Articles

8(3) 2015 issue
 
May 2015 issue
[Uncorrected Proof]
Southern Cross Publishing Group©2015
Australia




Plant Omics | May 2015
>>>Return to home page
Direct sequencing of RAPD products provides a set of SCAR markers for discrimination of sweet potato cultivars

Hye Min Lee, Young Hoon Park, Tae Hwan Jun, Soon Wook Kwon, In Soo Choi, Yong Chul Kim, Ravi Gupta, Mi Nam Chung, Sun Hyung Kim, Ping Yang, Yiming Wang, Sun Tae Kim*

Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 627-707, South Korea
Department of Horticultural Bioscience, Pusan National University, Miryang, 627-707, South Korea
Bioenergy Crop Research Center, NICS, RDA, Miryang, 627-803, South Korea
Department of Environmental Horticulture, University of Seoul, Seoul, 130-743, South Korea
Genome Diversity, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraίe 3, 06466, Stadt Seeland (OT) Gatersleben, Germany
Division of Applied Life Science, Gyeongsang National University, Jinju, 660-701, Korea

Abstract
Here, we analyzed 200 pairs of the random amplified polymorphic DNA (RAPD) markers to uncover the polymorphisms in sweet potato and subsequently developed 13 pairs of sequence-characterized amplified region (SCAR) markers. In contrast to the random amplification of RAPD markers, the newly-developed SCAR markers revealed lower ratio of polymorphisms, but showed higher repeatability, user-friendly and were sequence-specific. Furthermore, we employed these markers to exploit the genetic diversity of 27 Korean sweet potato cultivars, which could be distinguished and grouped. Overall, these results show that the newly-developed and sequence-specific SCAR markers could be used for marker-assisted selection (MAS) for breeding for elite sweet potato varieties in South Korea.

Pages 195-200 | Full Text PDF | Supplementary Data PDF
………………………………………………………………………………………………………………………………………..

Proteomic analysis of ageing in black gram (Vigna mungo L.) seeds and its relation to seed viability

Sekar Sathish, Rayees Ahamed, Natesan Senthil*, Nagappan Arulkumar, Hyeon Soo Park, Senthil Kalaiselvi, Renganathan Umarani, Muthurajan Raveendran, Muthusamy Bhaskaran, Gon Sup Kim

Department of Seed Science and Technology, Tamil Nadu Agricultural University, Coimbatore, India
Department of Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
Department of Seed Science and Technology, Forest College and Research Institute, Tamil Nadu Agricultural University, Mettupalayam, India
Department of Biochemistry, Avinasilingam Institute for Home Science and Higher Education for Women, Coimbatore, India
Research Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, 900 Gajwadong, Jinju, Gyeongnam 660-701, Republic of Korea

Abstract 
The aim of this study is to investigate, using 2D-PAGE analysis, the possible proteome changes in black gram seeds when their germination rate falls below 75%  and thereby, identify proteins that correlate with loss of seed viability during seed ageing. Firstly, in order to obtain seed samples with germination rate less than 75%, for 2D-PAGE analysis, we analyzed the proteomic (using SDS-PAGE) and physiological changes in seeds, which were artificially aged for 1 to 10 days at 98 ± 2% relative humidity and 40 ± 1° C temperature. The results revealed the major physiological and protein changes occurs from sixth day onwards and germination rate falls below 75% at sixth day, suggesting that 2D-PAGE seed samples can be obtained from 6-day-artificially aged seeds. Secondly, we carried out 2D-PAGE analysis using fresh and 6-day-artificially aged seeds and characterized 16 differentially expressed proteins in aged seeds.

Pages 201-211 | Full Text PDF
………………………………………………………………………………………………………………………………………..

Analysis of SSR markers linked with brown planthopper resistance genes (Bph) using high-resolution melting (HRM) in rice

Mahmoodreza Shabanimofrad, Mohd Y. Rafii*, Sadegh Ashkani, Mohamed M. Hanafi, Nur Azura Adam, Mohammad Abdul Latif, Harun A. Rahim, Mahbod Sahebi

Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
Department of Agronomy and Plant Breeding, Islamic Azad University of Yadegar-e-Imam Khomeini (RAH) Branch, Tehran, Iran
Department of Plant Protection, Faculty Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
Bangladesh Rice Research Institute, Gazipur-1701, Bangladesh
Malaysian Nuclear Agency, Bangi, 43000 Kajang, Selangor, Malaysia

Abstract

In the present study, 110 simple sequence repeat (SSR) markers that are associated with Bph resistance genes were selected from the Gramene database and used to develop SSR marker-based strategies for the reliable selection of BPH-resistant genotypes. Fifty-seven of the best polymorphic markers were used to identify the segregation ratio in 176 individual F2 rice progeny from a MR276 (susceptible) Χ Rathu Heenati (resistant) interspecific cross. Thirty-five SSR markers, including RM544, RM547, and RM8213, showed a good fit to the expected segregation ratio (1:2:1) for the single gene model (d.f. = 1.0, p = 0.05) in chi-square (?2) analyses.

Pages 212-219 | Full Text PDF
………………………………………………………………………………………………………………………………………..

Interactive effects of arsenic and chromium stresses on mineral and metal uptake in jute (Corchorus olitorius L.)

Muhammad Kamrul Islam, Mst. Salma Khanam, Si Young Lee, Tatoba R. Waghmode, Iftekhar Alam, Moo Ryong Huh*

Department of Horticulture, College of Agriculture and Life Science, Gyeongsang National University, Jinju 660-701, Korea
Department of Agronomy, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
National Institute of Biotechnology, Ganakbari, Savar, Dhaka 1349, Bangladesh
Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju 660-701, Korea

Abstract
Here, we report the effects of combined As and Cr stresses on plant biomass, photosynthesis, metal and nutrient uptake compared to As or Cr stress alone. Chromium tolerant variety, O-795, had significantly (p=0.05) higher Cr and As levels in roots, stems and leaf tissues than Cr sensitive variety, O-9897. Roots had much higher As and Cr contents than above-ground parts. Arsenic stress reduced potassium (K+), magnesium (Mg2+), iron (Fe3+), copper (Cu2+), manganese (Mn2+) and zinc (Zn2+) contents in the roots and inhibited calcium (Ca2+), and from being translocated into shoots and leaves. Chromium stress resulted in decreased concentration of K+, Mg2+, Fe3+, Zn2+, Cu2+ and Mn2+ and increased concentrations of Ca2+ concentration in the root tissues.

Pages 220-231 | Full Text PDF
………………………………………………………………………………………………………………………………………..

Improving sweet leaf (Stevia rebaudiana var. Bertoni) resistance to bialaphos herbicide via bar gene transfer

M. Mubarak, Y. El Halmouch*, A. Belal, M. Abd Elfadeel, T. Nasr EL-Din, S. F. Mahmoud, M. E. El Sharnouby, E. El Sarag

Department of Plant Production, Faculty of Environmental Agricultural Sciences, Suez Canal University, Egypt
Department of Botany, Faculty of Science, Damanhour University, Damanhour 22511, Egypt
Department of Biotechnology, Faculty of Science, Taif University, Taif, P.O. Box 21974, Kingdom of Saudi Arabia
Natural Products Department, National Centre for Radiation Research, and Technology, Cairo, Egypt
Department of Genetic Transformation, Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Cairo, Egypt

Abstract
The main objective of the present study was to improve the productivity of sweet leaf (Stevia rebaudiana var. Bertoni) through in vitro propagation and transformation methods.  Production of transgenic resistance to herbicide sweet leaf was achieved using bar gene. This was gained by biolistic bombardment gene delivery system. Histochemical assay and PCR analysis were used for detection the transformed tissue. The results of the study showed that 66.7% of transformed S. rebaudiana survived at 3 mg l-1 of bialaphos. However, only 4% of un-transformed explants were survived.

Pages 232-237 | Full Text PDF
………………………………………………………………………………………………………………………………………..

Genome-wide analyses of abiotic stress-related microRNAs and their targets in Arabidopsis thaliana

Kaibin Xie, Tianhai Zhang, Xue Zhou*, Guoxiang Chen*

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
Taizhou College, Nanjing Normal University, Taizhou 225300, China

Abstract
In this study, we systematically investigated stress-related miRNAs and their targets in Arabidopsis thaliana. We identified 94 putative stress-related miRNA genes, in which 8 miRNAs were new identified with stress-related response function based on targets prediction. Sequence analysis of these miRNA genes showed that most stress-related miRNAs possess TATA boxes in their promoters, and more than half contain at least two promoters. We also demonstrated that most stress-related miRNA genes contain stress-related elements in their promoters.

Pages 238-243 | Full Text PDF | Supplementary Data PDF
………………………………………………………………………………………………………………………………………..

Comparative analyses of osmotically and ionically adapted cell lines of rice and their response to regeneration

Azhar Hussain Shah*, Safdar Hussain Shah, Habib Ahmad, Ikram Muhammad, Uzma Khan

Department of Botany, Hazara University, Mansehra Pakistan
IBGE, The University of Agriculture Peshawar, Pakistan
Department of Genetics, Hazara University, Mansehra Pakistan

Abstract
In the present study, cell lines of Oryza sativa variety indica, cv. Swat-1 were adapted to osmotic (20% PEG) and ion toxicity (20mM LiCl) stresses by incremental increase of PEG and LiCl concentrations in the medium. Analyses of these cell lines revealed a substantial increase in Ca2+ level and significant reduction in Mg2+ contents on adaptation to PEG stress, while no prominent differences in accumulating organic and inorganic cytosolutes were observed between unadapted and LiCl adapted  cell lines. SDS-PAGE results revealed that adaptation to PEG and LiCl was evident by appearance of six different polypeptides, among these four polypeptide bands 15, 17, 26 and 68 kDa were common, while other two polypeptide bands of 60 kDa and 32 kDa were present only in PEG and LiCl adapted cell lines, respectively.

Pages 244-249 | Full Text PDF
………………………………………………………………………………………………………………………………………..

Ectopic expression of CisAF7, an Alfin1-like gene from Citrus sinensis, confers tolerance to several abiotic stresses in Escherichia coli

Jin-Wang Qu, Li-Ping Liu, Jian Wu, Qiao-Qiao Yin, Tian-Tian Wu, Xiao-Hong Guo, Jun-Lin Zhang, Fei-Rong Yuan, Na Li, Zi-Niu Deng*

Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, P. R. China
National Center for Citrus Improvement, Hunan Agricultural University, Changsha 410128, P. R. China
College of Life Science and Technology, Wuhan Institute of Bioengineering, Wuhan 430415, P. R. China
Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan 430415, P. R. China

Abstract
In order to identify the function of a sweet orange (Citrus sinensis [L.] Osbeck cv. Valencia) Alfin1-like (AL) gene, CisAL7, in vitro functional analyses were performed using a procaryotic heterologous expression system (Escherichia coli). CisAL7 was cloned and expressed in a pET28a(+) system. E. coli cells containing the recombinant plasmid or empty vector as a control were treated by multiple stresses. In LB (Luria-Bertani) solid media, Escherichia coli harboring CisAL7 gene was remarkably more tolerant to stresses, including high salinity (0.6 M NaCl or 0.6 M KCl), high temperature (50°C), and low temperature (4°C), than control cells. These results indicate that CisAL7 protein may play a positive role in responsive to abiotic stresses above. This provides the first experimental evidence that AL7 enhances abiotic tolerance of E. coli cells.

Pages 250-256 | Full Text PDF
………………………………………………………………………………………………………………………………………..

Cloning and characterization of two major blast resistance genes Pi-b and Pi-kh from Malaysian rice variety Pongsu Seribu 2

Fatah  A. Tanweer, Mohd Y. Rafii*, Kamaruzaman Sijam, Harun A. Rahim, Fahim Ahmed, Mohammad Abdul Latif

Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia 
Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia,43400 UPM Serdang, Selangor, Malaysia
Department of Plant Protections, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
Agrotechnology and Bioscience Division, Malaysian Nuclear Agency, 43000 Kajang, Selangor, Malaysia
Bangladesh Rice Research Institute, Gazipur 1701, Bangladesh
Department of Plant Breeding and Genetics, Faculty of Crop Production, Sindh Agriculture University Tandojam, Sindh, Pakistan

Abstract
In order to ensure the resistance of Pongsu Seribu 2, virulent pathotype of M. oryzae P7.2 was inoculated on Pongsu Seribu 2 and MR219 (susceptible used as control) where Pongsu Seribu 2 was found strongly resistance and MR219 susceptible. To determine the mechanism of resistance in PS2 cultivar, cloning and characterization of major blast resistance gene, Pi-b and Pi-kh were carried out. The results revealed that nucleotide sequence contain an open reading frame (ORF) and the same is also highly conserved in nature. Deduced amino acid sequence indicates that Pi-b contains zinc finger-containing protein domain and Pi-kh have Leucine rich repeat domain. The translated nucleotide sequence into amino acid produces significant homology average 76.8% with Pi-kh and 93.4% with Pi-b blast resistance genes present in different cultivars of rice.

Pages 257-263 | Full Text PDF
………………………………………………………………………………………………………………………………………..

Construction and classification of a cDNA Library from Miscanthus sinenesis (Eulalia) treated with UV-B

Eun Soo Seong, Ji Hye Yoo, Jae Hoo Choi, Nam Jun Kim, Hee Young Kim, Kweon Heo,
Chang Yeon Yu*

Bioherb Research Institute, Kangwon National University, Chuncheon 200-701, South Korea
Department of Applied Plant Sciences, College of Agriculture and Life Science, Kangwon National University, Chuncheon 200-701, South Korea


Abstract
  
The establishment of EST database is important to study classification and function of gene groups in Miscanthus. We isolated total RNA at 48 h after UV-B treatment to develop a gene expression profile of the entire Miscanthus plant (except for the root). A cDNA library was prepared from mature mRNAs, and 1000 cDNA clones were partially sequenced using a DNA sequence kit (BigDye TM Terminator Cycle Sequencing Ready Reaction mixture). A total of 827 unigenes, including 72 contigs and 755 singletons, were identified after assembly of the expressed sequence tags (ESTs). The functional classification sequences belonged to 15 categories including metabolism, energy, cell cycle, transcription, protein synthesis, protein fate, protein with binding function, regulation of metabolism and protein function, cell transport, signal transduction, cell defense, interaction with the environment, cell fate, biogenesis of cellular components, and subcellular localization, which were considered to be of interest for UV-response signaling.

Pages 264-269 | Full Text PDF | Supplementary Data PDF
………………………………………………………………………………………………………………………………………..

Quantitative expression analysis of TaMPK4 and TaTIP1 genes in drought tolerant and non-tolerant wheat (Triticum aestivum L.) cultivars

Birsen Cevher-Keskin*, Yasemin Yildizhan, Oktay Kulen, Selma Onarici

TUBITAK, The Scientific and Technical Research Council of Turkey, Marmara Research Center, Genetic Engineering and Biotechnology Institute, Plant Molecular Biology Laboratory; P.O Box: 21, 41470 Gebze, Kocaeli Turkey

Abstract
The mitogen-activated protein kinase (MPK) cascade elements and tonoplast intrinsic proteins (TIPs) take place in abiotic signaling pathway and water movement regulation, respectively. We aim to show the expression patterns of MPK4 and TIP1 mRNA in drought tolerant and non-tolerant T. aestivum cultivars treated with two different shock dehydration stresses using qRT-PCR technique. The patterns of MPK4 and TIP1 mRNA accumulation was different in non-tolerant wheat cultivar, up-regulated in 4 and 8h drought-stressed root and leaf tissues. The reason for early response to drought stress in the cultivar Atay might be related to drought sensitivity. Drought tolerant cultivars showed MPK4 up-regulation in 8h stressed roots implying that, increased expression of MPK4 might play an important role in drought tolerance of T.aestivum by regulating the stress signaling.

Pages 270-277 | Full Text PDF
………………………………………………………………………………………………………………………………………..

A novel eukaryotic translation initiation factor 5A gene from Populus simonii x P. nigra confers CuSO4 and NaCl stress tolerance in Arabidopsis thaliana

Tangchun Zheng, Lina Zang, Lijuan Dai, Chuanping Yang*, Guan-Zheng Qu*

State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China

Abstract
In the present study, we cloned and characterized a PsneIF5A2 from poplar (Populus simonii Χ P. nigra) leaves. With the support of bioinformatics prediction, the results showed the domain structures of PsneIF5A2, which was predicted by multiple alignment analysis. It has a S1_eIF5A motif, which is an ortholog of eIF5A1 in Arabidopsis. The plant expression vector of PsneIF5A2 was transformed into Arabidopsis using Agrobacterium tumefaciens strain EHA105. Ectopic expression of PsneIF5A2 in Arabidopsis significantly conferred CuSO4 and NaCl stress tolerance. Furthermore, PsneIF5A2-transgenic Arabidopsis exhibited enhanced SOD and POD activities, lower MDA content and electrolyte leakage under CuSO4 and NaCl stress, compared with control plants. Our results suggested that the PsneIF5A2 gene (GenBank No. KC521463) is an excellent candidate for genetic engineering to improve salt and heavy metal tolerance in agricultural plants.

Pages 278-286 | Full Text PDF