysian node of the Human Variome Project (MyHVP) and the Singapore Genome Variation Project (SGVP). In particular, genotype data from a total of 165 Malay individuals were analyzed, comprising data on 117 individual genotypes from the Affymetrix SNP-6 SNP array platform and data on 48 individual genotypes from the OMNI 2.5 Illumina SNP array platform. The HapMap phase 3 database (1397 individuals from 11 populations) was used as a reference for comparison with the Malay genotype data. The accuracy of each resulting Malay AIM panel was evaluated using a machine learning "ancestry-predictive model" constructed by using WEKA, a comprehensive machine learning platform written in Java. A total of 1250 SNPs were finally selected, which successfully identified Malay individuals from other world populations with an accuracy of 90%, but the accuracy decreased to 80% using 157 SNPs according to the pairwise FST method, while a panel of 200 SNPs selected using In and PCAIMs could be used to identify Malay individuals with an accuracy of approximately 80%.
  2. Yahya P, Sulong S, Harun A, Wan Isa H, Ab Rajab NS, Wangkumhang P, et al.
    Forensic Sci Int Genet, 2017 09;30:152-159.
    PMID: 28743033 DOI: 10.1016/j.fsigen.2017.07.005
    Malay, the main ethnic group in Peninsular Malaysia, is represented by various sub-ethnic groups such as Melayu Banjar, Melayu Bugis, Melayu Champa, Melayu Java, Melayu Kedah Melayu Kelantan, Melayu Minang and Melayu Patani. Using data retrieved from the MyHVP (Malaysian Human Variome Project) database, a total of 135 individuals from these sub-ethnic groups were profiled using the Affymetrix GeneChip Mapping Xba 50-K single nucleotide polymorphism (SNP) array to identify SNPs that were ancestry-informative markers (AIMs) for Malays of Peninsular Malaysia. Prior to selecting the AIMs, the genetic structure of Malays was explored with reference to 11 other populations obtained from the Pan-Asian SNP Consortium database using principal component analysis (PCA) and ADMIXTURE. Iterative pruning principal component analysis (ipPCA) was further used to identify sub-groups of Malays. Subsequently, we constructed an AIMs panel for Malays using the informativeness for assignment (In) of genetic markers, and the K-nearest neighbor classifier (KNN) was used to teach the classification models. A model of 250 SNPs ranked by In, correctly classified Malay individuals with an accuracy of up to 90%. The identified panel of SNPs could be utilized as a panel of AIMs to ascertain the specific ancestry of Malays, which may be useful in disease association studies, biomedical research or forensic investigation purposes.
  3. Wada Y, Irekeola AA, E A R ENS, Yusof W, Lih Huey L, Ladan Muhammad S, et al.
    Antibiotics (Basel), 2021 Jan 31;10(2).
    PMID: 33572528 DOI: 10.3390/antibiotics10020138
    Antimicrobial resistance in companion animals is a major public health concern worldwide due to the animals' zoonotic potential and ability to act as a reservoir for resistant genes. We report on the first use of meta-analysis and a systematic review to analyze the prevalence of vancomycin-resistant Enterococcus (VRE) in companion animals. Databases such as MedLib, PubMed, Web of Science, Scopus, and Google Scholar were searched. The information was extracted by two independent reviewers and the results were reviewed by a third. Two reviewers independently assessed the study protocol using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) checklist and the study quality using the Joanna Briggs Institute (JBI) critical appraisal checklist for prevalence data. OpenMeta analyst and comprehensive meta-analysis (CMA) were used for the meta-analysis. The random effect model was used, and publication bias was assessed using the Eggers test and funnel plot. Between-study heterogeneity was assessed, and the sources were analyzed using the leave-one-out meta-analysis, subgroup analysis and meta-regression. Twenty-two studies met the eligibility criteria, but because some studies reported the prevalence of VRE in more than one companion animal, they were considered as individual studies, and 35 studies were therefore added to the final meta-analysis. Sampling period of the included studies was from 1995-2018. Of the 4288 isolates tested in the included studies, 1241 were VRE. The pooled prevalence of VRE in companion animals was estimated at 14.6% (95% CI; 8.7-23.5%; I2 = 97.10%; p < 0.001). Between-study variability was high (t2 = 2.859; heterogeneity I2 = 97.10% with heterogeneity chi-square (Q) = 1173.346, degrees of freedom (df) = 34, and p < 0.001). The funnel plot showed bias, which was confirmed by Eggers test (t-value = 3.97165; p = 0.00036), and estimates from the leave-one-out forest plot did not affect the pooled prevalence. Pooled prevalence of VRE in dogs and cats were 18.2% (CI = 9.4-32.5%) and 12.3%, CI = 3.8-33.1%), respectively. More studies were reported in Europe than in any other continent, with most studies using feces as the sample type and disc diffusion as the detection method. With the emergence of resistant strains, new antimicrobials are required in veterinary medicine.
  4. Mohd Ali MR, Lih Huey L, Foo PC, Goay YX, Ismail AS, Mustaffa KMF, et al.
    Biomed Res Int, 2019;2019:9451791.
    PMID: 31355287 DOI: 10.1155/2019/9451791
    Melioidosis and leptospirosis, caused by two different bacteria, Burkholderia pseudomallei and Leptospira spp., are potentially fatal infections that share a very similar spectrum of clinical features and cause significant mortality and morbidity in humans and livestock. Early detection is important for better clinical consequences. To our knowledge, there is no diagnostic tool available to simultaneously detect and differentiate melioidosis and leptospirosis in humans and animals. In this study, we described a duplex TaqMan probe-based qPCR for the detection of B. pseudomallei and Leptospira spp. DNA. The performance of the assay was evaluated on 20 B. pseudomallei isolates, 23 Leptospira strains, and 39 other microorganisms, as well as two sets of serially diluted reference strains. The duplex qPCR assay was able to detect 0.02 pg (~ 4 copies) Leptospira spp. DNA and 0.2 pg (~ 25.6 copies) B. pseudomallei DNA. No undesired amplification was observed in other microorganisms. In conclusion, the duplex qPCR assay was sensitive and specific for the detection of B. pseudomallei & Leptospira spp. DNA and is suitable for further analytical and clinical evaluation.
  5. Rahman ZA, Harun A, Hasan H, Mohamed Z, Noor SS, Deris ZZ, et al.
    Eye Contact Lens, 2013 Sep;39(5):355-60.
    PMID: 23982472 DOI: 10.1097/ICL.0b013e3182a3026b
    Ocular surface infections that include infections of conjunctiva, adnexa, and cornea have the potential risk of causing blindness within a given population. Empirical antibiotic therapy is usually initiated based on epidemiological data of common causative agents. Thus, the aims of this study were to determine the bacterial agents and their susceptibility patterns of isolates from ocular surface specimens in our hospital.
  6. Yap PSX, Chong CW, Ponnampalavanar S, Ramli R, Harun A, Tengku Jamaluddin TZM, et al.
    PeerJ, 2023;11:e16393.
    PMID: 38047021 DOI: 10.7717/peerj.16393
    BACKGROUND: The high burden of extended-spectrum beta-lactamase-producing (ESBL)-producing Enterobacterales worldwide, especially in the densely populated South East Asia poses a significant threat to the global transmission of antibiotic resistance. Molecular surveillance of ESBL-producing pathogens in this region is vital for understanding the local epidemiology, informing treatment choices, and addressing the regional and global implications of antibiotic resistance.

    METHODS: Therefore, an inventory surveillance of the ESBL-Escherichia coli (ESBL-EC) isolates responsible for infections in Malaysian hospitals was conducted. Additionally, the in vitro efficacy of flomoxef and other established antibiotics against ESBL-EC was evaluated.

    RESULTS: A total of 127 non-repetitive ESBL-EC strains isolated from clinical samples were collected during a multicentre study performed in five representative Malaysian hospitals. Of all the isolates, 33.9% were isolated from surgical site infections and 85.8% were hospital-acquired infections. High rates of resistance to cefotaxime (100%), cefepime (100%), aztreonam (100%) and trimethoprim-sulfamethoxazole (100%) were observed based on the broth microdilution test. Carbapenems remained the most effective antibiotics against the ESBL-EC, followed by flomoxef. Antibiotic resistance genes were identified by PCR. The blaCTX-M-1 was the most prevalent ESBL gene, with 28 isolates (22%) harbouring blaCTX-M-1 only, 27 isolates (21.3%) co-harbouring blaCTX-M-1 and blaTEM, and ten isolates (7.9%) co-harbouring blaCTX-M-1, blaTEM and blaSHV. A generalised linear model showed significant antibacterial activity of imipenem against different types of infection. Besides carbapenems, this study also demonstrated a satisfactory antibacterial activity of flomoxef (81.9%) on ESBL-EC, regardless of the types of ESBL genes.

  7. Md Zamri ASS, Saruddin MZ, Harun A, Abd Aziz SF, Aizad Za'bah AK, Dapari R, et al.
    PLoS One, 2023;18(6):e0287040.
    PMID: 37307252 DOI: 10.1371/journal.pone.0287040
    INTRODUCTION: Occupational asthma (OA) is a type of Work-Related Asthma characterised by variable airflow limitation and/or inflammation due to causes and conditions attributable to a particular occupational environment, and not to stimuli encountered outside the workplace. There is an increasing need to extend the depth of knowledge of OA to better manage this condition, especially among food industry workers who are affected by it.

    OBJECTIVE: This systematic review aimed to determine the factors associated with occupational asthma among food industry workers by electronically collecting articles from two databases (Medline and Scopus).

    METHODS: This systematic review was prepared in accordance with the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta Analyses) updated guideline. Two independent reviewers screened the titles and abstracts of the collected data, which were then stored in Endnote20 based on the inclusion and exclusion criteria. The included articles have been critically appraised to assess the quality of the studies using the Mixed Methods Appraisal Tool (MMAT).

    RESULT: The search yielded 82 articles from Medline and 85 from SCOPUS, resulting in 167 unique hits. Only 22 articles have been included in the full-text assessment following a rigorous selection screening. Of the 22 articles identified, five were included in the final review. Several factors were found to have contributed to occupational asthma among food industry workers. They were classified into two categories: (1) work environment-related factors; and (2) individual factors.

    CONCLUSION: Several work environment and individual-related factors were found to be associated with OA among food industry workers. A better understanding of the development of the disease and its potential risk factors is needed because it can affect worker's quality of life. Pre-employment and periodic medical surveillance should be conducted to assess and detect any possible risk of developing occupational asthma among workers.

  8. Bagudo AI, Obande GA, Harun A, Singh KKB
    Asian Biomed (Res Rev News), 2020 Oct;14(5):177-186.
    PMID: 37551265 DOI: 10.1515/abm-2020-0026
    Acinetobacter species, particularly those within Acinetobacter calcoaceticus-A. baumannii complex (ACB complex), have emerged as clinically relevant pathogens in hospital environments worldwide. Early and quick detection and identification of Acinetobacter infections is challenging, and traditional culture and biochemical methods may not achieve adequate levels of speciation. Moreover, currently available techniques to identify and differentiate closely related Acinetobacter species are insufficient. The objective of this review is to recapitulate the current evolution in phenotypic and automated techniques used to identify the ACB complex. Compared with other automated or semiautomated systems of bacterial identification, matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) demonstrates a high level of Acinetobacter species identification and discrimination, including newly discovered species A. seifertii and A. dijkshoorniae.
  9. Lemlem M, Aklilu E, Mohamed M, Kamaruzzaman NF, Zakaria Z, Harun A, et al.
    BMC Microbiol, 2023 Dec 08;23(1):392.
    PMID: 38062398 DOI: 10.1186/s12866-023-03118-y
    BACKGROUND: Colistin is an antibiotic used as a last-resort to treat multidrug-resistant Gram-negative bacterial infections. Colistin had been used for a long time in veterinary medicine for disease control and as a growth promoter in food-producing animals. This excessive use of colistin in food animals causes an increase in colistin resistance. This study aimed to determine molecular characteristics of colistin-resistant Escherichia coli in broiler chicken and chicken farm environments.

    RESULTS: Four hundred fifty-three cloacal and farm environment samples were collected from six different commercial chicken farms in Kelantan, Malaysia. E. coli was isolated using standard bacteriological methods, and the isolates were tested for antimicrobial susceptibility using disc diffusion and colistin minimum inhibitory concentration (MIC) by broth microdilution. Multiplex PCR was used to detect mcr genes, and DNA sequencing was used to confirm the resistance genes. Virulence gene detection, phylogroup, and multilocus sequence typing (MLST) were done to further characterize the E. coli isolates. Out of the 425 (94%; 425/453) E. coli isolated from the chicken and farm environment samples, 10.8% (48/425) isolates were carrying one or more colistin-resistance encoding genes. Of the 48 colistin-resistant isolates, 54.2% (26/48) of the mcr positive isolates were genotypically and phenotypically resistant to colistin with MIC of colistin ≥ 4 μg/ml. The most prominent mcr gene detected was mcr-1 (47.9%; 23/48), followed by mcr-8 (18.8%; 9/48), mcr-7 (14.5%; 7/48), mcr-6 (12.5%; 6/48), mcr-4 (2.1%; 1/48), mcr-5 (2.1%; 1/48), and mcr-9 (2.1%; 1/48) genes. One E. coli isolate originating from the fecal sample was found to harbor both mcr-4 and mcr-6 genes and another isolate from the drinking water sample was carrying mcr-1 and mcr-8 genes. The majority of the mcr positive isolates were categorized under phylogroup A followed by phylogroup B1. The most prevalent sequence typing (ST) was ST1771 (n = 4) followed by ST206 (n = 3). 100% of the mcr positive E. coli isolates were multidrug resistant. The most frequently detected virulence genes among mcr positive E. coli isolates were ast (38%; 18/48) followed by iss (23%; 11/48). This is the first research to report the prevalence of mcr-4, mcr-5, mcr-6, mcr-7, and mcr-8 genes in E. coli from broiler chickens and farm environments in Malaysia.

    CONCLUSION: Our findings suggest that broiler chickens and broiler farm environments could be reservoirs of colistin-resistant E. coli, posing a risk to public health and food safety.

  10. Shareef BT, Harun A, Roziawati Y, Bahari IS, Deris ZZ, Ravichandran M
    J Contemp Dent Pract, 2008;9(3):114-20.
    PMID: 18335127
    This case report aims at describing an infection of the tongue as a manifestation of a Trichosporon asahii infection, its association with bronchial asthma and steroid administration, and to present a review of the literature pertaining to its antifungal susceptibility profile.
  11. Harun A, Vidyadaran S, Lim SM, Cole AL, Ramasamy K
    PMID: 26047814 DOI: 10.1186/s12906-015-0685-5
    Excessive production of inflammatory mediators such as nitric oxide (NO) and proinflammatory cytokines like tumour necrosis factor-alpha (TNF-α) from activated microglia contributes to uncontrolled inflammation in neurodegenerative diseases. This study investigated the protective role of five endophytic extracts (HAB16R12, HAB16R13, HAB16R14, HAB16R18 and HAB8R24) against LPS-induced inflammatory events in vitro. These endophytic extracts were previously found to exhibit potent neuroprotective effect against LPS-challenged microglial cells.
  12. Harun A, James RM, Lim SM, Abdul Majeed AB, Cole AL, Ramasamy K
    BMC Complement Altern Med, 2011 Sep 24;11:79.
    PMID: 21943123 DOI: 10.1186/1472-6882-11-79
    BACKGROUND: BACE1 was found to be the major β-secretase in neurons and its appearance and activity were found to be elevated in the brains of AD patients. Fungal endophytic extracts for BACE1 inhibitory activity and cytotoxicity against PC-12 (a rat pheochromocytoma with neuronal properties) and WRL68 (a non-tumorigenic human hepatic) were investigated.

    METHODS: Endophytes were isolated from plants collected from Kuala Pilah, Negeri Sembilan and the National Park, Pahang and the extracts were tested for BACE1 inhibition. For investigation of biological activity, the pure endophytic cultures were cultivated for 14 days on PDA plates at 28°C and underwent semipolar extraction with ethyl acetate.

    RESULTS: Of 212 endophytic extracts (1000 μg/ml), 29 exhibited more than 90% inhibition of BACE1 in the preliminary screening. Four extracts from isolates HAB16R13, HAB16R14, HAB16R18 and HAB8R24 identified as Cytospora rhizophorae were the most active with IC(50(BACE1)) values of less than 3.0 μg/ml. The most active extract HAB16R13 was shown to non-competitively inhibit BACE1 with K(i) value of 10.0 μg/ml. HAB16R13 was considered non-potent against PC-12 and WRL68 (IC(50(CT))) of 60.0 and 40.0 μg/ml, respectively).

    CONCLUSIONS: This first report on endophytic fungal extract with good BACE1 inhibitory activity demonstrates that more extensive study is required to uncover the potential of endophytes.

  13. Alexander MJ, Sinnatamby AS, Rohaimah MJ, Harun AH, Ng JS
    Ann Acad Med Singap, 1990 May;19(3):344-6.
    PMID: 2393233
    Brunei Darussalam has a mixed population with entirely different cultures and religions. The overall incidence of Hepatitis B virus (HBV) infection is 6%. A racial analysis of the incidence of HBV infection in Brunei shows a significantly higher incidence in Chinese compared to the other races. This is consistent with the incidence in the neighbouring countries.
  14. Salmuna ZN, Hashim S, Hasan H, Harun A, Abdul Rahman Z, Ismail N, et al.
    IIUM Medical Journal Malaysia, 2019;18(3):144-152.
    MyJurnal
    Influenza-like illnesses (ILI) were defined as a triad of cough, sore throat and fever. The aim of this study is to determine the changes in knowledge, perceptions and practices towards preventive measures of succumbing to ILI before and after hajj among Malaysian hajj pilgrims.Methodology: An open-labeled randomized control trial study performed on five hundred Malaysian hajj pilgrims in the year 2013. After validated pre-hajj questionnaires completed, 250 subjects were given health education, benzalkonium-based handrub and demonstration of the handrub usage together with pamphlets and labelled as an intervention group. Another 250 subjects from another flight batch were given the same questionnaires without health education with unmedicated hand lotion as a control group. The knowledge, perception, practices and compliances to the handrub practice in both groups were compared with the pre-hajj results. Results: No significant difference between pre and post hajj knowledge and practice among hajj pilgrims in intervention group. Pre hajj perception score [ M (IQR) = 30 (5.00), Z= -2.441, p < 0.05 ] is much higher compared to post hajj perception [ M (IQR) = 29 (6.00), Z = -2.441, p < O.O5 ]. No significant difference between pre and post hajj knowledge, perception and practices among hajj pilgrims in control group. Hand hygiene compliance was not improved with provision of health education and free handrub supply. Conclusion: No significant changes in knowledge, perceptions and practices of Malaysian hajj pilgrims pre and post-hajj in both groups. Provision of handrub did not improved hajj pilgrims compliance.
  15. Harun A, Kan A, Schwabenbauer K, Gilgado F, Perdomo H, Firacative C, et al.
    PMID: 35024355 DOI: 10.3389/fcimb.2021.761596
    Scedosporium spp. are the second most prevalent filamentous fungi after Aspergillus spp. recovered from cystic fibrosis (CF) patients in various regions of the world. Although invasive infection is uncommon prior to lung transplantation, fungal colonization may be a risk factor for invasive disease with attendant high mortality post-transplantation. Abundant in the environment, Scedosporium aurantiacum has emerged as an important fungal pathogen in a range of clinical settings. To investigate the population genetic structure of S. aurantiacum, a MultiLocus Sequence Typing (MLST) scheme was developed, screening 24 genetic loci for polymorphisms on a tester strain set. The six most polymorphic loci were selected to form the S. aurantiacum MLST scheme: actin (ACT), calmodulin (CAL), elongation factor-1α (EF1α), RNA polymerase subunit II (RPB2), manganese superoxide dismutase (SOD2), and β-tubulin (TUB). Among 188 global clinical, veterinary, and environmental strains, 5 to 18 variable sites per locus were revealed, resulting in 8 to 23 alleles per locus. MLST analysis observed a markedly high genetic diversity, reflected by 159 unique sequence types. Network analysis revealed a separation between Australian and non-Australian strains. Phylogenetic analysis showed two major clusters, indicating correlation with geographic origin. Linkage disequilibrium analysis revealed evidence of recombination. There was no clustering according to the source of the strains: clinical, veterinary, or environmental. The high diversity, especially amongst the Australian strains, suggests that S. aurantiacum may have originated within the Australian continent and was subsequently dispersed to other regions, as shown by the close phylogenetic relationships between some of the Australian sequence types and those found in other parts of the world. The MLST data are accessible at http://mlst.mycologylab.org. This is a joined publication of the ISHAM/ECMM working groups on "Scedosporium/Pseudallescheria Infections" and "Fungal Respiratory Infections in Cystic Fibrosis".
  16. Wan KF, Radu S, Cheah YK, Benjamin PG, Ling CM, Hon SF, et al.
    PMID: 15115139
    Enteropathogenic Escherichia coli (EPEC) is a leading cause of diarrhea among infants in developing countries. A total of 38 EPEC isolates, obtained from diarrhea patients of Hospital Miri, Sarawak, were investigated through plasmid profile, antibiotic resistance and randomly amplified polymorphic DNA (RAPD) analysis. From the 8 types of antibiotics used, all isolates were 100% resistant to furoxime, cephalothin and sulphamethoxazole and showed high multiple antibiotic resistant (MAR) indexes, ranging from 0.5 to 1.0. In plasmid profiling, 22 isolates (58%) showed the presence of one or more plasmids in the range 1.0 to 30.9 mDa. The dendrogram obtained from the results of the RAPD-PCR discriminated the isolates into 30 single isolates and 3 clusters at the level of 40% similarity. The EPEC isolates were highly diverse, as shown by their differing plasmid profiles, antibiotic resistance patterns and RAPD profiles.
  17. Abdullah JM, Wan Ismail WFN, Mohamad I, Ab Razak A, Harun A, Musa KI, et al.
    Malays J Med Sci, 2020 Mar;27(2):1-9.
    PMID: 32308536 DOI: 10.21315/mjms2020.27.2.1
    When the first report of COVID-19 appeared in December 2019 from Wuhan, China, the world unknowingly perceived this as another flu-like illness. Many were surprised at the extreme steps that China had subsequently taken to seal Wuhan from the rest of the world. However, by February 2020, the SARS-CoV-2 virus, which causes COVID-19, had spread so quickly across the globe that the World Health Organization officially declared COVID-19 a pandemic. COVID-19 is not the first pandemic the world has seen, so what makes it so unique in Malaysia, is discussed to avoid a future coronacoma.
  18. Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Latif MA
    C. R. Biol., 2015 Feb;338(2):83-94.
    PMID: 25553855 DOI: 10.1016/j.crvi.2014.11.003
    Backcross breeding is the most commonly used method for incorporating a blast resistance gene into a rice cultivar. Linkage between the resistance gene and undesirable units can persist for many generations of backcrossing. Marker-assisted backcrossing (MABC) along with marker-assisted selection (MAS) contributes immensely to overcome the main limitation of the conventional breeding and accelerates recurrent parent genome (RPG) recovery. The MABC approach was employed to incorporate (a) blast resistance gene(s) from the donor parent Pongsu Seribu 1, the blast-resistant local variety in Malaysia, into the genetic background of MR219, a popular high-yielding rice variety that is blast susceptible, to develop a blast-resistant MR219 improved variety. In this perspective, the recurrent parent genome recovery was analyzed in early generations of backcrossing using simple sequence repeat (SSR) markers. Out of 375 SSR markers, 70 markers were found polymorphic between the parents, and these markers were used to evaluate the plants in subsequent generations. Background analysis revealed that the extent of RPG recovery ranged from 75.40% to 91.3% and from 80.40% to 96.70% in BC1F1 and BC2F1 generations, respectively. In this study, the recurrent parent genome content in the selected BC2F2 lines ranged from 92.7% to 97.7%. The average proportion of the recurrent parent in the selected improved line was 95.98%. MAS allowed identification of the plants that are more similar to the recurrent parent for the loci evaluated in backcross generations. The application of MAS with the MABC breeding program accelerated the recovery of the RP genome, reducing the number of generations and the time for incorporating resistance against rice blast.
  19. Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Islam KhN, et al.
    Int J Mol Sci, 2013;14(11):22499-528.
    PMID: 24240810 DOI: 10.3390/ijms141122499
    Over the last few decades, the use of molecular markers has played an increasing role in rice breeding and genetics. Of the different types of molecular markers, microsatellites have been utilized most extensively, because they can be readily amplified by PCR and the large amount of allelic variation at each locus. Microsatellites are also known as simple sequence repeats (SSR), and they are typically composed of 1-6 nucleotide repeats. These markers are abundant, distributed throughout the genome and are highly polymorphic compared with other genetic markers, as well as being species-specific and co-dominant. For these reasons, they have become increasingly important genetic markers in rice breeding programs. The evolution of new biotypes of pests and diseases as well as the pressures of climate change pose serious challenges to rice breeders, who would like to increase rice production by introducing resistance to multiple biotic and abiotic stresses. Recent advances in rice genomics have now made it possible to identify and map a number of genes through linkage to existing DNA markers. Among the more noteworthy examples of genes that have been tightly linked to molecular markers in rice are those that confer resistance or tolerance to blast. Therefore, in combination with conventional breeding approaches, marker-assisted selection (MAS) can be used to monitor the presence or lack of these genes in breeding populations. For example, marker-assisted backcross breeding has been used to integrate important genes with significant biological effects into a number of commonly grown rice varieties. The use of cost-effective, finely mapped microsatellite markers and MAS strategies should provide opportunities for breeders to develop high-yield, blast resistance rice cultivars. The aim of this review is to summarize the current knowledge concerning the linkage of microsatellite markers to rice blast resistance genes, as well as to explore the use of MAS in rice breeding programs aimed at improving blast resistance in this species. We also discuss the various advantages, disadvantages and uses of microsatellite markers relative to other molecular marker types.
  20. Mazid MS, Rafii MY, Hanafi MM, Rahim HA, Latif MA
    Physiol Plant, 2013 Nov;149(3):432-47.
    PMID: 23521023 DOI: 10.1111/ppl.12054
    A field experiment was carried out in order to evaluate genetic diversity of 41 rice genotypes using physiological traits and molecular markers. All the genotypes unveiled variations for crop growth rate (CGR), relative growth rate (RGR), net assimilation rate (NAR), yield per hill (Yhill(-1)), total dry matter (TDM), harvest index (HI), photosynthetic rate (PR), leaf area index (LAI), chlorophyll-a and chlorophyll-b at maximum tillering stage. The CGR values varied from 0.23 to 0.76 gm cm(-2) day(-1). The Yhill(-1) ranged from 15.91 to 92.26 g, while TDM value was in the range of 7.49 to 20.45 g hill(-1). PR was found to vary from 9.40 to 22.34 µmol m(-2) s(-1). PR expressed positive relation with Yhill(-1). Significant positive relation was found between CGR and TDM (r = 0.61**), NAR and CGR (r = 0.62**) and between TDM and NAR (r = 0.31**). High heritability was found in RGR and Yhill(-1). Cluster analysis based on the traits grouped 41 rice genotypes into seven clusters. A total of 310 polymorphic loci were detected across the 20 inter-simple sequence repeats (ISSR) markers. The UPGMA dendrogram grouped 41 rice genotypes into 11 clusters including several sub-clusters. The Mantel test revealed positive correlation between quantitative traits and molecular markers (r = 0.41). On the basis of quantitative traits and molecular marker analyses parental genotypes, IRBB54 with MR84, IRBB60 with MR84, Purbachi with MR263, IRBB65 with BR29, IRBB65 with Pulut Siding and MRQ74 with Purbachi could be hybridized for future breeding program.
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