PLANT OMICS


Comprehensive analysis of the NAC gene family in Elaeis guineensis

Yong Xiao*, Haikuo Fan*, Jianwei Ma*, Xintao Lei, Yong Wang, Hongxin Cao, Lixia Zhou, Yong Zhang, Wei Xia

Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, P.R. China
Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, P.R. China
College of Horticulture, Sichuan Agricultural University, Chengdu, P.R. China


Abstract
The NAC gene family encode transcriptional regulator that contain a conserved NAM domain near the N-terminus and participate in the regulation of plant development and response to different abiotic stresses. In this study, 129 EgNAC genes were identified from the genome sequence of Elaeis guineensis and 97 EgNAC located on the chromsomes with an average of 4.56 EgNAC genes per chromosome. About 60% of EgNACs contained three exons and the gene sizes varied from 541 bp to 37,294 bp. Genomic duplication analysis showed that 10 EgNAC genes were involved in segmental duplication events and two genes were from tandem duplication. The gene expression profiles of EgNACs based on transcriptome database for different oil palm tissues showed that 30 EgNACs with low or no expression and 24 EgNACs were specifically expressed in one tissue. The trancriptome comparison between the control and cold stress samples demonstrated that thirty-seven EgNACs were down-regulated and 82 EgNACs were up-regulated under cold stress. Further RT-qPCR showed that the expression for 24 out of 32 validated EgNACs were induced under both cold, drought and salt stresses. Our comprehensive analysis of EgNAC genes has provided clues for candidate genes involved in abiotic stress tolerance.

Pages 120-127 | Full Text PDF| Supplementary Data | doi: 10.21475/poj.11.03.18.p1037
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Biosynthesis of novel phytochemicals in tobacco plant infected with tobacco mosaic tobamovirus (TMV)

Reham M. Mostafa, Heba S. Essawy

Botany Department Faculty of Sciences Benha University, Egypt

Abstract
The main purpose of this work was to study the effect of TMV infection on physiology of active gradient photochemicals and protein expression in infected tobacco plants. Impact of Tobacco mosaic tobamovirus (TMV) on active gradient photochemicals quantitative and qualitative was evaluated in Nicotiana tobaccum cv. white burly. First, the TMV samples were isolated from single local lesions of infected leaves of N. glutinosa. Then, the N. tobaccum cv. white burly plants were inoculated with TMV. The infected plants showed severe systemic mosaic symptoms and reduction of leave size. We used Datura metel as a diagnostic tool-plant (indicator) for mosaic virus because of its vast exhibitory ability to show the symptoms incited by viruses. It was confirmed that these symptoms were due to the effect of TMV virus, comparing with Datura plant (as control). Analysis of TMV infected leaves by GC-mass detected biosynthesis of novel photochemicals (2-cyclopenten-1-one, Furfural, Indene, Pyrrole, Benzonitrile, Guaiacol and Oxime, methoxy-phenyl) that could not be detected in healthy plants. Furthermore, a 56.17% decreased in nicotine content was observed in infected plants compared with healthy ones. Also, increase of soluble protein contents was observed in infected leaves in response to TMV infection, compared with healthy ones. Alterations in protein patterns were observed in N. tabaccum leaves in response to TMV infection using SDS PAGE. Several secondary bioactive compounds were also found to hold important functions in infected plants. For example, flavonoids could protect against free radicals generated during photosynthesis. Terpenoids may attract pollinators or seed dispersers, or inhibit competing plants. Alkaloids usually ward-off herbivore animals or insect attacks (phytoalexins).

Pages 128-134 | Full Text PDF| doi: 10.21475/poj.11.03.18.p1186
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Genetic diversity of endangered terrestrial orchids Spathoglottis plicata in Peninsular Malaysia based on AFLP markers

Florence C Ginibun*, Paul Arens, Ben Vosman, Subha Bhassu, Norzulaani Khalid and Rofina Yasmin Othman*

Centre for Research in Biotechnology for Agriculture (CEBAR), Department of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
Wageningen UR Plant Breeding, Wageningen University and Research Center, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
Department of Agriculture, Level 7-17, Wisma Tani, Lot 4G2, No.30, Persiaran Perdana. Presint 4, 62624 Putrajaya, Malaysia


Abstract
Spathoglottis plicata is an endangered terrestrial orchid species that have experienced severe threats to its habitat as wild forest sites come under pressure from industrialisation and natural disasters. This orchid species chosen to evaluate their levels of genetic diversity and population genetic structure, which 25-30 accession collected in the different location with different geographical, altitude and habitat. Genomic DNA was extracted from six natural populations (n=172) in Peninsular Malaysia using eleven AFLP markers of EcoRI+3 bases/MseI+3 base primer combinations. Based on 279 polymorphic bands, a significant degree of genetic population differentiation was found, with a 78.5% variation within populations as measured by AMOVA, indicating a potential restricted gene flow. Two distinct clades generated from a UPGMA dendrogram were further investigated through a Bayesian analysis using STRUCTURE software, producing an estimated population structure at optimal value K=4. These results point to the presence of four genetic structures in the Spathoglottis plicata population. The Pahang and Terengganu population revealed a higher than average genetic variation (60.25%), indicating that there may be a robust structural division between the population samples and a possible hybridisation between the Northern (Kedah), Southern (Negeri Sembilan and Johor) and Central (Selangor) region populations. In sum, these results suggest that geographical distance is the primary factor contributing to differences among populations and the need for conservation measures to protect the Spathoglottis plicata species.

Pages 135-144 | Full Text PDF| doi: 10.21475/poj.11.03.18.p1227
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Transcriptome analysis identified genes involved in anthocyanin biosynthesis in Rainbow bamboo (Indosasa hispida MeClure cv. ‘Rainbow’)

Yi Wang, YuMing Yang, Juan Wang*, Yuan XiaoLong

Key Laboratory of Yunnan Provincial for Forest Plant Cultivation and Utilization, and Key Laboratory of the State Forestry Administration for Conservation of Yunnan Rare, Endangered & Endemic Plant, Yunnan Academy of Forestry, Kunming650204, China

Abstract
Rainbow bamboo (Indosasa hispida) is an ornamental plant, which contains unique red to purple anthocyanin in its culm. However, the biosynthesis and function of anthocyanin in bamboo remains unclear. In this study, RNA-seq was used to investigate the transcriptome of the species and compare the gene expression profiles of red and white culms. The expression levels of genes involved in the anthocyanin biosynthesis pathway were detected using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). In total, 5.92 billion reads were obtained from the culm of Rainbow bamboo, which were assembled into 60,716 unigenes. qRT-PCR showed that the expression levels of anthocyanin biosynthesis-related genes in the red and white culms were higher than that in green leaves and that their levels in the red culm without sheath were higher than that in the white culm with sheath. Transcriptome analysis and qRT-PCR showed that the differences in the expression of genes encoding chalcone isomerase (CHI), dihydroflavonol reductase (DFR), flavonoid 3'-hydroxylase (F3'H), and anthocyanidin 3-O-glycosyltransferase (A3GT) between the culm and leaf were significant. This implies that CHI, DFR, F3'H, and A3GT play important roles in anthocyanin synthesis and accumulation in the culm of Rainbow bamboo.

Pages 145-152 | Full Text PDF| doi: 10.21475/poj.11.03.18.p1442
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Effects of silver nitrate (AgNO3) on growth and anatomical structure of vegetative organs of liquorice (Glycyrrhiza glabra L.) under in vitro condition

Farnaz Tahoori, Ahamd Majd*, Taher Nejadsattari, Hamideh Ofoghi, Alireza Iranbakhsh

Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
Department of Biology, North Tehran Branch, Islamic Azad University, Tehran, Iran
Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran


Abstract
Liquorice (Glycyrrhiza glabra L.) has been used worldwide as a medicine for a long time. In this research, the effect of silver nitrate (AgNO3) as a growth regulator and anti-ethylene in in vitro culture was investigated on growth and anatomical structure of vegetative organs (root, hypocotyl, shoot, leaf) as well as the number of stomata and trichomes in the leaves of liquorice under vitro culture condition. The seeds were cultured in MS culture media containing different concentrations of AgNO3 (0, 2, 4, 8, and 10 mg L-1). Investigations on 20-day seedlings after three replications showed a significant increase in length and growth of roots, hypocotyls and shoots, and decreased number of stomata and trichomes in the samples treated with AgNO3 (P≤0.05). The effects of AgNO3 on anatomical structures of the organs included the increased cell division in root and shoot tips, reduced vascular tissues and sclerenchyma-fiber (with lignified cell walls), increased thickness of Casparian strip and cell walls of endodermis, reduced thickness of epidermis and increased intercellular spaces in mesophyll. The leaf area was measured in the 4-month plantlets, showing a significant increase in the samples treated with AgNO3. Furthermore, there was significant difference in increased leaf area applying 10 mg L-1 treatment and other concentrations as well as between the concentrations of 2 and 8 mg L-1. It seems that these results are due to the inhibitory effects of AgNO3 on the production and function of ethylene and the plant strategy to increase the tolerance against silver metal.

Pages 153-160 | Full Text PDF| doi: 10.21475/poj.11.03.18.p1548


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