Zamri Zainal

Universiti Kebangsaan Malaysia | ukm · School of Biological Sciences and Biotechnology

Rice is frequently subjected to various environmental stresses, resulting in significant production losses, with drought and salinity are the leading causes of plant damage globally. This study aims to characterize and understand the function of rice high-affinity potassium transporters ( HKTs ) genes in response to salinity stress. Initially, the...

The application of miRNA mimic technology for silencing mature miRNA began in 2007. This technique originated from the discovery of the INDUCED BY PHOSPHATE STARVATION 1 (IPS1) gene, which was found to be a competitive mimic that prevents the cleavage of the targeted mRNA by miRNA inhibition at the post-transcriptional level. To date, various studi...

Nitrate transporter (NRT) is responsible for the molecular mechanism of the root nitrate (NO3-) uptake system for plant development. Although several NRT genes are identified and characterised in plants, knowledge of the NRT2 gene family and its nitrogen use efficiency (NUE) function in drought stress has remained elusive in rice. This study conduc...

In higher plants, the complexity of a system and the components within and among species are rapidly dissected by omics technologies. Multi-omics datasets are integrated to infer and enable a comprehensive understanding of the life processes of organisms of interest. Further, growing open-source datasets coupled with the emergence of high-performan...

Auxin receptor plays a significant role in the plant auxin signalling pathway in response to abiotic stress. Recently, we found that transgenic rice overexpressing ABP57 had higher drought tolerance than the wild-type cultivar, MR219, due to the fact of its enhanced leaf photosynthetic rate and yields under drought stress. We performed a microarray...

Abstract Sulfur is an essential element required for plant growth and development, physiological processes and stress responses. Sulfur-encoding biosynthetic genes are involved in the primary sulfur assimilation pathway, regulating various mechanisms at the gene, cellular and system levels, and in the biosynthesis of sulfur-containing compounds (SC...

Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a...

Abstract This study focuses on the growth and morpho-physiological responses of the Malaysian commercial variety MR219 rice to salinity stress during the early vegetative stages, specifically during germination and the five-leaf stage. For germination responses, MR219 seeds were grown for 10 days in different salt concentrations. Low salinity sign...

Mangoes comes in different sizes and consumer are often favour those with bigger, fleshy mango. Many genes are plays an important role in determining the growth, final size and shapes of the mango. To further understand the roles of genes that play roles in fruit development, a de novo transcriptomic analysis was performed at two stages of fruit de...

The red palm weevil (RPW; Rhynchophorus ferrugineus Olivier (Coleoptera Curculionidae)) is an invasive insect pest that is difficult to manage due to its nature of infesting the host palm trees from within. A holistic, molecular-based approach to identify proteins that correlate with RPW infestation could give useful insights into the vital process...

Basal stem rot (BSR) disease caused by pathogenic fungus Ganoderma boninense is a significant concern in the oil palm industry. G. boninense infection in oil palm induces defense-related genes. To understand oil palm defense mechanisms in response to fungal invasion, we analyzed differentially expressed genes (DEGs) derived from RNA-sequencing (RNA...

Auxin Binding Protein 57 (ABP57) is one of the molecular components involved in rice response to abiotic stress. The ABP57 gene encodes an auxin receptor which functions in activating the plasma membrane H+-ATPase. Biochemical properties of ABP57 have been characterized; however, the function of ABP57, particularly on stress and hormone responses i...

The ubiquitin-mediated proteolysis via Arg N-degron branch regulates various plant developmental processes and responds to multiple stresses. Nevertheless, limited information is available on the significance of the pathway during fruit ripening. This study reports that the suppression of PROTEOLYSIS6 (PRT6) E3 ligase in tomato through RNAi altered...

Key message Transcript profiling during the early induction phase of oil palm tissue culture and RNAi studies in a model somatic embryogenesis system showed that EgENOD93 expression is essential for somatic embryogenesis. AbstractMicropropagation of oil palm through tissue culture is vital for the generation of superior and uniform elite planting m...

MR219 transgenic rice line which overexpressed an auxin-binding protein (ABP57) and its wild-type cultivar, MR219, were screened under well-watered (WW) and drought stress (DS) conditions at the early reproductive stage. This study was conducted with the standard planting distance and under a normal environment to assess the yield advantages based...

Background: Rice tungro disease (RTD) is a viral disease mainly affecting rice in Asia. RTD caused by Rice tungro bacilliform virus and Rice tungro spherical virus. To date, there are only 5 RTSV isolates have been reported. Objectives: In this study, we aimed to report the complete nucleotide sequence of Malaysian isolate of Rice tungro spheric...

Numerous potyvirus studies, including virus biology, transmission, viral protein function, as well as virus–host interaction, have greatly benefited from the utilization of reverse genetic techniques. Reverse genetics of RNA viruses refers to the manipulation of viral genomes, transfection of the modified cDNAs into cells, and the production of liv...

The red palm weevil (RPW) is a stem boring Coleoptera that decimates host palm trees from within. The challenge of managing this pest is due to a lack of physical symptoms during the early stages of infestation. Investigating the physiological changes that occur within RPW-infested palm trees may be useful in establishing a new approach in RPW dete...

The genomics and genetic data of pigmented and non-pigmented Malaysian rice varieties are still limited. Hence, we performed the genome resequencing of two black rice varieties (Bali, Pulut Hitam 9), two red rice varieties (MRM16, MRQ100) and two white rice varieties (MR297 and MRQ76) using Illumina HiSeq 4000 platform with 30x sequencing coverage....

Monosaccharide transporter (MSTs) is a large family of integral membrane proteins that plays a crucial role in cell-to-cell and long-distance distribution of sugars throughout the plant. It has long been regarded as one of the most essential components in a myriad of plant physiological functions such as carbohydrate partitioning, sugar signaling,...

Pigmented rice is enriched with antioxidants, macro- and micronutrients. A comprehensive investigation of the gene expression patterns among the pigmented rice varieties would help to understand the cellular mechanism and biological processes of rice grain pigmentation. Hence, we performed RNA sequencing and analysis on the whole grain of dehusked...

The SCF complex is a widely studied multi-subunit ring E3 ubiquitin ligase that tags targeted proteins with ubiquitin for protein degradation by the ubiquitin 26S-proteasome system (UPS). The UPS is an important system that generally keeps cellular events tightly regulated by purging misfolded or damaged proteins and selectively degrading important...

Mangosteen (Garcinia mangostana L.) is an apomictic tropical fruit tree species which asexually produces recalcitrant seeds that are sensitive to desiccation and not viable for long-term storage. It is important to understand seed germination to inform strategy for the propagation and conservation of important plants, especially for recalcitrant sp...

CURT1 proteins in Arabidopsis thaliana have been reported to be important for inducing grana curvature. Currently, we have identified transcript encoding CURT1A from Oryza sativa cv. indica through RNA-seq analysis and characterised using heterologous system in Arabidopsis. The OsCURT1A gene shares 80% of its amino acid sequence with Arabidopsis At...

Abiotic stress is one of major constraints in crop production worldwide. Drought is the most important abiotic stress that has a huge impact on plant growth and productivity. Rice is one of the crops that is sensitive to water limited conditions and prolong drought stress causes yield loss. Many genes are also affected by drought stress and informa...

The prototypic cyclotide (Kalata B1), isolated from African plant Oldenlandia affinis (Rubiceae), exhibits molluscicidal property against golden apple snails. Given their naturally high mollucicidal activities against golden apple snail, and reports on the introduction of the Oak 1 gene into various plant species, there is a possibility to generate...

Agarwood is a resinous part of the non-timber Aquilaria tree, which is a highly valuable product for medicine and fragrance purposes. To protect the endangered Aquilaria species, mass plantation of Aquilaria trees has become a sustainable way in Asian countries to obtain the highly valuable agarwood. As only physiologically triggered Aquilaria tree...

Citral is a mixture of neral and geranial, which are of great interest to the fragrance industry due to its lemon-scented aroma. A newly characterized nerol dehydrogenase of Persicaria minor (PmNeDH) from our recent findings has shown a capacity to convert citral from nerol. Differential gene expression analysis revealed that the expression level o...

F-box proteins containing variable C-terminal domains make an essential part of SKP1-Cullin-Ring box-F box (SCF) complex. SCF complex catalyzes the final step to link the ubiquitin tag with the target protein, destined for degradation, through F-box protein that confer overall substrate specificity to the complex. In this study, we analyzed the rol...

Auxin plays important roles in many aspects of plant growth and development. It is known that auxin binds to auxin-binding protein (Abp57) and activates the plasma membrane H⁺-ATPases. In order to elucidate the biological function of rice Abp57 in plants, overexpression transgenic arabidopsis lines were generated. We found overexpression transgenic...

The efficacy of Citrus hystrix, Azadirachta indica and Cymbopogon citratus essential oils were evaluated for controlling the growth of mycelia and spore germination of Colletotrichum gloeosporioides. In order to determine the best essential oil (EO) and suitable concentration of essential oil, in vitro experiment was conducted by preparing a pure c...

In current era, majority of microRNA (miRNA) are being discovered through computational approaches which are more confined towards model plants. Here, for the first time, we have described the identification and characterization of novel miRNA in a non-model plant,Persicaria minor(P.minor) using computational approach. Unannotated sequences from de...

Green leaf volatiles (GLV) are important factors in plant defense, and plant–plant and plant–insect interactions. Kelch-repeat containing F-box proteins (KFB) are plant-specific proteins, which recruit substrates for protein degradation. The present study was conducted to evaluate the role of AtSKIP11, an Arabidopsis KFB, in the expression of hydro...

Geraniol degradation pathway has long been elucidated in microorganisms through bioconversion studies, yet weakly characterised in plants; enzyme with specific nerol-oxidising activity has not been reported. A novel cDNA encodes nerol dehydrogenase (PmNeDH) was isolated from Persicaria minor. The recombinant PmNeDH (rPmNeDH) is a homodimeric enzyme...

Alcohol dehydrogenases exist as a multigene family. Two isogenes, PmADHa and PmADHb were obtained from Persicaria minor via RACE-PCR were highly identical at the 5′-UTR and ORF region and highly divergent at the 3′-UTR. With the length of 1077 and 1163 bp respectively, PmADHa and PmADHb have 801 bp ORF length, encodes 266 amino acid residues. Four...

Garcinia mangostana is a tropical fruit plant rich in antioxidant and bears recalcitrant seeds. The extent of water loss and low temperature tolerable by recalcitrant seed varies from regular orthodox seeds. Present study generates transcriptome resources for G.mangostana to postulate potential transcriptome differences between recalcitrant and ort...

Increased tolerance to multiple abiotic stresses in plants is a key target for food security. OsSAP8 is a member of the stress-associated protein (SAP) gene family in rice and is characterized by the presence of two zinc finger domains, A20 and AN1. In this research, we aim to understand the regulatory mechanism of OsSAP8 in response to multiple st...

Drought stress is the main abiotic factor affecting rice production. Rain-fed upland rice which is grown on unbounded fields and totally dependent on rainfall for moisture is more prone to drought stress compared to rice from other ecosystems. However, upland rice has adapted to this limited water condition, thus are more drought tolerant than rice...

The dataset presented in this article describes microarray experiment of Auxin-binding protein 57, Abp57-overexpressing transgenic rice. The gene expression profiles were generated using Affymetrix GeneChip® Rice (Cn) Gene 1.0 ST Arrays. Total RNA from seedlings tissue of transgenic rice and wildtype, which serve as control were used as starting ma...

Agrobacterium-mediated transformation of indica rice is undoubtedly a challenging task due to the rice recalcitrant nature to transformation process. Therefore, optimization of the transformation protocol is important for specific indica rice cultivar to ensure effectiveness of the transformation. In this study, crucial parameters affecting Agrobac...

Persicaria minor (Kesum) is an important medicinal plant with high level of secondary metabolite contents, especially, terpenoids and flavonoids. Previous studies have revealed that application of exogenous phytohormone could increase secondary metabolite contents of the plant. MicroRNAs (miRNAs) are small RNAs that play important regulatory roles...

Persicaria minor (kesum) is an important medicinal plant and commonly found in southeast countries; Malaysia, Thailand, Indonesia, and Vietnam. This plant is enriched with a variety of secondary metabolites (SMs), and among these SMs, terpenoids are in high abundance. Terpenoids are comprised of many valuable biomolecules which have well-establishe...

Recent achievements in plant microRNA (miRNA), a large class of small and non-coding RNAs, are very exciting. A wide array of techniques involving forward genetic, molecular cloning, bioinformatic analysis, and the latest technology, deep sequencing have greatly advanced miRNA discovery. A tiny miRNA sequence has the ability to target single/multip...

Persicaria minor is one of the native aromatic plants in Malaysia and widely used in traditional foods and medicines. Previous studies have shown that treatment of P. minor with jasmonic acid upregulated genes involved in the secondary metabolites production and also gene encoding an F-box protein named PmFbox-1. It is known that F-box proteins pla...

Background Polygonum minus is an herbal plant in the Polygonaceae family which is rich in ethnomedicinal plants. The chemical composition and characteristic pungent fragrance of Polygonum minus have been extensively studied due to its culinary and medicinal properties. There are only a few transcriptome sequences available for species from this imp...

Data S1. KEGG pathway mapping results.

Supplementary Tables.

Data S2. RSEM estimation of transcript abundance in the leaf and root tissues with functional annotation.

Supplementary Figures.

Data S3. Profiling of candidate genes related to the biosynthesis of phenylpropanoids and flavonoids.

Plants possess different mechanisms in stress response, where induction of stress-responsive genes provides tolerance to unfavorable conditions. Stress-responsive genes are characterized for functional and regulatory genes that help in overcoming stress by molecular, biochemical and morphological adaptations. NAC transcription factors are one of th...

Ficus deltoidea (moraceae) is a herbal plant with medicinal values. Previous studies reported that the F. deltoidea contains a high level of bioactive compounds such as flavonoids. A cDNA encodes for chalcone isomerase was identified from F. deltoidea, designated as FdCHI, which involved in the isomerization of naringenin chalcone to naringenin. Na...

There is increased interest in the consumption of hot pepper (Capsicum annuum cv. Kulai) due to its high antioxidant content; however, pepper is also highly susceptible to postharvest losses. The goal of this study was to evaluate the combined effect of 1-methylcyclopropene (1-MCP) and modified-atmosphere packaging (MAP) compared to MAP alone in ma...

Delta 6-fatty acid desaturase and delta12-fatty acid desaturase are enzymes required for the desaturation steps during gamma-linolenic acid (GLA) biosynthesis in oleaginous fungi. The objectives of this study were to analyse the expression profiles of genes which encode for the delta 6-fatty acid desaturase (des6) and delta 12-fatty acid desaturase...

Terpenoids represent an important class of plant secondary metabolites, serving as component of plant defense against various biotic and abiotic stresses. A large number of structurally diverse terpenoid compounds have been identified from Persicaria minor (P. minor), an aromatic plant native to Malaysia. However, number of studies focusing on the...

Regeneration system via organogenesis has been developed for Malaysian chilli (Capsicum annuum L) var. CB4. Hypocotyls, cotyledons and petioles from In vitro germinated seedlings were cultured on medium comprising of Murashige and Skoog’s basal medium supplemented with 5 mg/l BAP, 1 mg/l IAA and 25 g/L DJ nutrient. Hypocotyls and petioles were foun...

Fruit constitutes an important part of the daily diet, thus contributing to its demand in local and worldwide markets. Consumer awareness, relative to food and health, has led to a demand for foods of high nutritional quality. This has encouraged many molecular biologists to study the complexity of fruit ripening so that the plants can be genetical...

Polygonum minus plant is rich in secondary metabolites, especially terpenoids and flavonoids. Present study generates transcriptome resource for P. minus to decipher its secondary metabolite biosynthesis pathways. Raw reads and the transcriptome assembly project have been deposited at GenBank under the accessions SRX313492 (root) and SRX669305 (lea...

This paper discusses the concepts and the contents of intervention program modules for integrative Science, Technology, Engineering and Mathematics (STEM) Education based on tauhid – the integration of Aqli and Naqli knowledge. This integration is designed to produce Ulul Albab (those deeply rooted in knowledge). The Ulul Albab Empowerment Modules...

Persicaria minor (Polygonaceae) is an important aromatic plant and due to its very strong taste and odor, leaves of P. minor are conventionally used to add flavor to certain foods in South East Asian countries. Traditionally; it is used for sprains and body aches by pounding with rice powder to make a paste. In this study we used UPLC/MS to examine...

Ubiquitination of regulatory proteins, catalysed by three enzyme complexes, E1, E2 and E3, renders the target proteins vulnerable to degradation by 26S proteasome system. SCF (SKP1-Cullin1-F-box) is one of the best characterized among many E3 (ubiquitin ligase) complexes, which catalyse the transfer of ubiquitin to the substrate protein. F-box prot...

To identify salt-responsive genes, we constructed a cDNA subtractive library from a salt-tolerant rice cultivar, MR219. Treatments of the whole plant were carried out with 150 mM sodium chloride for 0, 2, 4, 8, 12 and 24 h. The extraction of total RNA from 14-day-old seedlings was conducted on the shoots and roots of both treated and untreated plan...

Plants have evolved numerous constitutive and inducible defence mechanisms to cope with biotic and abiotic stresses. These stresses induce the expression of various genes to activate defence-related pathways that result in the release of defence chemicals. One of these defence mechanisms is the oxylipin pathway, which produces jasmonates, divinylet...

The stress-associated protein (SAP) family provides salinity stress tolerance in plants. We performed functional studies of SAP MR219, which is a member of the SAP family that is induced after salinity stresses. Computational analysis of the SAP MR219 cDNA clone that was isolated from rice root and shoot revealed significant homology with the SAP g...

Aromatic rice variety namely MRQ 74, MRQ 80 and MRQ 50 are the most popular rice in Malaysia. Establishing an efficient regeneration protocols via somatic embryogenesis is required for varietal improvements. An efficient somatic embryogenesis system has been established for three aromatic rice varieties using mature seeds. MS-B5 medium containing 1...

A method for hairy root induction of Persicaria minor, was developed and investigated, and a qualitative evaluation of the sesquiterpenes in the culture medium was performed. The transgenic status was confirmed by PCR analysis using rolB and virD specific primers. The efficiency with which four different strains of Agrobacterium rhizogenes (A4, ATC...

This study was directed at the understanding of the function of CCoAOMT isolated from Acacia auriculiformis x Acacia mangium. Full length cDNA of the Acacia hybrid CCoAOMT (AhCCoAOMT) was 1024-bp long, containing 750-bp coding regions, with one major open reading frame of 249 amino acids. On the other hand, full length genomic sequence of the CCoAO...

The floral-dip transformation method for Arabidopsis thaliana has long been established. Following transformation, an important step is involving the selection for transgenic plants through antibiotics or herbicides. Hygromycin has been widely applied for transgenic plants selection. However, the concentrations used were varied between laboratories...

Background: The somatic embryogenesis tissue culture process has been utilized to propagate high yielding oil palm. Due to the low callogenesis and embryogenesis rates, molecular studies were initiated to identify genes regulating the process, and their expression levels are usually quantified using reverse transcription quantitative real-time PCR...

The floral-dip transformation method for Arabidopsis thaliana has long been established. Following transformation, an important step is involving the selection for transgenic plants through antibiotics or herbicides. Hygromycin has been widely applied for transgenic plants selection. However, the concentrations used were varied between laboratories...

Polygonum minus is an aromatic plant, which contains high abundance of terpenoids, especially the sesquiterpenes C15H24. Sesquiterpenes were believed to contribute to the many useful biological properties in plants. This study aimed to functionally characterize a full length sesquiterpene synthase gene from P. minus. P. minus sesquiterpene synthase...

Tomato (Solanum Lycopersicum L.) is the second most cultivated vegetable in the world and widely used as a system for studying the role of ethylene during fruit ripening. Our objective was to study the oxidative stress and antioxidative metabolism during ripening of non transgenic tomato and transgenic line-21 tomato which reduced ethylene. The lin...

Stearoyl-acyl-carrier-protein (ACP) desaturase gene plays an important role in oil palm mesocarp where main substrate stearic acid is converted to oleic acid. In this study, β-glucuronidase (GUS) activity regulated by the oil palm stearoyl-ACP desaturase promoter (Des) and the effects of gibberellic acid (GA3) treatment on promoter activation were...

The success of Agrobacterium-mediated genetic tansformation depends on the efficiency of gene delivery, plant regeneration systems and selection agents. The effects of hygromycin B (hyg B), a selection agent that is commonly used in plant genetic transformation, on embryogenic calli and somatic embryos of indica rice var MR219 was evaluated. Embryo...

Ripening of climacteric fruit such as papaya (Carica papaya L. cv.Sekaki) fruit depends on the ethylene action which later accompanied by softening process that can influence postharvest quality and storability of the fruit. Ethylene action inhibitors, 1-Methylcyclopropene (1-MCP) has been found to inhibit ethylene action and thus it can delay the...

1-Methylcyclopropene (1-MCP) has been found to inhibit ethylene action and thus it can delay the fruit ripening process. The effects of 1-MCP (90 ppb for 12 h) on softening related changes were determined through physiological changes, fruit firmness and activities of the cell wall degrading enzymes including α-galactosidase, β-galactosidase, pecti...

Chitin is a structural polysaccharide which can be degraded by chitinolytic enzymes to various derivatives that can be utilised in medicine, agriculture and water treatment. The identification and characterisation of Trichoderma virens UKM1 genes encoding for enzymes involved in crustacean chitin degradation were carried out by generating expressed...

Polygonum minus has been reported to contain valuable metabolites and to date, there is no report on using cell culture technique for metabolite production in P. minus. Naphthalene acetic acid (NAA) concentrations in the range of 2–6 mg L−1 were used in a matrix of combinations with dichlorophenoxyacetic acid (2,4-D) concentrations in the range of...

Flavonoids are secondary metabolites that are present at high levels in the Polugonum minus. In recent years, flavonoids have attracted the interest of researchers because of their antioxidant properties .Flavonoids are synthesised via the condensation of 4 coumaryl-CoA and 3 malonyl-CoA by the action of Chalcone synthase. A cDNA encoding a chalcon...

Ripening of climacteric fruit such as papaya (Carica papaya L. cv.Sekaki) fruit depends on the ethylene action which later accompanied by softening process that can influence postharvest quality and storability of the fruit. Ethylene action inhibitors, 1-Methylcyclopropene (1-MCP) has been found to inhibit ethylene action and thus it can delay the...

This study aimed to determine the effects of different concentrations and combinations of the phytohormones 2,4-dichlorophenoxy acetic acid (2,4-D), kinetin, 6-benzylaminopurine (BAP), and 1-naphthaleneacetic acid (NAA) on callus induction and to demonstrate the role of elicitors and exogenous precursors on the production of mitragynine in a Mitrag...

The present study describes a direct shoot regeneration-based micropropagation procedure for Vanilla planifolia. Two types of explant (i.e. shoot apex and stem nodal segment) were screened for their shoot induction potential following a three-month treatment with 6-benzylaminopurine (BAP) and &#945-Naphthaleneacetic acid (NAA). Results indicated th...

Tiger's Milk mushroom has been used for medicinal purposes by local aborigines to treat asthma, breast cancer, cough, fever and food poisoning. Molecular phylogenetic analysis utilizing RNA polymerase II, second largest subunit (RPB2) gene, identified the wild Tiger's Milk mushrooms collected from the state of Pahang in Malaysia for this study as L...