Displaying publications 1 - 20 of 36 in total

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  1. Transcriptomics-based analysis using RNA-Seq of the coconut (Cocos nucifera) leaf in response to yellow decline phytoplasma infection
    Nejat N, Cahill DM, Vadamalai G, Ziemann M, Rookes J, Naderali N
    Mol Genet Genomics, 2015 Oct;290(5):1899-910.
    PMID: 25893418 DOI: 10.1007/s00438-015-1046-2
    Invasive phytoplasmas wreak havoc on coconut palms worldwide, leading to high loss of income, food insecurity and extreme poverty of farmers in producing countries. Phytoplasmas as strictly biotrophic insect-transmitted bacterial pathogens instigate distinct changes in developmental processes and defence responses of the infected plants and manipulate plants to their own advantage; however, little is known about the cellular and molecular mechanisms underlying host-phytoplasma interactions. Further, phytoplasma-mediated transcriptional alterations in coconut palm genes have not yet been identified. This study evaluated the whole transcriptome profiles of naturally infected leaves of Cocos nucifera ecotype Malayan Red Dwarf in response to yellow decline phytoplasma from group 16SrXIV, using RNA-Seq technique. Transcriptomics-based analysis reported here identified genes involved in coconut innate immunity. The number of down-regulated genes in response to phytoplasma infection exceeded the number of genes up-regulated. Of the 39,873 differentially expressed unigenes, 21,860 unigenes were suppressed and 18,013 were induced following infection. Comparative analysis revealed that genes associated with defence signalling against biotic stimuli were significantly overexpressed in phytoplasma-infected leaves versus healthy coconut leaves. Genes involving cell rescue and defence, cellular transport, oxidative stress, hormone stimulus and metabolism, photosynthesis reduction, transcription and biosynthesis of secondary metabolites were differentially represented. Our transcriptome analysis unveiled a core set of genes associated with defence of coconut in response to phytoplasma attack, although several novel defence response candidate genes with unknown function have also been identified. This study constitutes valuable sequence resource for uncovering the resistance genes and/or susceptibility genes which can be used as genetic tools in disease resistance breeding.
    Matched MeSH terms: Plant Leaves/genetics*
  2. Fulltext Transcriptome-wide shift from photosynthesis and energy metabolism upon endogenous fluid protein depletion in young Nepenthes ampullaria pitchers
    Goh HH, Baharin A, Mohd Salleh F', Ravee R, Wan Zakaria WNA, Mohd Noor N
    Sci Rep, 2020 04 20;10(1):6575.
    PMID: 32313042 DOI: 10.1038/s41598-020-63696-z
    Carnivorous pitcher plants produce specialised pitcher organs containing secretory glands, which secrete acidic fluids with hydrolytic enzymes for prey digestion and nutrient absorption. The content of pitcher fluids has been the focus of many fluid protein profiling studies. These studies suggest an evolutionary convergence of a conserved group of similar enzymes in diverse families of pitcher plants. A recent study showed that endogenous proteins were replenished in the pitcher fluid, which indicates a feedback mechanism in protein secretion. This poses an interesting question on the physiological effect of plant protein loss. However, there is no study to date that describes the pitcher response to endogenous protein depletion. To address this gap of knowledge, we previously performed a comparative RNA-sequencing experiment of newly opened pitchers (D0) against pitchers after 3 days of opening (D3C) and pitchers with filtered endogenous proteins (>10 kDa) upon pitcher opening (D3L). Nepenthes ampullaria was chosen as a model study species due to their abundance and unique feeding behaviour on leaf litters. The analysis of unigenes with top 1% abundance found protein translation and stress response to be overrepresented in D0, compared to cell wall related, transport, and signalling for D3L. Differentially expressed gene (DEG) analysis identified DEGs with functional enrichment in protein regulation, secondary metabolism, intracellular trafficking, secretion, and vesicular transport. The transcriptomic landscape of the pitcher dramatically shifted towards intracellular transport and defence response at the expense of energy metabolism and photosynthesis upon endogenous protein depletion. This is supported by secretome, transportome, and transcription factor analysis with RT-qPCR validation based on independent samples. This study provides the first glimpse into the molecular responses of pitchers to protein loss with implications to future cost/benefit analysis of carnivorous pitcher plant energetics and resource allocation for adaptation in stochastic environments.
    Matched MeSH terms: Plant Leaves/genetics
  3. The oil palm metallothionein promoter contains a novel AGTTAGG motif conferring its fruit-specific expression and is inducible by abiotic factors
    Omidvar V, Abdullah SN, Izadfard A, Ho CL, Mahmood M
    Planta, 2010 Sep;232(4):925-36.
    PMID: 20635097 DOI: 10.1007/s00425-010-1220-z
    The 1,053-bp promoter of the oil palm metallothionein gene (so-called MSP1) and its 5' deletions were fused to the GUS reporter gene, and analysed in transiently transformed oil palm tissues. The full length promoter showed sevenfold higher activity in the mesocarp than in leaves and 1.5-fold more activity than the CaMV35S promoter in the mesocarp. The 1,053-bp region containing the 5' untranslated region (UTR) gave the highest activity in the mesocarp, while the 148-bp region was required for minimal promoter activity. Two positive regulatory regions were identified at nucleotides (nt) -953 to -619 and -420 to -256 regions. Fine-tune deletion of the -619 to -420 nt region led to the identification of a 21-bp negative regulatory sequence in the -598 to -577 nt region, which is involved in mesocarp-specific expression. Gel mobility shift assay revealed a strong interaction of the leaf nuclear extract with the 21-bp region. An AGTTAGG core-sequence within this region was identified as a novel negative regulatory element controlling fruit-specificity of the MSP1 promoter. Abscisic acid (ABA) and copper (Cu(2+)) induced the activity of the promoter and its 5' deletions more effectively than methyl jasmonate (MeJa) and ethylene. In the mesocarp, the full length promoter showed stronger inducibility in response to ABA and Cu(2+) than its 5' deletions, while in leaves, the -420 nt fragment was the most inducible by ABA and Cu(2+). These results suggest that the MSP1 promoter and its regulatory regions are potentially useful for engineering fruit-specific and inducible gene expression in oil palm.
    Matched MeSH terms: Plant Leaves/genetics
  4. Fulltext Subcellular localization and interactions among rubber particle proteins from Hevea brasiliensis
    Brown D, Feeney M, Ahmadi M, Lonoce C, Sajari R, Di Cola A, et al.
    J Exp Bot, 2017 Nov 02;68(18):5045-5055.
    PMID: 29036360 DOI: 10.1093/jxb/erx331
    Natural rubber (polyisoprene) from the rubber tree Hevea brasiliensis is synthesized by specialized cells called laticifers. It is not clear how rubber particles arise, although one hypothesis is that they derive from the endoplasmic reticulum (ER) membrane. Here we cloned the genes encoding four key proteins found in association with rubber particles and studied their intracellular localization by transient expression in Nicotiana benthamiana leaves. We show that, while the cis-prenyltransferase (CPT), responsible for the synthesis of long polyisoprene chains, is a soluble, cytosolic protein, other rubber particle proteins such as rubber elongation factor (REF), small rubber particle protein (SRPP) and Hevea rubber transferase 1-REF bridging protein (HRBP) are associated with the endoplasmic reticulum (ER). We also show that SRPP can recruit CPT to the ER and that interaction of CPT with HRBP leads to both proteins relocating to the plasma membrane. We discuss these results in the context of the biogenesis of rubber particles.
    Matched MeSH terms: Plant Leaves/genetics
  5. Sequence analysis and gene expression of putative exo- and endo-glucanases from oil palm (Elaeis guineensis) during fungal infection
    Yeoh KA, Othman A, Meon S, Abdullah F, Ho CL
    J Plant Physiol, 2012 Oct 15;169(15):1565-70.
    PMID: 22854183 DOI: 10.1016/j.jplph.2012.07.006
    Glucanases are enzymes that hydrolyze a variety β-d-glucosidic linkages. Plant β-1,3-glucanases are able to degrade fungal cell walls; and promote the release of cell-wall derived fungal elicitors. In this study, three full-length cDNA sequences encoding oil palm (Elaeis guineensis) glucanases were analyzed. Sequence analyses of the cDNA sequences suggested that EgGlc1-1 is a putative β-d-glucan exohydolase belonging to glycosyl hydrolase (GH) family 3 while EgGlc5-1 and EgGlc5-2 are putative glucan endo-1,3-β-glucosidases belonging to GH family 17. The transcript abundance of these genes in the roots and leaves of oil palm seedlings treated with Ganoderma boninense and Trichoderma harzianum was profiled to investigate the involvement of these glucanases in oil palm during fungal infection. The gene expression of EgGlc1-1 in the root of oil palm seedlings was increased by T. harzianum but suppressed by G. boninense; while the gene expression of both EgGlc5-1 and EgGlc5-2 in the roots of oil palm seedlings was suppressed by G. boninense or/and T. harzianum.
    Matched MeSH terms: Plant Leaves/genetics
  6. RNA-Seq transcriptomic analysis of the Morus alba L. leaves exposed to high-level UVB with or without dark treatment
    Guan Q, Yu J, Zhu W, Yang B, Li Y, Zhang L, et al.
    Gene, 2018 Mar 01;645:60-68.
    PMID: 29274907 DOI: 10.1016/j.gene.2017.12.045
    Ultraviolet-B (UVB) irradiation induces oxidative stress in plant cells due to the generation of excessive reactive oxygen species. Morus alba L. (M. abla) is an important medicinal plant used for the treatment of human diseases. Also, its leaves are widely used as food for silkworms. In our previous research, we found that a high level of UVB irradiation with dark incubation led to the accumulation of secondary metabolites in M. abla leaf. The aim of the present study was to describe and compare M. alba leaf transcriptomics with different treatments (control, UVB, UVB+dark). Leaf transcripts from M. alba were sequenced using an Illumina Hiseq 2000 system, which produced 14.27Gb of data including 153,204,462 paired-end reads among the three libraries. We de novo assembled 133,002 transcripts with an average length of 1270bp and filtered 69,728 non-redundant unigenes. A similarity search was performed against the non-redundant National Center of Biotechnology Information (NCBI) protein database, which returned 41.08% hits. Among the 20,040 unigenes annotated in UniProtKB/SwissProt database, 16,683 unigenes were assigned 102,232 gene ontology terms and 6667 unigenes were identified in 287 known metabolic pathways. Results of differential gene expression analysis together with real-time quantitative PCR tests indicated that UVB irradiation with dark incubation enhanced the flavonoid biosynthesis in M. alba leaf. Our findings provided a valuable proof for a better understanding of the metabolic mechanism under abiotic stresses in M. alba leaf.
    Matched MeSH terms: Plant Leaves/genetics
  7. Proteome analysis of abundant proteins extracted from the leaf of Gynura procumbens (Lour.) Merr
    Hew CS, Gam LH
    Appl Biochem Biotechnol, 2011 Dec;165(7-8):1577-86.
    PMID: 21938418 DOI: 10.1007/s12010-011-9377-x
    Gynura procumbens (Lour.) Merr. is a traditionally used medicinal plant to decrease cholesterol level, reduce high blood pressure, control diabetics, and for treatment of cancer. In our present study, a proteomic approach was applied to study the proteome of the plant that had never analyzed before. We have identified 92 abundantly expressed proteins from the leaves of G. procumbens (Lour.) Merr. Amongst the identified proteins was miraculin, a taste-masking agent with high commercial value. Miraculin made up ∼0.1% of the total protein extracted; the finding of miraculin gave a great commercial value to G. procumbens (Lour.) Merr. as miraculin's natural source is limited while the production of recombinant miraculin faced challenges of not being able to exhibit the taste-masking effect as in the natural miraculin. We believe the discovery of miraculin in G. procumbens (Lour.) Merr., provides commercial feasibility of miraculin in view of the availability of G. procumbens (Lour.) Merr. that grow wildly and easily in tropical climate.
    Matched MeSH terms: Plant Leaves/genetics
  8. Fulltext Oil palm (Elaeis guineensis Jacq.) tissue culture ESTs: identifying genes associated with callogenesis and embryogenesis
    Low ET, Alias H, Boon SH, Shariff EM, Tan CY, Ooi LC, et al.
    BMC Plant Biol, 2008 May 29;8:62.
    PMID: 18507865 DOI: 10.1186/1471-2229-8-62
    BACKGROUND: Oil palm (Elaeis guineensis Jacq.) is one of the most important oil bearing crops in the world. However, genetic improvement of oil palm through conventional breeding is extremely slow and costly, as the breeding cycle can take up to 10 years. This has brought about interest in vegetative propagation of oil palm. Since the introduction of oil palm tissue culture in the 1970s, clonal propagation has proven to be useful, not only in producing uniform planting materials, but also in the development of the genetic engineering programme. Despite considerable progress in improving the tissue culture techniques, the callusing and embryogenesis rates from proliferating callus cultures remain very low. Thus, understanding the gene diversity and expression profiles in oil palm tissue culture is critical in increasing the efficiency of these processes.

    RESULTS: A total of 12 standard cDNA libraries, representing three main developmental stages in oil palm tissue culture, were generated in this study. Random sequencing of clones from these cDNA libraries generated 17,599 expressed sequence tags (ESTs). The ESTs were analysed, annotated and assembled to generate 9,584 putative unigenes distributed in 3,268 consensi and 6,316 singletons. These unigenes were assigned putative functions based on similarity and gene ontology annotations. Cluster analysis, which surveyed the relatedness of each library based on the abundance of ESTs in each consensus, revealed that lipid transfer proteins were highly expressed in embryogenic tissues. A glutathione S-transferase was found to be highly expressed in non-embryogenic callus. Further analysis of the unigenes identified 648 non-redundant simple sequence repeats and 211 putative full-length open reading frames.

    CONCLUSION: This study has provided an overview of genes expressed during oil palm tissue culture. Candidate genes with expression that are modulated during tissue culture were identified. However, in order to confirm whether these genes are suitable as early markers for embryogenesis, the genes need to be tested on earlier stages of tissue culture and a wider range of genotypes. This collection of ESTs is an important resource for genetic and genome analyses of the oil palm, particularly during tissue culture development.

    Matched MeSH terms: Plant Leaves/genetics
  9. Fulltext Morpho-physiological and biochemical attributes of Chili (Capsicum annum L.) genotypes grown under varying salinity levels
    Butt M, Sattar A, Abbas T, Hussain R, Ijaz M, Sher A, et al.
    PLoS One, 2021;16(11):e0257893.
    PMID: 34735478 DOI: 10.1371/journal.pone.0257893
    Climate change is causing soil salinization, resulting in huge crop losses throughout the world. Multiple physiological and biochemical pathways determine the ability of plants to tolerate salt stress. Chili (Capsicum annum L.) is a salt-susceptible crop; therefore, its growth and yield is negatively impacted by salinity. Irreversible damage at cell level and photo inhibition due to high production of reactive oxygen species (ROS) and less CO2 availability caused by water stress is directly linked with salinity. A pot experiment was conducted to determine the impact of five NaCl salinity levels, i.e., 0,1.5, 3.0, 5.0 and 7.0 dS m-1 on growth, biochemical attributes and yield of two chili genotypes ('Plahi' and 'A-120'). Salinity stress significantly reduced fresh and dry weight, relative water contents, water use efficiency, leaf osmotic potential, glycine betaine (GB) contents, photosynthetic rate (A), transpiration rate (E), stomatal conductance (Ci), and chlorophyll contents of tested genotypes. Salinity stress significantly enhanced malondialdehyde (MDA) contents and activities of the enzymatic antioxidants such as superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD). In addition, increasing salinity levels significantly reduced the tissue phosphorus and potassium concentrations, while enhanced the tissue sodium and chloride concentrations. Genotype 'Plahi' had better growth and biochemical attributes compared to 'A-120'. Therefore, 'Plahi' is recommended for saline areas to improve chili production.
    Matched MeSH terms: Plant Leaves/genetics
  10. Fulltext Morpho-anatomical characterization and DNA barcoding of Artemesia vulgaris L
    Wahyuni DK, Indriati DT, Ilham M, Murtadlo AAA, Purnobasuki H, Junairiah, et al.
    Braz J Biol, 2024;84:e278393.
    PMID: 38422290 DOI: 10.1590/1519-6984.278393
    Artemisia vulgaris L. belongs to Asteraceae, is a herbal plant that has various benefits in the medical field, so that its use in the medical field can be explored optimally, the plant must be thoroughly identified. This study aims to identify A. vulgaris both in terms of descriptive morpho-anatomy and DNA barcoding using BLAST and phylogenetic tree reconstruction. The morpho-anatomical character was observed on root, stem, and leaf. DNA barcoding analysis was carried out through amplification and alignment of the rbcL and matK genes. All studies were conducted on three samples from Taman Husada (Medicinal Plant Garden) Graha Famili Surabaya, Indonesia. The anatomical slide was prepared by the paraffin method. Morphological studies revealed that the leaves of A. vulgaris both on the lower-middle part and on the upper part of the stem have differences, especially in the character of the stipules, petioles, and incisions they have. Meanwhile, from the study of anatomy, A. vulgaris has an anomocytic type of stomata and its distribution is mostly on the ventral part of the leaves. Through the BLAST process and phylogenetic tree reconstruction, the plant sequences being studied are closely related to several species of the genus Artemisia as indicated by a percentage identity above 98% and branch proximity between taxa in the reconstructed phylogenetic tree.
    Matched MeSH terms: Plant Leaves/genetics
  11. Microsatellite-based evidences of genetic bottlenecks in the cryptic species "Andrographis paniculata Nees": a potential anticancer agent
    Valdiani A, Javanmard A, Talei D, Tan SG, Nikzad S, Kadir MA, et al.
    Mol Biol Rep, 2013 Feb;40(2):1775-84.
    PMID: 23086278 DOI: 10.1007/s11033-012-2231-6
    Andrographis paniculata (AP) is a medicinal plant species introduced into Malaysia. To address the genetic structure and evolutionary connectedness of the Malaysian AP with the Indian AP, a DNA sequence analysis was conducted based on 24 microsatellite markers. Out of the 24 primer sets, seven novel microsatellite primers were designed and amplified intra-specifically according to the available Indian AP sequences at the National Centre for Biotechnology Information (NCBI), where 17 of them were amplified using the cross-species strategy by employing the primers belonging to Acanthus ilicifolius Linn (Acanthaceae) and Lumnitzera racemosa Wild (Combretaceae). The primers were then applied on the Malaysian AP accessions. Sixteen of the new microsatellite loci were amplified successfully. Analysis of these microsatellite sequences, revealed some significant differences between the Indian and Malaysian AP accessions in terms of the size and type of the repeat motifs. These findings depicted the cryptic feature of this species. Despite identifying several heterozygous alleles no polymorphism was observed in the detected loci of the selected accessions. This situation was in concordance with the presence of "fixed heterozygosity" phenomenon in the mentioned loci. Accordingly, this was fully consistent with the occurrence of the genetic bottleneck and founder effect within Malaysian AP population. Apart from the amplification of new microsatellites in this species, our observations could be in agreement with the risk of genetic depletion and consequently extinction of this precious herb in Malaysia. This issue should be taken into consideration in the future studies.
    Matched MeSH terms: Plant Leaves/genetics*
  12. Mapping of the quantitative trait locus (QTL) conferring partial resistance to rice leaf blast disease
    Ashkani S, Rafii MY, Rahim HA, Latif MA
    Biotechnol Lett, 2013 May;35(5):799-810.
    PMID: 23315158 DOI: 10.1007/s10529-012-1130-1
    Malaysian rice, Pongsu Seribu 2, has wide-spectrum resistance against blast disease. Chromosomal locations conferring quantitative resistance were detected by linkage mapping with SSRs and quantitative trait locus (QTL) analysis. For the mapping population, 188 F3 families were derived from a cross between the susceptible cultivar, Mahsuri, and a resistant variety, Pongsu Seribu 2. Partial resistance to leaf blast in the mapping population was assessed. A linkage map covering ten chromosomes and consisting of 63 SSR markers was constructed. 13 QTLs, including 6 putative and 7 putative QTLs, were detected on chromosomes 1, 2, 3, 5, 6, 10, 11 and 12. The resulting phenotypic variation due to a single QTL ranged from 2 to 13 %. These QTLs accounted for approx. 80 % of the total phenotypic variation within the F3 population. Therefore, partial resistance to blast in Pongsu Seribu 2 is due to combined effects of multiple loci with major and minor effects.
    Matched MeSH terms: Plant Leaves/genetics
  13. Light-harvesting complexes in photosystem II regulate glutathione-induced sensitivity of Arabidopsis guard cells to abscisic acid
    Jahan MS, Nozulaidi M, Khairi M, Mat N
    J Plant Physiol, 2016 May 20;195:1-8.
    PMID: 26970687 DOI: 10.1016/j.jplph.2016.03.002
    Light-harvesting complexes (LHCs) in photosystem II (PSII) regulate glutathione (GSH) functions in plants. To investigate whether LHCs control GSH biosynthesis that modifies guard cell abscisic acid (ABA) sensitivity, we evaluated GSH content, stomatal aperture, reactive oxygen species (ROS), weight loss and plant growth using a ch1-1 mutant that was defective of LHCs and compared this with wild-type (WT) Arabidopsis thaliana plants. Glutathione monoethyl ester (GSHmee) increased but 1-chloro-2,4 dinitrobenzene (CDNB) decreased the GSH content in the guard cells. The guard cells of the ch1-1 mutants accumulated significantly less GSH than the WT plants. The guard cells of the ch1-1 mutants also showed higher sensitivity to ABA than the WT plants. The CDNB treatment increased but the GSHmee treatment decreased the ABA sensitivity of the guard cells without affecting ABA-induced ROS production. Dark and light treatments altered the GSH content and stomatal aperture of the guard cells of ch1-1 and WT plants, irrespective of CDNB and GSHmee. The ch1-1 mutant contained fewer guard cells and displayed poor growth, late flowering and stumpy weight loss compared with the WT plants. This study suggests that defective LHCs reduced the GSH content in the guard cells and increased sensitivity to ABA, resulting in stomatal closure.
    Matched MeSH terms: Plant Leaves/genetics
  14. Leaf transcriptomic signatures for somatic embryogenesis potential of Elaeis guineensis
    Ooi SE, Feshah I, Nuraziyan A, Sarpan N, Ata N, Lim CC, et al.
    Plant Cell Rep, 2021 Jul;40(7):1141-1154.
    PMID: 33929599 DOI: 10.1007/s00299-021-02698-1
    KEY MESSAGE: Potentially embryogenic oil palms can be identified through leaf transcriptomic signatures. Differential expression of genes involved in flowering time, and stress and light responses may associate with somatic embryogenesis potential. Clonal propagation is an attractive approach for the mass propagation of high yielding oil palms. A major issue hampering the effectiveness of oil palm tissue culture is the low somatic embryogenesis rate. Previous studies have identified numerous genes involved in oil palm somatic embryogenesis, but their association with embryogenic potential has not been determined. In this study, differential expression analysis of leaf transcriptomes from embryogenic and non-embryogenic mother palms revealed that transcriptome profiles from non- and poor embryogenic mother palms were more similar than highly embryogenic palms. A total of 171 genes exhibiting differential expression in non- and low embryogenesis groups could also discriminate high from poor embryogenesis groups of another tissue culture agency. Genes related to flowering time or transition such as FTIP, FRIGIDA-LIKE, and NF-YA were up-regulated in embryogenic ortets, suggesting that reproduction timing of the plant may associate with somatic embryogenesis potential. Several light response or photosynthesis-related genes were down-regulated in embryogenic ortets, suggesting a link between photosynthesis activity and embryogenic potential. As expression profiles of the differentially expressed genes are very similar between non- and low embryogenic groups, machine learning approaches with several candidate genes may generate a more sensitive model to better discriminate non-embryogenic from embryogenic ortets.
    Matched MeSH terms: Plant Leaves/genetics*
  15. Isolation and characterization of an oil palm constitutive promoter derived from a translationally control tumor protein (TCTP) gene
    Masura SS, Parveez GK, Ti LL
    Plant Physiol Biochem, 2011 Jul;49(7):701-8.
    PMID: 21549610 DOI: 10.1016/j.plaphy.2011.04.003
    We have characterized an oil palm (Elaeis guineensis Jacq.) constitutive promoter that is derived from a translationally control tumor protein (TCTP) gene. The TCTP promoter was fused transcriptionally with the gusA reporter gene and transferred to monocot and dicot systems in order to study its regulatory role in a transient expression study. It was found that the 5' region of TCTP was capable of driving the gusA expression in all the oil palm tissues tested, including immature embryo, embryogenic callus, embryoid, young leaflet from mature palm, green leaf, mesocarp and stem. It could also be used in dicot systems as it was also capable of driving gusA expression in tobacco leaves. The results indicate that the TCTP promoter could be used for the production of recombinant proteins that require constitutive expression in the plant system.
    Matched MeSH terms: Plant Leaves/genetics
  16. Fulltext Increasing leaf vein density by mutagenesis: laying the foundations for C4 rice
    Feldman AB, Murchie EH, Leung H, Baraoidan M, Coe R, Yu SM, et al.
    PLoS One, 2014;9(4):e94947.
    PMID: 24760084 DOI: 10.1371/journal.pone.0094947
    A high leaf vein density is both an essential feature of C4 photosynthesis and a foundation trait to C4 evolution, ensuring the optimal proportion and proximity of mesophyll and bundle sheath cells for permitting the rapid exchange of photosynthates. Two rice mutant populations, a deletion mutant library with a cv. IR64 background (12,470 lines) and a T-DNA insertion mutant library with a cv. Tainung 67 background (10,830 lines), were screened for increases in vein density. A high throughput method with handheld microscopes was developed and its accuracy was supported by more rigorous microscopy analysis. Eight lines with significantly increased leaf vein densities were identified to be used as genetic stock for the global C4 Rice Consortium. The candidate population was shown to include both shared and independent mutations and so more than one gene controlled the high vein density phenotype. The high vein density trait was found to be linked to a narrow leaf width trait but the linkage was incomplete. The more genetically robust narrow leaf width trait was proposed to be used as a reliable phenotypic marker for finding high vein density variants in rice in future screens.
    Matched MeSH terms: Plant Leaves/genetics
  17. Fulltext Identification of functionally important microRNAs from rice inflorescence at heading stage of a qDTY4.1-QTL bearing Near Isogenic Line under drought conditions
    Cheah BH, Jadhao S, Vasudevan M, Wickneswari R, Nadarajah K
    PLoS One, 2017;12(10):e0186382.
    PMID: 29045473 DOI: 10.1371/journal.pone.0186382
    A cross between IR64 (high-yielding but drought-susceptible) and Aday Sel (drought-tolerant) rice cultivars yielded a stable line with enhanced grain yield under drought screening field trials at International Rice Research Institute. The major effect qDTY4.1 drought tolerance and yield QTL was detected in the IR77298-14-1-2-10 Backcrossed Inbred Line (BIL) and its IR87705-7-15-B Near Isogenic Line (NIL) with 93.9% genetic similarity to IR64. Although rice yield is extremely susceptible to water stress at reproductive stage, currently, there is only one report on the detection of drought-responsive microRNAs in inflorescence tissue of a Japonica rice line. In this study, more drought-responsive microRNAs were identified in the inflorescence tissues of IR64, IR77298-14-1-2-10 and IR87705-7-15-B via next-generation sequencing. Among the 32 families of inflorescence-specific non-conserved microRNAs that were identified, 22 families were up-regulated in IR87705-7-15-B. Overall 9 conserved and 34 non-conserved microRNA families were found as drought-responsive in rice inflorescence with 5 conserved and 30 non-conserved families induced in the IR87705-7-15-B. The observation of more drought-responsive non-conserved microRNAs may imply their prominence over conserved microRNAs in drought response mechanisms of rice inflorescence. Gene Ontology annotation analysis on the target genes of drought-responsive microRNAs identified in IR87705-7-15-B revealed over-representation of biological processes including development, signalling and response to stimulus. Particularly, four inflorescence-specific microRNAs viz. osa-miR5485, osa-miR5487, osa-miR5492 and osa-miR5517, and two non-inflorescence specific microRNAs viz. osa-miR169d and osa-miR169f.2 target genes that are involved in flower or embryonic development. Among them, osa-miR169d, osa-miR5492 and osa-miR5517 are related to flowering time control. It is also worth mentioning that osa-miR2118 and osa-miR2275, which are implicated in the biosynthesis of rice inflorescence-specific small interfering RNAs, were induced in IR87705-7-15-B but repressed in IR77298-14-1-2-10. Further, gene search within qDTY4.1 QTL region had identified multiple copies of NBS-LRR resistance genes (potential target of osa-miR2118), subtilisins and genes implicated in stomatal movement, ABA metabolism and cuticular wax biosynthesis.
    Matched MeSH terms: Plant Leaves/genetics
  18. Fulltext Identification of four functionally important microRNA families with contrasting differential expression profiles between drought-tolerant and susceptible rice leaf at vegetative stage
    Cheah BH, Nadarajah K, Divate MD, Wickneswari R
    BMC Genomics, 2015;16:692.
    PMID: 26369665 DOI: 10.1186/s12864-015-1851-3
    Developing drought-tolerant rice varieties with higher yield under water stressed conditions provides a viable solution to serious yield-reduction impact of drought. Understanding the molecular regulation of this polygenic trait is crucial for the eventual success of rice molecular breeding programmes. microRNAs have received tremendous attention recently due to its importance in negative regulation. In plants, apart from regulating developmental and physiological processes, microRNAs have also been associated with different biotic and abiotic stresses. Hence here we chose to analyze the differential expression profiles of microRNAs in three drought treated rice varieties: Vandana (drought-tolerant), Aday Sel (drought-tolerant) and IR64 (drought-susceptible) in greenhouse conditions via high-throughput sequencing.
    Matched MeSH terms: Plant Leaves/genetics
  19. Fulltext Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs
    Graham NS, Hammond JP, Lysenko A, Mayes S, O Lochlainn S, Blasco B, et al.
    Plant Cell, 2014 Jul;26(7):2818-30.
    PMID: 25082855 DOI: 10.1105/tpc.114.128603
    Although Ca transport in plants is highly complex, the overexpression of vacuolar Ca(2+) transporters in crops is a promising new technology to improve dietary Ca supplies through biofortification. Here, we sought to identify novel targets for increasing plant Ca accumulation using genetical and comparative genomics. Expression quantitative trait locus (eQTL) mapping to 1895 cis- and 8015 trans-loci were identified in shoots of an inbred mapping population of Brassica rapa (IMB211 × R500); 23 cis- and 948 trans-eQTLs responded specifically to altered Ca supply. eQTLs were screened for functional significance using a large database of shoot Ca concentration phenotypes of Arabidopsis thaliana. From 31 Arabidopsis gene identifiers tagged to robust shoot Ca concentration phenotypes, 21 mapped to 27 B. rapa eQTLs, including orthologs of the Ca(2+) transporters At-CAX1 and At-ACA8. Two of three independent missense mutants of BraA.cax1a, isolated previously by targeting induced local lesions in genomes, have allele-specific shoot Ca concentration phenotypes compared with their segregating wild types. BraA.CAX1a is a promising target for altering the Ca composition of Brassica, consistent with prior knowledge from Arabidopsis. We conclude that multiple-environment eQTL analysis of complex crop genomes combined with comparative genomics is a powerful technique for novel gene identification/prioritization.
    Matched MeSH terms: Plant Leaves/genetics
  20. Functional characterization of the gene promoter for an Elaeis guineensis phosphate starvation-inducible, high affinity phosphate transporter in both homologous and heterologous model systems
    Ahmadi F, Akmar Abdullah SN, Kadkhodaei S, Ijab SM, Hamzah L, Aziz MA, et al.
    Plant Physiol Biochem, 2018 Jun;127:320-335.
    PMID: 29653435 DOI: 10.1016/j.plaphy.2018.04.004
    Oil palm is grown in tropical soils with low bioavailability of Pi. A cDNA clone specifically expressed under phosphate-starvation condition in oil palm roots was identified as a high-affinity phosphate transporter (EgPHT1). The deduced amino acid sequence has 6 transmembrane domains each at the N- and C-termini separated by a hydrophilic linker. Comparison of promoter motifs within 1500 bp upstream of ATG of 10 promoters from high- and low-affinity phosphate transporter from both dicots and monocots including EgPHT1 was performed. The EgPHT1 promoter was fused to β-glucuronidase (GUS) reporter gene and its activity was analysed by histochemical and fluorometric GUS assays in transiently transformed oil palm tissues and T3 homozygous transgenic Arabidopsis plants. In response to Pi-starvation, no GUS activity was detected in oil palm leaves, but a strong inducible activity was observed in the roots (1.4 times higher than the CaMV35S promoter). GUS was specifically expressed in transgenic Arabidopsis roots under Pi deficiency and starvation of the other macronutrients (N and K) did not induce GUS activity. Eight motifs including ABRERATCAL (abscisic-acid responsive), RHERPATEXPA7 (root hair-specific), SURECOREATSULTR11 (sulfur-deficiency response), LTRECOREATCOR15 (temperature-stress response), MYB2CONSENSUSAT and ACGTATERD1 (water-stress response) as well as two novel motifs, 3 (TAAAAAAA) and 26 (TTTTATGT) identified through pattern discovery, occur at significantly higher frequency (p 
    Matched MeSH terms: Plant Leaves/genetics
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