5(4) June 2012 issue
July 2012 issue
Plant Omics Journal | July 2012 issue
Southern Cross Publishing Group©2012

Identification of self-incompatibility related proteins in the pistil of Japanese pear [Pyrus pyrifolia (Burm.f.)] by proteome analysis

Asuka Uchida, Hidenori Sassa, Satoshi Takenaka, Yoichi Sakakibara, Masahito Suiko, Hisato Kunitake

The Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki 889-2192, Japan
Graduate School of Horticulture, Chiba University, Chiba, 271-8510, Japan
Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan


The differences between stylar protein of the Japanese pear [Pyrus pyrifolia (Burm.f.)] cultivars ‘Kosui’ (S4S5) and ‘Kikusui’ (S2S4) were compared by two-dimensional difference gel electrophoresis (2-D DIGE), and were labelled and visualized with different fluorescent dyes (IC3-OSu, IC5-OSu) on a single 2-D gel. The individual different expressed proteins spots were subjected to identification. The proteins were analyzed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) to identify proteins related to gametophytic self-incompatibility
(GSI). S4-RNase and thaumatin-like protein 1 were successfully detected as expected in the pistils of ‘Kosui’ and ‘Kikusui’. S5-RNase was also detected in the pistils of ‘Kosui’. However, we could not detect S2-RNase in ‘Kikusui’ in this study, possibly because the level of expression of S2-RNase might be minuscule, or the estimated isoelectric point (pI) of S2-RNase (pI:9.26) was more basic than S4-RNase (pI: 9.17) and S5-RNase (pI: 9.01). These results indicate that proteomic studies are effective tools for detection of the expected proteins and might be helpful for finding the unknown key proteins related to the mechanism of self-incompatibility (SI) in many other SI plants.

Pages 320-325 | Full Text PDF
Identification and promoter analysis of some important storage protein genes from wheat (Triticum aestivum L.)

Jiarui Li, Baoyan An, Xiansheng Zhang

Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
Department of Plant Pathology, Kansas State University, Manhattan, Kansas State, 66502, USA
College of Veterinary Medicine, Kansas State University, Manhattan, Kansas State, 66502, USA


A cDNA library was constructed using wheat seeds from a cultivar PH82-2-2 with superior bread-making quality, and differential hybridization was conducted by using RNA probes of unpollinated ovary, embryo and endosperm with 10, 000 clones from the cDNA library. 99 out of 800 clones, representing 22 unique genes, were identified as storage protein genes through sequencing blast. These 22 genes encode low molecular weight glutenin subunits (LMW-GS), high molecular weight glutenin subunits (HMW-GS), gliadin and avenins. Three clones 6A4, 6H11 and 8G17 encoding storage proteins were confirmed to express specifically in endosperm via Northern blot analysis. Southern blot result indicated there are at least three copies of 6A4 in wheat genome. A 2-kb promoter of 8G17 was isolated by Universal GenomeWalkerTM Kit. The analysis of cis-acting elements revealed 8G17 promoter contained endosperm related transcriptional elements. The functional genomics data in this paper will provide valuable information for improvement of wheat flour quality.

Pages 326-332 | Full Text PDF | Supplementary data
Activities of chitinase enzymes in the oil palm (Elaeis guineensis Jacq.) in interactions with pathogenic and non-pathogenic fungi

Laila Naher, Soon Guan Tan, Umi Kalsom Yusuf, Chai Ling Ho, Shafiquzzaman Siddiquee

Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia
Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia
Institute of tropical Agriculture, Universiti Putra Malaysia, 43400 UPM, Selangor, Malaysia
Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, 
Kota Kinabalu, Sabah, Malaysia


Ganoderma boninense
Pat. is a fungal pathogen that causes basal stem rot disease in the oil palm (Elaeis guineensis jacq.). Chitinases are important defence enzymes in plants. In this study, the activities of chitinase was analyzed at various time points in roots and leaves of oil palm in the presence of G. boninense and Trichoderma harzianum (a biocontrol fungus used to combat G. boninense infection), either alone or together. At two weeks post infection, G. boninense alone treatment showed significant chitinase activity of 35.28 and 30.83 U/mg in the roots and in leaves of oil palms, respectively. In the treatments with T. harzianum alone or in combination with G. boninense the chitinase activity was significantly increased (compared to control plants) to 15.14 and 18.8 U/mg in leaf tissue, and 26.11 and 22.08 U/mg in root tissue, respectively at two weeks post inoculation. This suggests that the chitinase enzyme activity induced by T. harzianum in oil palms may have a role in the defence response against microbial pathogen infections. 

Pages 333-336 | Full Text PDF
Combining ability and heritability analysis for yield and yield contributing characters in chilli (Capsicum annuum) landraces

M. Hasanuzzaman, M. A. Hakim, Jannatul Fersdous, M. M. Islam and L. Rahman

Department of Genetics and plant Breeding, HSTU, Dinajpur 5200, Bangladesh
Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM serdang Selangor, Malaysia,
Department of Forest Management, Faculty of Forestry, Universiti Putra Malaysia, 43400 UPM serdang Selangor, Malaysia, 4Dept. of Genetics and plant Breeding, BAU, Mymensingh, Bangladesh


Six different homozygous divergent parents, CCA 2, CCA 5, BARI Morich 1, CCA 11, CCA 15 and CCA 19 were evaluated for combining ability using 6×6 diallel cross excluding reciprocals. The results showed that the general combining ability (GCA) was significant for all days to 50% flowering, fruit length, fruit width, fruit weight, days to fruit maturity (green), days to maturity (ripe), plant height, plant canopy width, number of seeds per plant, number of fruits per plant and yield per plant. Significant specific combining ability (SCA) was also observed for all the measured variables except fruit width. Both additive and non-additive effects influenced the performance of the hybrid in all the traits. The non-additive effects played a more important role than additive effects in studied traits. The parents CCA 5, BARI Morich 1 and CCA 19 were found as the reliable general combiners. Considering the SCA effects and mean performance, hybrids 36 and 23 were the best genotypes. Top two yield were obtained in hybrids 36 (BARI Morich 1× CCA 19) (898.87g yield per plant) and 23 (CCA 5× BARI Morich) (833.63g yield per plant). No parent and cross had significant GCA and SCA effects, respectively in all the traits studied. Broad sense heritability of all the 11 characters was above 90% indicating that all traits are highly heritable. Narrow sense heritability of days to 50% flowering, fruit length, fruit width, fruit weight, days to fruit maturity (green), days to maturity (ripe), plant height, plant canopy width were high (37.34-81.26), whereas the  number of seeds per plant, number of fruits per plant and yield per plant were in medium range of narrow sense heritability (18.42-29.19). Estimates of heritability by mid parent-offspring regression indicated that all the studied traits were highly heritable.

Pages 337-344 | Full Text PDF
Encapsulation-vitrification of Dendrobium sonia-28 supported by histology

L.P. Ching, J.J.J. Antony, R. Poobathy, S. Subramaniam

School of Biological Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia


In vitro protocorm-like bodies (PLBs) of Dendrobium sonia-28 were cryopreserved through an encapsulation-vitrification method. One to two and 3-4mm PLBs were precultured in half-strength semi-solid Murashige and Skoog (MS) medium supplemented with various sucrose concentrations (0, 0.25, 0.5, 0.75 and 1.0M) at different periods (0, 3, 6 and 9 days). Precultured PLBs were encapsulated and osmoprotected for 24 hours, and then dehydrated in plant vitrification solution 2 (PVS2, 0ºC) at different periods (0, 30, 60, 90, 120, 150, 180 and 210 minutes) prior to storage in liquid nitrogen (LN, -196ºC) for at least 24 hours. After rapid thawing (40±2ºC) for two minutes, the beads were unloaded with 1.2M sucrose and then cultured on half-strength semi-solid MS medium devoid of growth regulators. The 2,3,5-triphenyltetrazolium chloride (TTC) assay was used to determine the viability of the treated PLBs after two weeks of recovery. Histological analyses of non-cryopreserved and cryopreserved PLBs were conducted to assess the impact of the cryopreservation procedure on the in vitro PLB cultures. Observations indicated that cryopreserved PLBs underwent anatomical changes expressed as changes in the cell structure, cell wall, nucleus and cytoplasm. The optimised encapsulation-vitrification parameters involved in this study were the preculture of 3-4mm PLBs for six days in 0.5M sucrose, followed by dehydration in PVS2 at 0ºC for 150 minutes. Thus, this method was deemed promising for cryopreservation of PLBs of Dendrobium sonia-28.

Pages 345-350 | Full Text PDF
Analysis of GDSL lipase (GLIP) family genes in rice (Oryza sativa)

Yunyun Jiang, Rongjun Chen, Jiali Dong, Zhengjun Xu, Xiaoling Gao

Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan 611130, China


Lipase is one of the lipid hydrolyzing enzymes, distributed broadly throughout plants, animal and microorganisms. GDSL-lipases is one of the lipases that exhibit a GDSL motif GxSxxxxG, in which the active site Serine is located near the N-terminus and display a Gly-Asp-Ser-(Leu) [GDS(L)] motif in conserved block I. However, the knowledge about their roles in developmental processes and response to various stimuli are still very limited in rice. A systematic analysis revealed the presence of at least 113 GDSL lipase (GLIP) genes in the rice genome. The tandem gene duplications have contributed a major role in expansion of this gene family. Phylogenetic analysis classed proteins into three groups; OsGLIP group B contained 56 genes, 50 in group A and only 2 genes in group C. The organization of putative motifs indicated potential diverse functions of GLIP gene family members in rice. Microarray data analysis revealed tissue and developmental stage-specific expression patterns of several OsGLIP genes. 38 OsGLIP genes were especially expressed in stigma and seed germination, several genes expressed exclusively in root and 17 OsGLIP genes were induced by any of three stresses. Our analysis also suggests differential accumulation of cluster genes during these processes. Our analyses indicated OsGLIP genes may have potential roles in rice development and abiotic stresses.

Pages 351-358 | Full Text PDF
R-RAP: a retrotransposon-based DNA fingerprinting technique in plants

Ali Aalami, Samira Safiyar, Babak Abdollahi Mandoulakani

Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Guilan, Rasht, Iran
Department of Agronomy and Plant Breeding, Faculty of Agriculture, Urmia University, Urmia, Iran  
Department of Agricultural Biotechnology, Institute of Biotechnology, Urmia University, Urmia, Iran 


The present research is aimed at testing a new retrotransposon-based marker, RAPD-retrotransposon amplified polymorphism (R-RAP), which used the combination of RAPD and LTR retrotransposon primers. Banding patterns which are obtained by R-RAP primer combinations were different from amplicons by IRAP and RAPD, demonstrating detection of different genomic regions that are not covered by the other molecular marker systems. The used LTR rertrotransposons had been previously isolated from barley and wheat, hence, twelve accessions of three species of Triticum aestivum, Hordeum vulgare, and Aegilops tauschii were used to evaluate the efficiency of this method. Ten polymorphic R-RAP primer combinations generated 141 loci, of which 114 were polymorphic. The studied species were divided with 66 % similarity into 3 clusters according to their species and even some sub-clusters within species. High polymorphism was observed in both between and within species. Polymorphic information content (PIC) ranged from 0.28 to 0.40. Reproducibility of each primer combination, tested 4 times in different conditions, was approximately 100%. Agarose gel was used to separate PCR products and showed good resolving ability. We showed that R-RAP can be used as an efficient marker as with other retrotransposon-based markers and can be applied in a similar way for DNA fingerprinting, genetic diversity, genome mapping, and gene tagging in plants. This method also represents a departure for IRAP and RAPD limitations.

Pages 359-364 | Full Text PDF
Differentially expressed proteins in sugarcane leaves in response to water deficit stress

Ni-on Ngamhui, Chutipong Akkasaeng, Yun J. Zhu, Nathpapat Tantisuwichwong, Sittiruk Roytrakul, and Taksina Sansayawichai

Department of Plant Science and Agricultural Resources, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
Hawaii Agriculture Research Center, 94-340 Kunia Road, Waipahu, Hawaii, 96797, USA
Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
Genome Institute, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Pathumthani, 12120, Thailand
Khon Kaen Field Crops Research Center, Department of Agriculture, Ministry of Agriculture and Cooperatives, Khon Kaen, 40000, Thailand


In many areas of the world, water stress is the major constraint limiting the productivity of sugarcane. The objective of this study was to identify proteins that were differentially expressed in sugarcane leaves in response to a water deficit treatment to describe the sugarcane responses at the cellular and molecular levels. Drought-tolerant sugarcane cultivar Khon Kaen 3 stalk cuttings were grown under a controlled environment in a growth chamber where a water deficit treatment was imposed by withholding watering for 5 days. The treatment group continuously received an adequate water supply. Soil moisture content (SMC), leaf water potential (LWP) and relative water content (RWC) were recorded to quantify the water deficit stress. Leaf proteins from non- and water-stressed plants were separated using two-dimensional electrophoresis (2-DE). Image analysis was performed on the electrophoresis gel to locate proteins that were differentially expressed between treatments, which were then identified using liquid chromatography coupled with electrospray ionization ion trap subjected to mass spectrometry/mass spectrometry analysis (LC-ESI-IT-MS/MS) and characterized. Two proteins involved in light-dependent reactions, chlorophyll a-b binding protein 1B-21 and chloroplastic and oxygen-evolving enhancer protein 1, were up-regulated by the stress treatment. Enzymes known to participate in antioxidant networks, including chloroplastic copper-zinc superoxide dismutase (CuZn-SOD), two-cysteine peroxiredoxin (2-Cys Prx) BAS1, superoxide dismutase [manganese] (SOD [Mn]) 3.1, SOD [Mn] 3.4, and isoflavone reductase (IFR) homolog IRL, were also up-regulated. These enzymes all used NADPH as the reducing equivalent, suggesting that linear electron flow (LEF) may dominate the total electron transport activities in sugarcane leaves under water deficit. In addition, two isoforms of ATP synthase beta and ATP synthase alpha subunits were up-regulated under water deficit, indicating that LEF was coupled to the generation of electrochemical gradients across the thylakoid membranes, leading to an increased abundance of ATP synthase beta and ATP synthase alpha subunits. There was increased abundance of a 16.9 kDa class I heat shock protein (HSP) and two isoforms of the elongation factor (EF-Tu) proteins, which are associated with heat tolerance. The identification of proteins regulated by water stress could lead to a better understanding of the cellular response to dehydration, which is an important and fundamental part of improving the stress tolerance of crops.

Pages 365-371| Full Text PDF | Supplementary data
Recombinant Arabidopsis WHY2 protein binds unspecifically to single-stranded DNA and is phosphorylated by mitochondrial protein kinases

Vladislav I. Tarasenko, Alexandr I. Katyshev, Irina Y. Subota, and Yuri M. Konstantinov

Siberian Institute of Plant Physiology and Biochemistry, Siberian Division of the Russian Academy of Sciences, Lermontova 132, Irkutsk 664033, Russia


Whirly proteins comprise a unique family of plant-specific DNA-binding proteins which are localized in both the nucleus and organelles. We have obtained a recombinant AtWHY2 protein, a mitochondrially targeted member of the Arabidopsis Whirly family, by the heterologous expression of WHY2 gene in E. coli and subsequent purification. The purified protein bound efficiently to single-stranded DNA probes in vitro, but failed to bind double-stranded DNA probes. The binding of the AtWHY2 to single-stranded DNA probes did not depend on DNA sequence. It bound with similar efficiency to mitochondrial gene promoter regions, the protein-encoding part of COB gene lacking regulatory elements, and the nuclear elicitor response element. We have also demonstrated the phosphorylation of the AtWHY2 protein in vitro by mitochondrial protein kinases from maize and Arabidopsis. This finding suggests that activity of AtWHY2 and other Whirly family members could be regulated by phosphorylation that would be an interesting subject for further research.

Pages 372-375 | Full Text PDF
Improvement of ornamental characteristics in Rehmannia elata through Agrobacterium rhizogenes-mediated transformation

Young Seon Kim, Yong Kyoung Kim, Hui Xu, Md. Romij Uddin, Nam Il Park, Haeng Hoon Kim, Soo Cheon Chae, Sang Un Park

Department of Crop Science, College of Agriculture & Life Sciences, , Chungnam National University, 79 Daehangno, Yuseong-Gu, Daejeon, 305-764, Korea
Wildlife Genetic Resources Center, National Institute of Biological Resources, 42 Nanji-ro, Seo-gu, Incheon, 404-708, Korea

Department of Well-being Resources, Sunchon National University, 413 Jungangno, Suncheon, Jeollanam-do, 540-742, Korea
Department of Horticultural Science, College of Industrial Sciences, Kongju National University, 1 Daehoe-ri, Yesan-kun, Chungnam, 340-720, Korea


An attempt was initiated to develop short stature bushy transgenic ornamental plant Rehmannia elata from hairy roots culture. Transgenic plants were regenerated by infecting leaf explants with Agrobacterium rhizogenes R1000 from hairy roots culture. PCR amplification confirmed the presence of root loci (rol) genes from the root-inducing (Ri) plasmid in the transgenic R. elata. Three transgenic lines were characterized in the greenhouse trial. Several morphological traits such as the plant height, the size and number of leaves and flowers of these tranformants had changed in terms of ornamental value. The transgenic had different phenotype from that of the wild-type plants: the internodes were clearly shorter in the transformants, with a short, bushy, and compact growth with plenty of flowers. Among the transformants, T2 transformant contained 8-fold higher stem number, 5-fold higher flower number and 3 fold higher leaf number compared to wild-type. Such compact plants with numerous flowers can be used effectively for further breeding.

Pages 376-380 | Full Text PDF
Agrobacterium rhizogenes-mediated genetic transformation of radish (Raphanus sativus L. cv. Valentine) for accumulation of anthocyanin

Hanhong Bae, Yeon Bok Kim, Nam Il Park, Haeng Hoon Kim, Young Seon Kim, Mi Young Lee, Sang Un Park

School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Korea
Department of Crop Science, Chungnam National University, 79 Daehangno, Yuseong-gu, Daejeon, 305-764, Korea
Wildlife Genetic Resources Center, National Institute of Biological Resources, 42 Nanji-ro, Seo-gu, Incheon, 404-708, Korea
Department of Well-being Resources, Sunchon National University, 413 Jungangno, Suncheon, Jeollanam-do, 540-742, Korea
Aging Research Center, Korea Insititute of Oriental Medicine, Yuseong-Gu, Daejeon 305-811, Korea


An efficient protocol for the transformation of radish (Raphanus sativus L. cv. Valentine) hairy root cultures was initiated using cotyledon explants and infected by Agrobacterium rhizogenes R1000, a strain with the binary vector pBI121. Kanamycin-resistant roots appeared on explants at 4 weeks after infection with A. rhizogenes and these roots were maintained on hormone-free selection medium. PCR analysis of the neomycin phosphotransferase (NTPII) gene confirmed transformation in 15 plants of kanamycin-resistant hairy root cultures from a total 20 plants. Detection of high levels of ß-glucuronidase (GUS) transcripts and enzyme activity, as well as GUS histochemical localization, also confirmed the stable genetic transformation. We inoculated isolated hairy roots in liquid medium to promote rapid growth and production of anthocyanin. Among the different auxin treatments, 1.0 mg/L 2,4-D treatment resulted the highest production of anthocyanin (30.9 mg/L) that was 26 times higher as compared to control (1.2 mg/L). Transgenic root cultures of R. sativus L. cv. Valentine will allow investigation of the molecular and metabolic regulation of anthocyanin biosynthesis and evaluation of the genetic engineering potential of this species.

Pages 381-385 | Full Text PDF
Comparative Artemisinin analysis in Artemisia dubia transformed with two different Agrobacteria harbouring rol ABC genes

Bushra Hafeez Kiani, Naila Safdar, Abdul Mannan, Bushra Mirza

Department of Biochemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
Department of Pharmaceutical Sciences, COMSATS Institute of Information Technology, Abbottabad, 22060, Pakistan


Artemisinin, a potent antimalarial drug and a major constituent of Artemisia, is effective against quinine resistant strains of Plasmodium. The aim of the present study was to enhance artemisinin production in the roots of Artemisia dubia through transformation with rol genes by using Agrobacterium tumefaciens and Agrobacterium rhizogenes. Agrobacterium tumefaciens strain LBA4404 containing pRT99 and Agrobacterium rhizogenes strain LBA8196 and 9402 harboring rol ABC genes were used for the transformation experiments. PCR and Southern hybridization confirmed the T-DNA integration events in Artemisia dubia roots. The transformed roots proliferated two fold more as compared to untransformed roots. After 30 days of roots proliferation, the HPLC analysis showed higher concentration of artemisinin (36.581 µg/g DW) in roots of Artemisia dubia transformed with A. rhizogenes (strain 9402) compared to that of roots transformed with A. tumefaciens (0.855 µg/g DW) while no artemisinin was observed in control roots.

Pages 386-391 | Full Text PDF
Differential expression of kenaf phenylalanine ammonia-lyase (PAL) ortholog during developmental stages and in response to abiotic stresses

Mi-Jeong Jeong, Bo Sung Choi, Dong Won Bae, Sung Chul Shin, Sang Un Park, Hyoun-Sub Lim, Jongkee Kim, Joon Bum Kim, Byoung-Kwan Cho, Hanhong Bae

National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea
School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Korea
Central Laboratory, Gyeongsang National University, Jinju, 660-701, Korea
Department of Chemistry, Gyeongsang National University, Jinju 660-701, Korea
Department of Crop Science, Chungnam National University, Daejeon 305-754, Korea
Department of Applied Biology, Chungnam National University, Daejeon 305-764, Korea
Department of Applied Plant Science, Chung-Ang University, Anseong 456-756, Korea
Warm-Temperate Forest Research Center, Korea Forest Research Institute, Seogwipo 697-050, Korea
Department of Biosystems and Machinery Engineering, Chungnam National University, Daejeon 305-764, Korea


Phenylalanine ammonia-lyase (PAL) is a key enzyme in the phenylpropanoid pathway. A full-length of the gene putatively encoding phenylalanine ammonia-lyase (PAL) was cloned from kenaf (Hibiscus cannabinus L.) using degenerate primers and the RACE (rapid amplification of cDNA ends) method. The full-length PAL ortholog in kenaf consists of a 2,148 bp open reading frame encoding 715 amino acids (JQ779022). The deduced amino acid sequence showed high similarity to those of PAL from Ricinus communis (88%) and Vitis vinifera (86%). The expression of the PAL transcript was examined in different tissues, developmental stages, and after treatments with abiotic stresses (wound, NaCl, cold, H2O2, ABA, SA, MeJA and drought) using quantitative real-time reverse transcriptase polymerase chain reaction (QPCR). The PAL ortholog was differentially expressed in the different tissues and developmental stages. The highest transcript level of the PAL ortholog was observed in young (4-week-old) stem and mature flower tissues, with a certain level of expression in all tissues and organs tested. Three-week-old kenaf stem tissues were used to evaluate the effects of abiotic stresses on PAL ortholog expression. The highest transcript level of the PAL ortholog was observed at an early time point (1 or 6 h) after treatments with wound (1 h), H2O2 (6 h) and SA (6 h), while the highest transcript level was detected at the late time point (24 h) after treatments with NaCl, cold and ABA. The PAL ortholog was not significantly induced by MeJA, while drought repressed the PAL ortholog.

Pages 392-399 | Full Text PDF
Hydrogen cyanamide enhances MRI-measured water status in flower buds of peach (Prunus persica L.) during winter

Suravoot Yooyongwech, Akemi K Horigane, Mitsura Yoshida, Yoshihiro Sekozawa, Sumiko Sugaya, Suriyan Cha-um, Hiroshi Gemma

Pomology Laboratory, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
Department of Agricultural Science, Mahidol University, Kanchanaburi Campus, Kanchanaburi, Thailand
Molecular Structure and Dynamics Laboratory, National Food Research Institute, Tsukuba, Japan
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathumthani, Thailand


Braking bud dormancy in temperate fruit species using physical and chemical agents is a challenge issue. In present study, we investigated the interaction between hydrogen cyanamide (HC) and temperature in breaking dormancy to gain a basic knowledge on water status in peach (Prunus persica L.) floral buds. The water status, relaxation time (T2) and apparent diffusion coefficient (ADC), in the upper part (flower primordia and bud scales), basal part, and bud trace of flower buds were determined using the magnetic resonance imaging (MRI). Bulk water, which might flow through the bud trace, increased the water content in the basal part, and water molecular mobility as reflected by an increase in T2 in HC-treated buds after 1 week at 5
°C. The HC triggers the influx of water into the bud, where the basal part exhibited the highest level of water accumulation. The study provides significant insights into the status of water in floral buds and highlights the role of HC to solve the problems of produce in temperate fruits.

Pages 400-404 | Full Text PDF
In silico analysis for gene content in rice genomic regions mapped for the gall midge resistance genes

Arun Kumar Yasala, Nidhi Rawat, V. S. Arun Kumar Sama, Kudapa Himabindu, R. M. Sundaram, J. S. Bentur

Directorate of Rice Research, Rajendranagar, Hyderabad, Andhra Pradesh 500030, India


So far, 11 gall midge resistance genes (Gm1 through Gm11) have been identified in rice though classical inheritance studies and several of these have been mapped through linked markers. Nevertheless the exact identity of these genes is still eluding. Hence, the present study aimed to identify the potential candidate genes involved in rice-gall midge interactions by in silico analysis for gene content of 4.02 Mb genomic regions containing the gall midge R genes. The candidate genes were identified in terms of common genes among the different gall midge resistance regions, transcriptomics data analysis from earlier studies and, reported genes widely implicated in defense against plant-pathogen interactions. Results revealed, of the 375 annotated genes, five genes with one or more copy number common among these regions such as the genes encoding NBS-LRR class proteins, no apical meristem protein, F-box family protein, pentatricopeptide repeat containing protein and SET domain containing protein. Further, 15 genes from these regions have been reported in earlier transcriptomics studies implicated in incompatible (9 genes) and compatible (6 genes) rice-gall midge interactions and 22 genes were known to be implicated in different plant-pathogen interactions. From the present study, we have shortlisted 24 genes and developed 33 primer pairs. These primers are ready to use for conducting real time PCR validation.

Pages 405-413 | Full Text PDF | Supplementary data
Identification and expression analysis of a 3-hydroxy-3-methylglutaryl coenzyme A reductase gene from American ginseng

Qiong Wu, Chao Sun, Shilin Chen

College of Pharmacy, Institute of Materia Medica, Guilin Medical University, Guilin, 541004, China
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China


3-Hydroxy-3-methylgutary coenzyme A reductase (HMGR, EC catalyzes the NAD(P)H-dependent reduction of HMG-CoA to mevalonate, the first committed step in the isoprenoid pathway, which produces the largest group of contemporary natural products. We report the cloning and characterization of a full-length cDNA that encodes HMGR (designated as PqHMGR) from a 4-year-old Panax quinquefolius root, a ginsenoside-producing plant. The full-length cDNA of PqHMGR is 2327 bp, with a 1770 bp open reading frame that encodes a protein containing 589 amino-acids. Bioinformatics analyses revealed that the deduced PqHMGR protein contains two transmembrane domains and one catalytic domain. Three-dimensional modeling revealed that PqHMGR is a new HMGR with a spatial structure similar to that of Homo sapiens with a sequence identity of 57.7%. PqHMGR shows high homology to plant HMGRs, particularly with considerable similarity to the HMG-CoA reductase of Camptotheca acuminata, suggesting that this enzyme may have an important function in terpenoid biosynthesis in P. quinquefolius.
Expression analysis by real-time quantitative PCR indicates that PqHMGR is differentially expressed among tissues, with a strong expression in the leaf and low expression level in the stem. Our results suggest that leaves are crucial to terpenoid biosynthesis in P. quinquefolius. An evolutionary case of HMGR in plants is presented in this study. The results enable further elucidation of the genes involved in ginsenoside biosynthesis in a tissue-specific manner.

Pages 414-420 | Full Text PDF
Fingerprinting and variety identification of rice (Oryza sativa L.) based on simple sequence repeat markers

Yan-fang Zhu, Guo-chen Qin, Jin Hu, Yang Wang, Jian-cheng Wang and Shui-jin Zhu

Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China


Fingerprinting with molecular markers allows precise, objective and rapid variety identification. In this study, simple sequence repeat (SSR) markers were used to fingerprint the forty-eight main commercial rice cultivars under cultivation at present in Zhejiang Province, China, and identify indica and japonica subspecies including eight groups of closely related cultivars. Eighteen of the thirty-two SSR primer pairs were polymorphic and generated a total of 42 distinct reproducible bands with an average of 2.33 bands per primer pair. 41 (97.6%) of the 42 bands amplified were polymorphic. The number of polymorphic bands detected with each primer pair ranged from 1 to 4 with an average of 2.28 per primer pair. The polymorphic information content (PIC) values of each primer pair ranged from 0.10 to 0.50 with an average of 0.31. The UPGMA cluster analysis separated the 48 cultivars into two major groups. The first major cluster consisted of the 34 indica cultivars, and the leaving 14 japonica cultivars formed the second major cluster. Primer pair RM249 or RM250 was able to differentiate between indica and japonica subspecies, respectively. Most of the closely related cultivars were identified with the fingerprinting based on the polymorphic SSR primer pairs, apart from cultivars ‘Xiushui 09’ and ‘Xiushui 114’. The results revealed a narrow genetic diversity among the forty-eight main commercial rice cultivars in Zhejiang Province of China, and combination of SSR with other marker systems might be a potential strategy for fingerprinting database development and authentification of rice cultivars in further study.

Pages 421-426 | Full Text PDF | Supplementary data