PLANT OMICS JOURNAL OF PLANT MOLECULAR BIOLOGY AND OMICS


Comparative genomics and expression profile of lipid biosynthesis pathway genes in Camellia sinensis


Madhurjya Gogoi *, Afruza Zaman, Sangeeta Borchetia and Tanoy Bandyopadhyay

Department of Biotechnology, Tocklai Tea Research Institute, Tea Research Association, Jorhat- 785008, Assam, India


Abstract

The lipid biosynthesis pathway is directly associated with lipid content in plants. The genes involved in lipid biosynthesis of tea plant (Camellia sinensis) were identified through in-silico mining of available transcriptomic data in public domain. Seventy five homologous genes in tea were identified through comparative genomics and 56 sequences of them showed more than 50% sequence similarity with the Arabidopsis reference sequences. The expression pattern of five key genes biotin carboxylase (BC), Acyl CoA: diacylglycerol acyltransferase (DGAT), phosphatidylinositol synthase (PIS), monogalactosyldiacylglycerol synthase (MGDGS) and glycerol 3 phosphate dehydrogenase (G3PDH) were analysed through qRT-PCR in roots, leaves, flowers, and seeds of three Tocklai released tea varieties (TV1, TV17 and TV20). Relative expression analysis showed that all the five genes were highly up-regulated in the seeds compared to the other parts of the studied tea varieties. Except biotin carboxylase, other four genes showed highest expression in TV1 seeds compared to TV17 and TV20. The overall increased expression of four key lipid biosynthesis genes give an indication that TV1 seeds may contain higher lipid content than the others in this study. DGAT, PIS and G3PDH also showed upregulation in the leaves and roots of some of the studied varieties which is an indication of possible involvement of lipid biosynthesis genes in various growth and developmental processes.

 

Pages 295-303 | Read More| Supplementary Data| DOI: 10.21475/poj.09.05.16.pne50

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Proteomics analysis of the photo-oxidation mutant 812HS rice (Oryza sativa L.) exposed to high light intensity


Chunfang Lv, Jing Ma, Ze Yuan, Yuwen Wang, Guoxiang Chen, Zhiping Gao*Chuangen Lv*


School of Life Sciences, Nanjing Normal University, Nanjing 210023, China

Institute of Food and Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China


Abstract

The 812HS rice line, a mutant of two-line sterile rice, exhibits leaf photo-oxidation during the tillering-jointing stage since its chloroplasts are susceptible to damage induced by strong sunlight. To determine the proteomic response to light intensity, the 812HS rice line was exposed to natural light and shade (about one fourth natural light), and two-dimensional electrophoresis in combination with matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry was used to compare the proteomic expressions in the rice leaves. Although over 1000 reproducible proteins were detected, only 9.61 % of them displayed differential expression with 1.5-fold abundance. A search of the National Center for Biotechnology Information database revealed 53 proteins, 34 down-regulated and 19 up-regulated under highlight. Among these identified proteins, six ones were related to disease and defense, implying the defense and protection mechanism was built under strong light stress. The increase in S-adenosylmethionine synthetase involved in the biosynthesis of the phytohormone ethylene might contribute to the phenotypic modulation from green to etiolation in photo-oxidation-sensitive leaves. These results suggest the existence of a complex regulatory mechanism of the proteomes in photo-oxidation-sensitive 812HS rice under light stress.

 

Pages 304-310  | Read More| DOI: 10.21475/poj.09.05.16.pne80

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Genetic diversity, variety identification and gene detection in some Egyptian grape varieties by SSR and SCoT markers

 

Shafik D. Ibrahim*, S. S. Adawy, M. A. M Atia, A. M. Alsamman, M. M. Mokhtar

 

Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, Egypt

 

Abstract

Leaves of seven Egyptian grape varieties represent different range of agronomic and morphological traits were genotyped using Start-codon Targeted (SCoT) and Simple Sequence Repeats (SSR). The 24 SCoT primers generated 362 total fragments with 77.10% of polymorphism and 0.04 of average PIC. Dice coefficient that shows the genetic similarity and relationship was also used between the seven varieties. On one hand, SCoT analysis successfully characterized 73 unique positive and negative markers differentiating between the rootstock varieties especially those with green and red fruits. On the other hand, the seven SSR primers produced 73 fragments with 86.30% total polymorphism and 0.14 of average PIC. It also provided 19 unique positive and negative markers differentiating between the rootstock varieties. SO4 variety was identified by the highest number of positive unique markers (5). Both Scot and SSR analysis had covered 0.02% (0.10 Mbp) of V. vinifera genome. The SCoT covered 0.96 Mbp and SSR covered 846 bp. Together, the covered region encompassed about 22 genes of grape genome. Further, eight SCoT polymorphic bands were purified, cloned and sequenced. Of which, four SCoT sequences (SCoT3600, SCoT4450, SCoT6200 and SCoT12550) showed high similarity to some potential genes.

 

Pages 311-318 | Read More| Supplementary Data| DOI: 10.21475/poj.09.05.16.pne125

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In silico analysis of the LRR receptor-like serine threonine kinases subfamily in Morus notabilis

 

Antonios Zambounis*, Fotis E. Psomopoulos, Ioannis Ganopoulos, Evangelia Avramidou, Filippos A. Aravanopoulos, Athanasios Tsaftaris, Panagiotis Madesis

 

Laboratory of Genetics and Plant Breeding, Faculty of Agriculture, Forestry & Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, Thessaloniki GR-54124, Greece

Department of Electrical and Computer Engineering, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece

Laboratory of Forest Genetics and Tree Breeding, Faculty of Agriculture, Forestry & Natural Environment, Aristotle University of Thessaloniki, P.O. Box 238, Thessaloniki GR54006, Greece

Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki, 570 01, Greece

 

Abstract

Mulberries are important trees crops for orchards and agroforestry systems, which are plagued by many phytopathogenic fungal species. Leucine rich repeats (LRRs) receptor-like serine threonine kinases (LRR-RSTK) subfamily plays an important role in plant defense-related reactions against fungal attacks. In the present study, we mined this subfamily on Morus notabilis, a mulberry species whose relevant annotated genome assembly has recently become publicly available. Our aim was to decipher in silico the expansion and phylogeny of these genes, their homology relationships against their orthologous in woody angiosperm plant species, and the existence of positive selective pressures acting upon their LRRs. This subfamily was found to be quite abundant and diverged, comprising by 142 annotated gene members and containing a range of conserved functional domains in their C-termini, whilst their LRRs number ranged from one to 17 repeats. A phylogenetic investigation revealed 12 distinct clades based on their diverse structural profiles, mainly as a result of the fused functional domains at their C-termini. The interspecific expansion of these M. notabilis LRR-RSTKs has been investigated by a homology analysis across 12 other woody angiosperm species, showing that the highest proportion of homologous best BLAST hits observed primarily in Prunus persica, Malus domestica and Theobroma cacao. Using a series of maximum likelihood analyses, extensive episodes of positive selective pressures acting across the LRRs were observed. This overall evidence supports a potential crucial role of this diverged LRR-RSTK subfamily as a surveillance mechanism of M. notabilis against fungal attacks by providing rapidly evolving ligand-binding specificities.

 

Pages 319-326 | Read More| Supplementary Data| DOI: 10.21475/poj.09.05.16.pne126

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Expression analysis of five critical transcription factors (TFs) OsbHLH148, OsbZIP72, OsMYB2, OsNAC6 and TRAB1 in response to drought stress in contrasting Iranian rice genotypes.

 

Ahmad Mollazadeh Taghipour*, Alireza Tarang, Nasser Zare, Moslem Pourebrahim, Ramin Seighalani, Mahdi Ghasemi Selakjani

 

Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Bonn, Germany

Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Mohaghegh Ardabili, Ardabil, Iran

Gilan Branch, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREO), Rasht, Iran

Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Guilan, Rasht, Iran

 

Abstract

Drought stress causes great damage to the rice cultivation all over the world. Specific transcription factors (TFs) can regulate the expression of stress-related genes. In this research, we investigated the effect of drought stress on the expression of five specific transcription factors OsbHLH148, OsbZIP72, OsMYB2, OsNAC6 and TRAB1 at vegetative and reproductive stages in two Iranian rice cultivars with drought-sensitive and tolerant backgrounds; Hashemi and Neda. Using a real-time quantitative PCR (qPCR) approach, this study revealed that the expression of OsbZIP72, OsMYB2 and OsNAC6 were increased significantly in the Hashemi cultivar under drought stress at the vegetative stage. It seems that these three genes paly their roles in the drought sensitive cultivar Hashemi at the vegetative stage and do not play any role at the reproductive stage as the most sensitive stage to drought stress. The expression of TRAB1 was increased in Hashemi cultivar at the reproductive stage, while the expression of TRAB1 was decreased in Neda cultivar at the vegetative stage. This indicates that the expression of TRAB1 could respond sensitively to drought stress at the vegetative stage. Furthermore, there were statistically significant increases in expression of OsbHLH148, OsbZIP72, OsMYB2, OsNAC6 and TRAB1 in Neda (tolerant) cultivar at the reproductive stage. Therefore, our study suggests that these five genes might be involved in drought tolerance of this cultivar to drought stress at the reproductive stage. Thus, they could be used as viable candidate TFs to develop additional varieties of drought-tolerant transgenic rice.

 

Pages 327-333 | Read More |  DOI: 10.21475/poj.09.05.16.pne158

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Research Note

 

Gene expression changes in response to drought stress in Ilex paraguariensis leaves

 

Raúl M. Acevedo, Oscar A. Ruiz, Pedro A. Sansberro*

 

Laboratorio de Biotecnología Aplicada y Genómica Funcional, Instituto de Botánica del Nordeste (CONICET), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Sargento Cabral 2131, CC: 209, W3402BKG, Corrientes, Argentina

Unidad de Biotecnología 1, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (UNSAM-CONICET). Av. Intendente Marino Km 8,200 CC: 164. B7130IWA, Chascomús, Buenos Aires, Argentina

 

Abstract

Ilex paraguariensis St. Hil. is recognized as a shade-tolerant tree, cultivated in north-eastern Argentina, south-eastern Brazil, and Paraguay. Its leaves and young shoots are industrialised and; hence, being used to prepare a traditional tea-like infusion (mate-tea) with various medicinal benefits. Under the prevailing agro-climatic conditions in NE Argentina and with the occurrence of high temperatures and scarce rains during spring or summer, I. paraguariensis plants are subjected to water stress, reducing their yield. Differential Display was used to compare differences in gene expression between stressed and unstressed (control) potted plants. We found 52 differentially expressed transcripts (DETs), analysing banding patterns of Differential Display polyacrylamide gels, in which 38 DETs were induced, and 14 DETs were repressed in response to drought. Sequence comparisons revealed that 19% of the fragments showed no homologies, whereas 40.5 % of the total number of fragments had strong similarities with database entries of known functions. The other DETs belonged to unclassified proteins or genes with unknown functions. Interestingly, 12% of the DNA sequences were related to signal transduction, and 2% of the sequences were identified as transcription factors. Approximately, 12% of the annotated sequences were involved in stress tolerance and metal homeostasis, while 7% of the DETs were associated with photosynthesis. Other groups, representing 12%, included those involved in secondary metabolism, lignin biosynthesis, cell walls and RNA stabilization/chaperone activity. When integrated with physiological data, our results suggest that the transcriptional activity of some of the studied genes could be related to the degree of drought tolerance/susceptibility of I. paraguariensis.

 

Pages 334-343 | Read More | DOI: 10.21475/poj.09.05.16.pne185

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Vascular expression of trehalose phosphate synthase1 (TPS1) induces flowering in Arabidopsis

 

Jorge-Luis Ruiz-Salas, Roberto Ruiz-Medrano, María del Carmen Montes-Horcasitas, Kenny Alejandra Agreda-Laguna, Jesús Hinojosa-Moya, Beatriz Xoconostle-Cázares*

 

Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional. Av. IPN San Pedro Zacatenco, 07360, Ciudad de México

Facultad de Ingeniería Química, Benemérita Universidad Autónoma de Puebla, Campus Acatzingo, Puebla, México

 

Abstract

Trehalose and Trehalose-6-phosphate (T6P) have been described as signaling molecules involved in plant growth, development, carbon partitioning, flowering and response to biotic and abiotic stress. In order to investigate the role of T6P in vascular tissue signaling, Arabidopsis, plants expressing the TPS1 gene under the control of the actin depolymerizing factor 3 promoter (At5g59880) were generated by Agroinfiltration. Flower development and silique production occurred earlier in overexpressing lines compared to wild type (WT) control plants, while accumulation of TPS1 transcripts in overexpressing plants was considerably higher in silique, rosette and cauline leaves than in WT plants. Flowering Locus T (FT, AT1g65480) transcript was detected in rosette and cauline leaves in tps1 overexpressing lines, which could cause the observed early flowering. Trehalose levels were higher in rosette and cauline leaves in TPS1 lines, although no differences were observed in photosynthesis rate.  These results suggest that the ectopic expression in the vasculature of the TPS1 gene induced trehalose accumulation in the vasculature, inducing flowering without compromising plant development.

 

Pages 344-351 | Read More | Supplementary Data | DOI: 10.21475/poj.09.05.16.pne188

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Salinity and drought-induced methylglyoxal detoxification in Brassica spp. and purification of a high active glyoxalase I from tolerant genotype

 

Md. Shahadat Hossain, Mirza Hasanuzzaman*, Md. Ekramul Hoque, Homayra Huq and Md. Motiar Rohman*

 

Department of Biotechnology, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka 1207, Bangladesh

Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka 1207, Bangladesh

Molecular Breeding Laboratory, Plant Breeding Division, Bangladesh Agricultural Research Institute, Gazipur, Bangladesh

 

Abstract

This experiment was conducted to study the role of glyoxalase system in conferring salinity and drought stress in Brassica spp. Two Brassica genotypes viz. BARI Sharisha16 (tolerant) and Tori7 (susceptible) were exposed to salt (16 dS m-1) and drought for 2, 4 and 6 day. The comparative study of two Brassica genotypes under salinity and drought stress revealed that BARI Sharisha16 is more tolerant than Tori7 in both stresses. Under drought stress and salinity stress, Gly I activity increased significantly in both genotypes. Notably, concomitant increased activities of Gly I and Gly II with increased methylglyoxal (MG) suggested their role in MG detoxification in Brassica Spp. At six-day of salt stress, it was remarkable that Gly I and Gly II activities were 49 and 36 % higher in BARI Sharisha16 than Tori7. In addition, Gly I and Gly II activities were 24 and 21 % higher in BARI Sharisha16 than Tori7 after sixth day of drought, and hence, using different column chromatography Gly I was purified from BARI Sharisha16 seedlings. In purification, the fraction eluted from affinity chromatography showed specific activity of 173.51 µM min-1mg-1 protein. In SDS-PAGE, the purified Gly I protein migrated as a single band on with an apparent molecular mass of 27 kDa. In final purification, the recovery of Gly I activity was 0.38% along with purification fold 112.7. In this study, role of glyoxalase system in detoxification of MG was observed and subsequently, Gly I was purified from tolerant genotypes.

 

Pages 352-359 | Read MoreDOI: 10.21475/poj.09.05.16.pne232

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Molecular cloning, characterization and expression pattern analysis of a jasmonic acid responsive sesquiterpene synthase gene from Persicaria minor

 

Chew Jin Kiat, Mehdi Farshad Ashraf, Muhammad Naeem-Ul-Hassan, Che Radziah Che Mohd Zain, Zamri Zainal, Ismanizan Ismail*


School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia

Institute of System Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia

 

Abstract

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 P. minor terpenoid metabolism, especially at the genetic level is still very scarce. In the present study, a cDNA sequence (KT192706) from the leaves of P. minor, encoding a sesquiterpene synthase (PmSS) gene was successfully cloned. The complete sequence of PmSS comprised of 1724 bp with a 1680 bp open reading frame, corresponding to a deduced protein of 559 amino acids. Under the normal conditions, PmSS gene was found to be differentially expressed in the organs of P. minor. Significantly higher expression level of PmSS was recorded in leaves and stems which are, respectively, about 98 folds and 49 folds higher than that in the roots. In addition, the present study has also shown that the expression of PmSS gene was responsive towards the exogenous application of jasmonic acid in all organs of the P. minor.


Pages 360-368 | Read MoreDOI: 10.21475/poj.09.05.16.pne271

 

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