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Lee W.S.,University of Malaya | Gudimella R.,University of Malaya | Wong G.R.,University of Malaya | Tammi M.T.,University of Malaya | And 3 more authors.
PLoS ONE | Year: 2015

Physiological responses to stress are controlled by expression of a large number of genes, many of which are regulated by microRNAs. Since most banana cultivars are salt-sensitive, improved understanding of genetic regulation of salt induced stress responses in banana can support future crop management and improvement in the face of increasing soil salinity related to irrigation and climate change. In this study we focused on determining miRNA and their targets that respond to NaCl exposure and used transcriptome sequencing of RNA and small RNA from control and NaCl-treated banana roots to assemble a cultivar-specific reference transcriptome and identify orthologous and Musa-specific miRNA responding to salinity. We observed that, banana roots responded to salinity stress with changes in expression for a large number of genes (9.5% of 31,390 expressed unigenes) and reduction in levels of many miRNA, including several novel miRNA and banana-specific miRNA-target pairs. Banana roots expressed a unique set of orthologous and Musa-specific miRNAs of which 59 respond to salt stress in a dose-dependent manner. Gene expression patterns of miRNA compared with those of their predicted mRNA targets indicated that a majority of the differentially expressed miRNAs were down-regulated in response to increased salinity, allowing increased expression of targets involved in diverse biological processes including stress signaling, stress defence, transport, cellular homeostasis, metabolism and other stress-related functions. This study may contribute to the understanding of gene regulation and abiotic stress response of roots and the high-throughput sequencing data sets generated may serve as important resources related to salt tolerance traits for functional genomic studies and genetic improvement in banana. © 2015 Lee et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Neoh B.K.,Sime Darby Technology Center Sdn Bhd | Teh H.F.,Sime Darby Technology Center Sdn Bhd | Ng T.L.M.,Sime Darby Technology Center Sdn Bhd | Tiong S.H.,Sime Darby Technology Center Sdn Bhd | And 2 more authors.
Journal of Plant Biochemistry and Biotechnology | Year: 2013

Adenosine phosphates (ATP, ADP, AMP) and nicotinamides (NAD, NADH, NADP and NADPH) are nucleotides that are involved in various plant biosynthetic pathways such as photosynthesis, nitrogen uptake, purine metabolism and lipid biosynthesis. In oil palm fruit formation, kernel and mesocarp are separated by a shell and differ mainly by lipid composition. Oil palm mesocarp and kernel tissues were extracted using a modified perchloric acid extraction and separated via HPLC to quantify the accumulation of these seven nucleotides in relation to lipid composition. Principal component analysis on palm mesocarp and kernel samples displayed clustering and indicated that palm mesocarp contained higher ATP and NAD+ than palm kernel. The higher levels of ATP and NADH may be attributable to the higher content of unsaturated and long chain fatty acids in found palm mesocarp. © 2013, Society for Plant Biochemistry and Biotechnology.

Ooi S.-E.,Malaysian Palm Oil Board | Ramli Z.,Malaysian Palm Oil Board | Syed Alwee S.S.R.,Felda Global Ventures R&D Sdn. Bhd. | Kulaveerasingam H.,Sime Darby Technology Center Sdn Bhd | Ong-Abdullah M.,Malaysian Palm Oil Board
Plant Gene | Year: 2016

The embryogenesis rate in oil palm tissue culture still averages at a low 6%. Hence, a better understanding of the regulatory mechanisms during somatic embryogenesis and identification of molecular markers may help to improve the oil palm cloning process. EgHOX1, a previously isolated cold plaque clone, was further characterized and identified to be a putative HD-Zip II gene. High levels of EgHOX1 transcripts were detected in early tissue culture stages involving embryogenesis induction. Transcripts accumulated preferentially in meristematic centers of embryogenic callus and then in the provascular regions of developing somatic embryos. EgHOX1 was modestly induced by exogenous auxin and highly induced by dehydration and osmotic stresses. However, its expression was down-regulated by light. Based on its expression patterns, this novel oil palm HD-Zip II gene may be involved during the acquisition of embryogenic competency in early somatic embryogenesis and in vascular development later on, similar to the roles of some HD-Zip genes in other plants. © 2016 Elsevier B.V.

Tan B.A.,Sime Darby Technology Center Sdn Bhd | Daim L.D.J.,Sime Darby Technology Center Sdn Bhd | Ithnin N.,Sime Darby Technology Center Sdn Bhd | Ooi T.E.K.,Sime Darby Technology Center Sdn Bhd | And 5 more authors.
Plant Gene | Year: 2016

The phenylpropanoid and flavonoid pathways are well known for their function towards plant development and defense. Oil palm seedlings from a single cross challenged with Ganoderma boninense displayed different severity of infection after six and fourteen months post inoculation (mpi). Transcripts from phenylpropanoid and flavonoid pathways, and transcription factors related to secondary cell wall formation were compared based on external and internal symptom classification. This long term infection study revealed that the oil palm roots responded to G. boninense and regulated both phenylpropanoid and flavonoid pathways during infection. The expression of PAL2 and PAL3 were significantly higher at 6 mpi in symptomatic compared to asymptomatic and control seedlings. However, the expression of all PAL genes were down-regulated at 14 mpi for both symptomatic and asymptomatic seedlings. In the monolignol and lignin pathways, down-regulation of COMT in symptomatic and CCR in asymptomatic seedlings was observed at 14 mpi but not at 6 mpi suggesting a possible change in lignin composition likely related to observed resistance. The expression of transcription factors for secondary cell wall and monolignol (MYB58, MYB63 and SND1) biosynthesis showed down-regulation in symptomatic seedlings, also suggesting a link between cell wall biosynthesis and disease resistance. Genes that regulate the flavonoid pathway were mostly down-regulated in both symptomatic seedlings at both 6 mpi and 14 mpi indicating a possibility of pathway suppression after challenge with G. boninense. Prolonged G. boninense exposure suggested that oil palm seedlings responded differently in terms of phenylpropanoid and flavonoid pathway expression in conferring defense and disease resistance. © 2016 Elsevier B.V.

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