Address: Dept. of Cell and Molecular Biology,
Faculty of Biotechnology and Biomolecular Sciences,
Universiti Putra Malaysia,
43400 UPM Serdang,
Malaysia
Trichoderma species are commercially applied
as biocontrol agents against numerous plant pathogen... more Trichoderma species are commercially applied as biocontrol agents against numerous plant pathogenic fungi due to their production of antifungal metabolites, competition for nutrients and space, and mycoparasitism. However, currently the identification of Trichoderma species from throughout the world based on micro-morphological descriptions is tedious and prone to error. The correct identification of Trichoderma species is important as several traits are species-specific. The Random Amplified Microsatellites (RAMS) analysis done using five primers in this study showed different degrees of the genetic similarity among 42 isolates of this genus. The genetic similarity values were found to be in the range of 12.50–85.11% based on a total of 76 bands scored in the Trichoderma isolates. Of these 76 bands, 96.05% were polymorphic, 3.95% were monomorphic and 16% were exclusive bands. Two bands (250 bp and 200 bp) produced by primer LR-5 and one band (250 bp) by primer P1A were present in all the Trichoderma isolates collected from healthy and infected oil palm plantation soils. Cluster analysis based on UPGMA of the RAMS marker data showed that T. harzianum, T. virens and T. longibrachiatum isolates were grouped into different clades and lineages. In this study we found that although T. aureoviride isolates were morphologically different when compared to T. harzianum isolates, the UPGMA cluster analysis showed that the majority isolates of T. aureoviride (seven from nine) were closely related to the isolates of T. harzianum.
Isozyme and protein electrophoresis data from mycelial extracts of 27 isolates of Trichoderma har... more Isozyme and protein electrophoresis data from mycelial extracts of 27 isolates of Trichoderma harzianum, 10 isolates of T. aureoviride, and 10 isolates of T. longibrachiatum from Southern Peninsular Malaysia were investigated. The eight enzyme and a single protein pattern systems were analyzed. Three isozyme and total protein patterns were shown to be useful for the detection of three Trichoderma species. The isozyme and protein data were analyzed using the Nei and Li Dice similarity coefficient for pairwise comparison between individual isolates, species isolate group, and for generating a distance matrix. The UPGMA cluster analysis showed a higher degree of relationship between T. harzianum and T. aureoviride than to T. longibrachiatum. These results suggested that the T.harzianum isolates had high levels of genetic variation compared with the other isolates of Trichoderma species.
The goal of this study is to determine whether sequence analysis of internal transcribed spacer -... more The goal of this study is to determine whether sequence analysis of internal transcribed spacer -1 region of the rDNA can be used to detect species level of Trichoderma harzianum. Internal transcribed spacer- 1 region (ITS 1) of the ribosomal DNA was amplified by polymerase chain reaction (PCR). To test the selected universal primers (ITS1 and ITS2) and conditions of the PCR, thirty-six of Malaysian Trichoderma isolates were used. The results of PCR product were positively performed purification. The PCR purification products were proved possible to amplify the ITS 1 region of all Trichoderma strains. The amplified DNA was sequenced and aligned against using ex-type strains sequencings from TrichoBLAST /GenBank and established Trichoderma taxonomy. Thirty-six isolates were positively identified as Trichoderma harzianum (32 strains) Trichoderma virens (3 strains) and Trichoderma longibrachiatum (1 strain) formed clearly defining phylogenetic analysis. T. virens and T. longibrachiatum which were used as an outgroup in these analyses. To this end, thus are proposed that the ITS-1 region sequences are used as the reference’s sequence for future study involving the identification and taxonomy of Trichoderma harzianum. Amplification of ITS 1 region of the rDNA has showed potential as a rapid technique for identifying Trichoderma harzianum successfully fungi in all cases.
A new electrochemical biosensor is described for voltammetric detection of gene sequence related ... more A new electrochemical biosensor is described for voltammetric detection of gene sequence related to Trichoderma harzianum. The sensor involves immobilization of a 20 base single-stranded probe (ssDNA), which is complementary to a specific gene sequence related to T. ...
Oil palm chloroplast is maternally inherited, making investigation of the chloroplast diversity a... more Oil palm chloroplast is maternally inherited, making investigation of the chloroplast diversity an interesting endeavor. This paper describes a method for extracting enriched oil palm chloroplast DNA (cpDNA) done on six palms of different origins from Angola, Nigeria, Ghana, Madagascar and Suriname. Restriction enzyme digestion was used to evaluate the successful extraction of the oil palm cpDNA. The use of a mitochondrial DNA specific- universal primer revealed that most of the cpDNA were free from mitochondrial DNA contamination. Three chloroplast- specific universal primers were also used to evaluate the cpDNA. Their amplicons were cloned and sequenced to confirm that the cpDNA was indeed amplified. A search against the public databases further confirmed that the primers amplied sequences of the Elaeis guineensis Jacq. chloroplast genome. Two of them gave consistent amplifications when tested on cpDNA from the Angolan, Nigerian, Ghanian, Madagascan and Suriname palms.
ABSTRACT Miyun Reservoir is the main raw water source for Beijing’s domestic water supply. Flow d... more ABSTRACT Miyun Reservoir is the main raw water source for Beijing’s domestic water supply. Flow discharge to Miyun Reservoir decreased drastically over a 50-year period, from 1956 to 2005, and had seriously affected Beijing’s water supply. Climate variability and human activity had been identified as the two main reasons for the decrease in flow. Here, climate variability refers to changes in precipitation and temperature. Impact of human activity includes direct withdrawal of water (referred to as “direct abstraction” in this paper) from the river (primary) or groundwater and indirect impact due to man-made changes in land use and vegetation in the upstream of the reservoir. According to the historical record, “direct abstraction” from the upstream of the reservoir has increased significantly since 1984. The study period was split into two sub-periods, from 1956 to 1983 and from 1984 to 2005. Based on the historical record, annual runoff in the upstream catchment of Miyun Reservoir (i.e., inflow into the reservoir) had decreased from 90.3 mm to 41.8 mm for the two sub-periods, a decrease of 48.5 mm. Over the same period, average annual “direct abstraction” increased from 2.2 mm to 13.4 mm, an increase of 11.2 mm. The latter accounted for 23% (11.2 mm/48.5 mm) of the decrease in inflow into the reservoir.This study utilised: (1) a distributed hydrological model (geomorphology-based hydrological model, or GBHM) and (2) a climate elasticity model to conduct a quantitative assessment of the impact of climate variability and the indirect impact of human activity on the inflow into the reservoir. Simulation results of GBHM and the climate elasticity model showed that climate impact was accountable for about 55% and 51% of the decrease in reservoir inflow, respectively. The indirect impact of human activity (mainly man-made land use and vegetation changes) accounted for 18% of the decrease in reservoir inflow.
Inter-simple sequence repeats (ISSRs) are regions in the genome flanked by microsatellite sequenc... more Inter-simple sequence repeats (ISSRs) are regions in the genome flanked by microsatellite sequences. PCR amplification of these regions using a single primer yields multiple amplification products that can be used as a dominant multilocus marker system for the study of genetic variation in various organisms. ISSR markers are easy to use, low-cost, and methodologically less demanding compared to other dominant markers, making it an ideal genetic marker for beginners and for organisms whose genetic information is lacking. Here, we comment upon some of the intricacies often overlooked in designing an ISSR experiment, clarify some misconceptions, and provide recommendations on using ISSR markers in genetic variation studies.
Horseshoe crabs are one of the oldest living organisms that still exist today. Given the overexpl... more Horseshoe crabs are one of the oldest living organisms that still exist today. Given the overexploitation of horseshoe crabs around the world, and the lack of information on their populations, it is crucial that genetic variation studies are done to assess their levels and patterns of genetic variation for continuous monitoring and management of their populations. Here, five populations of the Asian horseshoe crab Tachypleus gigas sampled from along the coasts of the Malay Peninsula were studied using simple-sequence repeat (SSR) and inter-simple-sequence repeat (ISSR) markers. Different results were obtained using the two different types of markers in terms of the levels of genetic variation estimated, but both concurred that most of the genetic variations were distributed at the individual level rather than among populations of the species. Inbreeding was also observed using the SSR data, although the presence of null alleles could have influenced the estimation. Finally, both marker types revealed that T. gigas could have been subjected to the land barrier effect of the Malay Peninsula that causes populations from the Indian Ocean to be genetically differentiated from the populations from the South China Sea. Key words: Dispersal, genetic monitoring, land barrier, peninsular Malaysia, population structure
Andrographis paniculata (AP) has been stated as a low-diverse, endangered and red-listed plant sp... more Andrographis paniculata (AP) has been stated as a low-diverse, endangered and red-listed plant species. Self-pollinated mating system, being an introduced species and experiencing a bottleneck as well as over exploitation cause such a consequence. Inter and intra-specific hybridizations have been suggested as essential techniques for generating genetic diversity. To test the effect of intra-specific hybridization on diversification and heterosis of AP, seven accessions were outcrossed manually in all 21 possible combinations. Three types of markers including morphological, phytochemical and RAPD markers were employed to evaluate the mentioned hypothesis. The results revealed that hybridization acted as a powerful engine for diversification of AP as it caused heterotic expression of the studied traits, simultaneously. Initially, it seems that additive and non-additive gene effects both can be considered as the genetic basis of heterosis in AP for the investigated traits. Agronomic an...
Andrographis paniculata Nees. (AP) is a self-pollinated medicinal herb with a wide range of pharm... more Andrographis paniculata Nees. (AP) is a self-pollinated medicinal herb with a wide range of pharmaceutical properties, facing a low diversity in Malaysia. Cross-pollination of AP accessions leads to considerable rates of heterosis in the agro-morphological characteristics and anticancer phytochemicals of this eminent medicinal herb. However, the poor crossability of the plant at the interpopulation or intraspecific levels is an obstacle from the evolutionary and breeding points of view as an average of 4.56% crossability was recorded for AP in this study. Hence, this research aimed to elicit the impact of parental genetic distances (GD) on the rate of crossability of AP using seven accessions in 21 possible cross combinations. To this end, a set of 55 randomly amplified polymorphic DNA (RAPD) primers and a total of 13 agro-morphological markers were employed to test the hypothesis. Twenty-two out of the 55 RAPD primers amplified a total of 257 bands of which 107 bands were found to be polymorphic. The principal component analysis (PCA) based on the RAPD markers revealed that the studied AP accessions were distributed to three distinct groups. Furthermore, it was noticed that even a minor increase in GD between two parents can cause a decline in their crossability. Unlike, the morphological-based GDs acted neutrally to crossability. This finding suggests that, despite the low genetic diversity among the Malaysian APs, a population prescreening using RAPD markers would be useful to enhance the rate of fruit set through selecting the genetically adjacent parents.
Understanding the genetic variation of the Plasmodium parasites could play an important
role in c... more Understanding the genetic variation of the Plasmodium parasites could play an important role in controlling and preventing this lethal infection. Inter simple sequence repeat (ISSR) markers have successfully been tested for investigating the genetic diversity of malaria vectors. It is hypothesized that ISSRs could lead to fruitful results in studying the genetic variation of Plasmodium species, as well. To illustrate the genetic diversity of two infectious Plasmodium species, including Plasmodium knowlesi and Plasmodium cynomolgi, infected and uninfected monkey blood samples were separately collected on filter papers (FTA cards), and used for DNA extraction. A total of 103 and 95 polymorphic ISSR loci were detected in infected and uninfected samples, respectively. Cluster analysis of the Plasmodium and Macaca fascicularis accessions both resulted in the generation of three clusters. However, the most significant result of the cluster analysis was revealing the high efficiency of ISSR markers in the discrimination of the two Plasmodium species from each other. The cluster analysis showed a wide range of genetic diversity among both Plasmodium and the long-tailed Macaque accessions. The principal component analysis (PCA) also confirmed the cluster analysis results.
study was conducted to ascertain the genetic structure and the level of heterozygosity of Acipen... more study was conducted to ascertain the genetic structure and the level of heterozygosity of Acipenser persicus in the Caspian Sea. A total of 167 fish were randomly collected from Turkmenistan, Russia and two regions of Iran. The number of alleles of eleven microsatellite markers ranged from 3 to 21 and the mean observed values of heterozygosity were 0.56 ± 0.20, 0.64 ± 0.14, 0.67 ± 0.16, and 0.64 ± 0.11. The observed heterozygosity was lower than the expected levels. The observed low genetic differentiation indicates that all populations are closely related. Hence, inbreeding is a potential problem, which should be taken into consideration in future breeding programs to avoid a further decline in genetic diversity.
Andrographis paniculata (AP) has been stated as a low-diverse, endangered and red-listed plant sp... more Andrographis paniculata (AP) has been stated as a low-diverse, endangered and red-listed plant species. Self-pollinated mating system, being an introduced species and experiencing a bottleneck as well as over exploitation cause such a consequence. Inter and intraspecific hybridization has been suggested as essential techniques for generating genetic diversity. To test the effect of intraspecific hybridization on diversification and heterosis of AP, seven accessions were outcrossed manually in all 21 possible combinations. Three types of markers including morphological, phytochemical and RAPD markers were employed to evaluate the mentioned hypothesis. The results revealed that hybridization acted as a powerful engine for diversification of AP as it caused heterotic expression of the studied traits, simultaneously. Initially, it seems that additive and non-additive gene effects both can be considered as the genetic basis of heterosis in AP for the investigated traits. Agronomic and morphological traits were differentiated from each other, while positive heterosis was recorded mainly for agronomic traits but not for the morphological traits. Intra-specific hybridization increased the genetic diversity in AP population. Nevertheless, a part of this variation could also be attributed to the negative heterosis. The current exploration demonstrated the first ever conducted manual intraspecific hybridization among AP accessions in a mass scale. However, the 17 RAPD primers produced a monomorph pattern, but perhaps increasing the number of markers can feature a new genetic profile in this plant.
Tomistoma schlegelii, also referred to as the “false gharial”, is one of the most exclusive and l... more Tomistoma schlegelii, also referred to as the “false gharial”, is one of the most exclusive and least known of the world’s fresh water crocodilians, limited to Southeast Asia. Indeed, lack of economic value for its skin has led to neglect the biodiversity of the species. The current study aimed to investigate the mentioned case using 40 Simple Sequence Repeat (SSR) primer pairs and 45 Inter Simple Sequence Repeat (ISSR) primers. DNA analysis of 17 T. schlegelii samples using the SSR and ISSR markers resulted in producing a total of 49 and 108 polymorphic bands, respectively. Furthermore, the SSR- and ISSR-based cluster analyses both generated two main clusters. However, the SSR based results were found more in line with the geographical distributions of the crocodile samples collected across the country as compared with the ISSR-based results. The observed heterozygosity (HO) and expected heterozygosity (HE) of the polymorphic SSRs ranged between 0.588-1 and 0.470-0.891, respectively. The present results suggest that the Malaysian T. schlegelii populations had originated from a core population of crocodiles. In cooperation with the SSR markers, the ISSRs showed high potential for studying the genetic variation of T. schlegelii, and these markers are suitable to be employed in conservation genetic programs of this endangered species. Both SSR- and ISSR-based STRUCTURE analyses suggested that all the individuals of T. schlegelii are genetically similar with each other.
Keywords: Tomistoma schlegelii, ISSR, SSR, Genetic variation, Genetic structure
Trichoderma species are commercially applied
as biocontrol agents against numerous plant pathogen... more Trichoderma species are commercially applied as biocontrol agents against numerous plant pathogenic fungi due to their production of antifungal metabolites, competition for nutrients and space, and mycoparasitism. However, currently the identification of Trichoderma species from throughout the world based on micro-morphological descriptions is tedious and prone to error. The correct identification of Trichoderma species is important as several traits are species-specific. The Random Amplified Microsatellites (RAMS) analysis done using five primers in this study showed different degrees of the genetic similarity among 42 isolates of this genus. The genetic similarity values were found to be in the range of 12.50–85.11% based on a total of 76 bands scored in the Trichoderma isolates. Of these 76 bands, 96.05% were polymorphic, 3.95% were monomorphic and 16% were exclusive bands. Two bands (250 bp and 200 bp) produced by primer LR-5 and one band (250 bp) by primer P1A were present in all the Trichoderma isolates collected from healthy and infected oil palm plantation soils. Cluster analysis based on UPGMA of the RAMS marker data showed that T. harzianum, T. virens and T. longibrachiatum isolates were grouped into different clades and lineages. In this study we found that although T. aureoviride isolates were morphologically different when compared to T. harzianum isolates, the UPGMA cluster analysis showed that the majority isolates of T. aureoviride (seven from nine) were closely related to the isolates of T. harzianum.
Isozyme and protein electrophoresis data from mycelial extracts of 27 isolates of Trichoderma har... more Isozyme and protein electrophoresis data from mycelial extracts of 27 isolates of Trichoderma harzianum, 10 isolates of T. aureoviride, and 10 isolates of T. longibrachiatum from Southern Peninsular Malaysia were investigated. The eight enzyme and a single protein pattern systems were analyzed. Three isozyme and total protein patterns were shown to be useful for the detection of three Trichoderma species. The isozyme and protein data were analyzed using the Nei and Li Dice similarity coefficient for pairwise comparison between individual isolates, species isolate group, and for generating a distance matrix. The UPGMA cluster analysis showed a higher degree of relationship between T. harzianum and T. aureoviride than to T. longibrachiatum. These results suggested that the T.harzianum isolates had high levels of genetic variation compared with the other isolates of Trichoderma species.
The goal of this study is to determine whether sequence analysis of internal transcribed spacer -... more The goal of this study is to determine whether sequence analysis of internal transcribed spacer -1 region of the rDNA can be used to detect species level of Trichoderma harzianum. Internal transcribed spacer- 1 region (ITS 1) of the ribosomal DNA was amplified by polymerase chain reaction (PCR). To test the selected universal primers (ITS1 and ITS2) and conditions of the PCR, thirty-six of Malaysian Trichoderma isolates were used. The results of PCR product were positively performed purification. The PCR purification products were proved possible to amplify the ITS 1 region of all Trichoderma strains. The amplified DNA was sequenced and aligned against using ex-type strains sequencings from TrichoBLAST /GenBank and established Trichoderma taxonomy. Thirty-six isolates were positively identified as Trichoderma harzianum (32 strains) Trichoderma virens (3 strains) and Trichoderma longibrachiatum (1 strain) formed clearly defining phylogenetic analysis. T. virens and T. longibrachiatum which were used as an outgroup in these analyses. To this end, thus are proposed that the ITS-1 region sequences are used as the reference’s sequence for future study involving the identification and taxonomy of Trichoderma harzianum. Amplification of ITS 1 region of the rDNA has showed potential as a rapid technique for identifying Trichoderma harzianum successfully fungi in all cases.
A new electrochemical biosensor is described for voltammetric detection of gene sequence related ... more A new electrochemical biosensor is described for voltammetric detection of gene sequence related to Trichoderma harzianum. The sensor involves immobilization of a 20 base single-stranded probe (ssDNA), which is complementary to a specific gene sequence related to T. ...
Oil palm chloroplast is maternally inherited, making investigation of the chloroplast diversity a... more Oil palm chloroplast is maternally inherited, making investigation of the chloroplast diversity an interesting endeavor. This paper describes a method for extracting enriched oil palm chloroplast DNA (cpDNA) done on six palms of different origins from Angola, Nigeria, Ghana, Madagascar and Suriname. Restriction enzyme digestion was used to evaluate the successful extraction of the oil palm cpDNA. The use of a mitochondrial DNA specific- universal primer revealed that most of the cpDNA were free from mitochondrial DNA contamination. Three chloroplast- specific universal primers were also used to evaluate the cpDNA. Their amplicons were cloned and sequenced to confirm that the cpDNA was indeed amplified. A search against the public databases further confirmed that the primers amplied sequences of the Elaeis guineensis Jacq. chloroplast genome. Two of them gave consistent amplifications when tested on cpDNA from the Angolan, Nigerian, Ghanian, Madagascan and Suriname palms.
ABSTRACT Miyun Reservoir is the main raw water source for Beijing’s domestic water supply. Flow d... more ABSTRACT Miyun Reservoir is the main raw water source for Beijing’s domestic water supply. Flow discharge to Miyun Reservoir decreased drastically over a 50-year period, from 1956 to 2005, and had seriously affected Beijing’s water supply. Climate variability and human activity had been identified as the two main reasons for the decrease in flow. Here, climate variability refers to changes in precipitation and temperature. Impact of human activity includes direct withdrawal of water (referred to as “direct abstraction” in this paper) from the river (primary) or groundwater and indirect impact due to man-made changes in land use and vegetation in the upstream of the reservoir. According to the historical record, “direct abstraction” from the upstream of the reservoir has increased significantly since 1984. The study period was split into two sub-periods, from 1956 to 1983 and from 1984 to 2005. Based on the historical record, annual runoff in the upstream catchment of Miyun Reservoir (i.e., inflow into the reservoir) had decreased from 90.3 mm to 41.8 mm for the two sub-periods, a decrease of 48.5 mm. Over the same period, average annual “direct abstraction” increased from 2.2 mm to 13.4 mm, an increase of 11.2 mm. The latter accounted for 23% (11.2 mm/48.5 mm) of the decrease in inflow into the reservoir.This study utilised: (1) a distributed hydrological model (geomorphology-based hydrological model, or GBHM) and (2) a climate elasticity model to conduct a quantitative assessment of the impact of climate variability and the indirect impact of human activity on the inflow into the reservoir. Simulation results of GBHM and the climate elasticity model showed that climate impact was accountable for about 55% and 51% of the decrease in reservoir inflow, respectively. The indirect impact of human activity (mainly man-made land use and vegetation changes) accounted for 18% of the decrease in reservoir inflow.
Inter-simple sequence repeats (ISSRs) are regions in the genome flanked by microsatellite sequenc... more Inter-simple sequence repeats (ISSRs) are regions in the genome flanked by microsatellite sequences. PCR amplification of these regions using a single primer yields multiple amplification products that can be used as a dominant multilocus marker system for the study of genetic variation in various organisms. ISSR markers are easy to use, low-cost, and methodologically less demanding compared to other dominant markers, making it an ideal genetic marker for beginners and for organisms whose genetic information is lacking. Here, we comment upon some of the intricacies often overlooked in designing an ISSR experiment, clarify some misconceptions, and provide recommendations on using ISSR markers in genetic variation studies.
Horseshoe crabs are one of the oldest living organisms that still exist today. Given the overexpl... more Horseshoe crabs are one of the oldest living organisms that still exist today. Given the overexploitation of horseshoe crabs around the world, and the lack of information on their populations, it is crucial that genetic variation studies are done to assess their levels and patterns of genetic variation for continuous monitoring and management of their populations. Here, five populations of the Asian horseshoe crab Tachypleus gigas sampled from along the coasts of the Malay Peninsula were studied using simple-sequence repeat (SSR) and inter-simple-sequence repeat (ISSR) markers. Different results were obtained using the two different types of markers in terms of the levels of genetic variation estimated, but both concurred that most of the genetic variations were distributed at the individual level rather than among populations of the species. Inbreeding was also observed using the SSR data, although the presence of null alleles could have influenced the estimation. Finally, both marker types revealed that T. gigas could have been subjected to the land barrier effect of the Malay Peninsula that causes populations from the Indian Ocean to be genetically differentiated from the populations from the South China Sea. Key words: Dispersal, genetic monitoring, land barrier, peninsular Malaysia, population structure
Andrographis paniculata (AP) has been stated as a low-diverse, endangered and red-listed plant sp... more Andrographis paniculata (AP) has been stated as a low-diverse, endangered and red-listed plant species. Self-pollinated mating system, being an introduced species and experiencing a bottleneck as well as over exploitation cause such a consequence. Inter and intra-specific hybridizations have been suggested as essential techniques for generating genetic diversity. To test the effect of intra-specific hybridization on diversification and heterosis of AP, seven accessions were outcrossed manually in all 21 possible combinations. Three types of markers including morphological, phytochemical and RAPD markers were employed to evaluate the mentioned hypothesis. The results revealed that hybridization acted as a powerful engine for diversification of AP as it caused heterotic expression of the studied traits, simultaneously. Initially, it seems that additive and non-additive gene effects both can be considered as the genetic basis of heterosis in AP for the investigated traits. Agronomic an...
Andrographis paniculata Nees. (AP) is a self-pollinated medicinal herb with a wide range of pharm... more Andrographis paniculata Nees. (AP) is a self-pollinated medicinal herb with a wide range of pharmaceutical properties, facing a low diversity in Malaysia. Cross-pollination of AP accessions leads to considerable rates of heterosis in the agro-morphological characteristics and anticancer phytochemicals of this eminent medicinal herb. However, the poor crossability of the plant at the interpopulation or intraspecific levels is an obstacle from the evolutionary and breeding points of view as an average of 4.56% crossability was recorded for AP in this study. Hence, this research aimed to elicit the impact of parental genetic distances (GD) on the rate of crossability of AP using seven accessions in 21 possible cross combinations. To this end, a set of 55 randomly amplified polymorphic DNA (RAPD) primers and a total of 13 agro-morphological markers were employed to test the hypothesis. Twenty-two out of the 55 RAPD primers amplified a total of 257 bands of which 107 bands were found to be polymorphic. The principal component analysis (PCA) based on the RAPD markers revealed that the studied AP accessions were distributed to three distinct groups. Furthermore, it was noticed that even a minor increase in GD between two parents can cause a decline in their crossability. Unlike, the morphological-based GDs acted neutrally to crossability. This finding suggests that, despite the low genetic diversity among the Malaysian APs, a population prescreening using RAPD markers would be useful to enhance the rate of fruit set through selecting the genetically adjacent parents.
Understanding the genetic variation of the Plasmodium parasites could play an important
role in c... more Understanding the genetic variation of the Plasmodium parasites could play an important role in controlling and preventing this lethal infection. Inter simple sequence repeat (ISSR) markers have successfully been tested for investigating the genetic diversity of malaria vectors. It is hypothesized that ISSRs could lead to fruitful results in studying the genetic variation of Plasmodium species, as well. To illustrate the genetic diversity of two infectious Plasmodium species, including Plasmodium knowlesi and Plasmodium cynomolgi, infected and uninfected monkey blood samples were separately collected on filter papers (FTA cards), and used for DNA extraction. A total of 103 and 95 polymorphic ISSR loci were detected in infected and uninfected samples, respectively. Cluster analysis of the Plasmodium and Macaca fascicularis accessions both resulted in the generation of three clusters. However, the most significant result of the cluster analysis was revealing the high efficiency of ISSR markers in the discrimination of the two Plasmodium species from each other. The cluster analysis showed a wide range of genetic diversity among both Plasmodium and the long-tailed Macaque accessions. The principal component analysis (PCA) also confirmed the cluster analysis results.
study was conducted to ascertain the genetic structure and the level of heterozygosity of Acipen... more study was conducted to ascertain the genetic structure and the level of heterozygosity of Acipenser persicus in the Caspian Sea. A total of 167 fish were randomly collected from Turkmenistan, Russia and two regions of Iran. The number of alleles of eleven microsatellite markers ranged from 3 to 21 and the mean observed values of heterozygosity were 0.56 ± 0.20, 0.64 ± 0.14, 0.67 ± 0.16, and 0.64 ± 0.11. The observed heterozygosity was lower than the expected levels. The observed low genetic differentiation indicates that all populations are closely related. Hence, inbreeding is a potential problem, which should be taken into consideration in future breeding programs to avoid a further decline in genetic diversity.
Andrographis paniculata (AP) has been stated as a low-diverse, endangered and red-listed plant sp... more Andrographis paniculata (AP) has been stated as a low-diverse, endangered and red-listed plant species. Self-pollinated mating system, being an introduced species and experiencing a bottleneck as well as over exploitation cause such a consequence. Inter and intraspecific hybridization has been suggested as essential techniques for generating genetic diversity. To test the effect of intraspecific hybridization on diversification and heterosis of AP, seven accessions were outcrossed manually in all 21 possible combinations. Three types of markers including morphological, phytochemical and RAPD markers were employed to evaluate the mentioned hypothesis. The results revealed that hybridization acted as a powerful engine for diversification of AP as it caused heterotic expression of the studied traits, simultaneously. Initially, it seems that additive and non-additive gene effects both can be considered as the genetic basis of heterosis in AP for the investigated traits. Agronomic and morphological traits were differentiated from each other, while positive heterosis was recorded mainly for agronomic traits but not for the morphological traits. Intra-specific hybridization increased the genetic diversity in AP population. Nevertheless, a part of this variation could also be attributed to the negative heterosis. The current exploration demonstrated the first ever conducted manual intraspecific hybridization among AP accessions in a mass scale. However, the 17 RAPD primers produced a monomorph pattern, but perhaps increasing the number of markers can feature a new genetic profile in this plant.
Tomistoma schlegelii, also referred to as the “false gharial”, is one of the most exclusive and l... more Tomistoma schlegelii, also referred to as the “false gharial”, is one of the most exclusive and least known of the world’s fresh water crocodilians, limited to Southeast Asia. Indeed, lack of economic value for its skin has led to neglect the biodiversity of the species. The current study aimed to investigate the mentioned case using 40 Simple Sequence Repeat (SSR) primer pairs and 45 Inter Simple Sequence Repeat (ISSR) primers. DNA analysis of 17 T. schlegelii samples using the SSR and ISSR markers resulted in producing a total of 49 and 108 polymorphic bands, respectively. Furthermore, the SSR- and ISSR-based cluster analyses both generated two main clusters. However, the SSR based results were found more in line with the geographical distributions of the crocodile samples collected across the country as compared with the ISSR-based results. The observed heterozygosity (HO) and expected heterozygosity (HE) of the polymorphic SSRs ranged between 0.588-1 and 0.470-0.891, respectively. The present results suggest that the Malaysian T. schlegelii populations had originated from a core population of crocodiles. In cooperation with the SSR markers, the ISSRs showed high potential for studying the genetic variation of T. schlegelii, and these markers are suitable to be employed in conservation genetic programs of this endangered species. Both SSR- and ISSR-based STRUCTURE analyses suggested that all the individuals of T. schlegelii are genetically similar with each other.
Keywords: Tomistoma schlegelii, ISSR, SSR, Genetic variation, Genetic structure
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Papers by Soon -Guan Tan
as biocontrol agents against numerous plant pathogenic
fungi due to their production of antifungal metabolites,
competition for nutrients and space, and mycoparasitism.
However, currently the identification of Trichoderma species
from throughout the world based on micro-morphological
descriptions is tedious and prone to error. The
correct identification of Trichoderma species is important
as several traits are species-specific. The Random Amplified
Microsatellites (RAMS) analysis done using five
primers in this study showed different degrees of the
genetic similarity among 42 isolates of this genus. The
genetic similarity values were found to be in the range of
12.50–85.11% based on a total of 76 bands scored in the
Trichoderma isolates. Of these 76 bands, 96.05% were
polymorphic, 3.95% were monomorphic and 16% were
exclusive bands. Two bands (250 bp and 200 bp) produced
by primer LR-5 and one band (250 bp) by primer P1A
were present in all the Trichoderma isolates collected from
healthy and infected oil palm plantation soils. Cluster
analysis based on UPGMA of the RAMS marker data
showed that T. harzianum, T. virens and T. longibrachiatum
isolates were grouped into different clades and lineages.
In this study we found that although T. aureoviride
isolates were morphologically different when compared to
T. harzianum isolates, the UPGMA cluster analysis showed
that the majority isolates of T. aureoviride (seven from
nine) were closely related to the isolates of T. harzianum.
PCR purification products were proved possible to amplify the ITS 1 region of all Trichoderma strains. The amplified DNA was sequenced and aligned against using ex-type strains sequencings from TrichoBLAST /GenBank and established Trichoderma taxonomy. Thirty-six isolates were positively identified as Trichoderma harzianum (32 strains) Trichoderma virens (3 strains) and Trichoderma longibrachiatum (1 strain) formed clearly defining phylogenetic analysis. T. virens and T. longibrachiatum which were used as an outgroup in these analyses. To this end, thus are proposed that the ITS-1 region sequences are used as the reference’s sequence for future study involving the identification and taxonomy of Trichoderma harzianum. Amplification of ITS 1 region of the rDNA has showed potential as a rapid technique for identifying Trichoderma harzianum successfully fungi in all cases.
PCR amplification of these regions using a single primer yields multiple amplification products that can
be used as a dominant multilocus marker system for the study of genetic variation in various organisms.
ISSR markers are easy to use, low-cost, and methodologically less demanding compared to other
dominant markers, making it an ideal genetic marker for beginners and for organisms whose genetic
information is lacking. Here, we comment upon some of the intricacies often overlooked in designing an
ISSR experiment, clarify some misconceptions, and provide recommendations on using ISSR markers
in genetic variation studies.
around the world, and the lack of information on their populations, it is crucial that genetic variation studies are done to
assess their levels and patterns of genetic variation for continuous monitoring and management of their populations. Here,
five populations of the Asian horseshoe crab Tachypleus gigas sampled from along the coasts of the Malay Peninsula were
studied using simple-sequence repeat (SSR) and inter-simple-sequence repeat (ISSR) markers. Different results were
obtained using the two different types of markers in terms of the levels of genetic variation estimated, but both concurred
that most of the genetic variations were distributed at the individual level rather than among populations of the species.
Inbreeding was also observed using the SSR data, although the presence of null alleles could have influenced the estimation.
Finally, both marker types revealed that T. gigas could have been subjected to the land barrier effect of the Malay Peninsula
that causes populations from the Indian Ocean to be genetically differentiated from the populations from the South
China Sea.
Key words: Dispersal, genetic monitoring, land barrier, peninsular Malaysia, population structure
role in controlling and preventing this lethal infection. Inter simple sequence repeat (ISSR)
markers have successfully been tested for investigating the genetic diversity of malaria
vectors. It is hypothesized that ISSRs could lead to fruitful results in studying the genetic
variation of Plasmodium species, as well. To illustrate the genetic diversity of two
infectious Plasmodium species, including Plasmodium knowlesi and Plasmodium
cynomolgi, infected and uninfected monkey blood samples were separately collected on
filter papers (FTA cards), and used for DNA extraction. A total of 103 and 95 polymorphic
ISSR loci were detected in infected and uninfected samples, respectively. Cluster analysis
of the Plasmodium and Macaca fascicularis accessions both resulted in the generation of
three clusters. However, the most significant result of the cluster analysis was revealing
the high efficiency of ISSR markers in the discrimination of the two Plasmodium species
from each other. The cluster analysis showed a wide range of genetic diversity among both
Plasmodium and the long-tailed Macaque accessions. The principal component analysis
(PCA) also confirmed the cluster analysis results.
Keywords: Tomistoma schlegelii, ISSR, SSR, Genetic variation, Genetic structure
as biocontrol agents against numerous plant pathogenic
fungi due to their production of antifungal metabolites,
competition for nutrients and space, and mycoparasitism.
However, currently the identification of Trichoderma species
from throughout the world based on micro-morphological
descriptions is tedious and prone to error. The
correct identification of Trichoderma species is important
as several traits are species-specific. The Random Amplified
Microsatellites (RAMS) analysis done using five
primers in this study showed different degrees of the
genetic similarity among 42 isolates of this genus. The
genetic similarity values were found to be in the range of
12.50–85.11% based on a total of 76 bands scored in the
Trichoderma isolates. Of these 76 bands, 96.05% were
polymorphic, 3.95% were monomorphic and 16% were
exclusive bands. Two bands (250 bp and 200 bp) produced
by primer LR-5 and one band (250 bp) by primer P1A
were present in all the Trichoderma isolates collected from
healthy and infected oil palm plantation soils. Cluster
analysis based on UPGMA of the RAMS marker data
showed that T. harzianum, T. virens and T. longibrachiatum
isolates were grouped into different clades and lineages.
In this study we found that although T. aureoviride
isolates were morphologically different when compared to
T. harzianum isolates, the UPGMA cluster analysis showed
that the majority isolates of T. aureoviride (seven from
nine) were closely related to the isolates of T. harzianum.
PCR purification products were proved possible to amplify the ITS 1 region of all Trichoderma strains. The amplified DNA was sequenced and aligned against using ex-type strains sequencings from TrichoBLAST /GenBank and established Trichoderma taxonomy. Thirty-six isolates were positively identified as Trichoderma harzianum (32 strains) Trichoderma virens (3 strains) and Trichoderma longibrachiatum (1 strain) formed clearly defining phylogenetic analysis. T. virens and T. longibrachiatum which were used as an outgroup in these analyses. To this end, thus are proposed that the ITS-1 region sequences are used as the reference’s sequence for future study involving the identification and taxonomy of Trichoderma harzianum. Amplification of ITS 1 region of the rDNA has showed potential as a rapid technique for identifying Trichoderma harzianum successfully fungi in all cases.
PCR amplification of these regions using a single primer yields multiple amplification products that can
be used as a dominant multilocus marker system for the study of genetic variation in various organisms.
ISSR markers are easy to use, low-cost, and methodologically less demanding compared to other
dominant markers, making it an ideal genetic marker for beginners and for organisms whose genetic
information is lacking. Here, we comment upon some of the intricacies often overlooked in designing an
ISSR experiment, clarify some misconceptions, and provide recommendations on using ISSR markers
in genetic variation studies.
around the world, and the lack of information on their populations, it is crucial that genetic variation studies are done to
assess their levels and patterns of genetic variation for continuous monitoring and management of their populations. Here,
five populations of the Asian horseshoe crab Tachypleus gigas sampled from along the coasts of the Malay Peninsula were
studied using simple-sequence repeat (SSR) and inter-simple-sequence repeat (ISSR) markers. Different results were
obtained using the two different types of markers in terms of the levels of genetic variation estimated, but both concurred
that most of the genetic variations were distributed at the individual level rather than among populations of the species.
Inbreeding was also observed using the SSR data, although the presence of null alleles could have influenced the estimation.
Finally, both marker types revealed that T. gigas could have been subjected to the land barrier effect of the Malay Peninsula
that causes populations from the Indian Ocean to be genetically differentiated from the populations from the South
China Sea.
Key words: Dispersal, genetic monitoring, land barrier, peninsular Malaysia, population structure
role in controlling and preventing this lethal infection. Inter simple sequence repeat (ISSR)
markers have successfully been tested for investigating the genetic diversity of malaria
vectors. It is hypothesized that ISSRs could lead to fruitful results in studying the genetic
variation of Plasmodium species, as well. To illustrate the genetic diversity of two
infectious Plasmodium species, including Plasmodium knowlesi and Plasmodium
cynomolgi, infected and uninfected monkey blood samples were separately collected on
filter papers (FTA cards), and used for DNA extraction. A total of 103 and 95 polymorphic
ISSR loci were detected in infected and uninfected samples, respectively. Cluster analysis
of the Plasmodium and Macaca fascicularis accessions both resulted in the generation of
three clusters. However, the most significant result of the cluster analysis was revealing
the high efficiency of ISSR markers in the discrimination of the two Plasmodium species
from each other. The cluster analysis showed a wide range of genetic diversity among both
Plasmodium and the long-tailed Macaque accessions. The principal component analysis
(PCA) also confirmed the cluster analysis results.
Keywords: Tomistoma schlegelii, ISSR, SSR, Genetic variation, Genetic structure