Articles

7(6) 2014 issue
 
November 2014 issue
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Plant Omics | November 2014
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Genetic and epigenetic diversity of wild and cultivated soybean in local populations in Northern Huang Huai region of China

Xuefei Yan, Xiaodong Liu, Jiandong Li, Hongkun Zhao, Qiyun Li, Yumin Wang, Cuiping Yuan, Ling Zhang, Yingshan Dong*

Jilin Academy of Agricultural Science, Changchun, Jilin 130033, People’s Republic of China
College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, People’s Republic of China

Summary
This study aimed to characterize genetic/epigenetic structures within and between cultivated and wild soybean at local population level in Northern Huang Huai region of China. We analyzed a total of 124 individuals including 94 wild accessions and 30 cultivars using 10 AFLP primer pairs and 8 MSAP primer pairs. The results revealed that the genetic and epigenetic diversity in cultivated soybean exceeded that of wild accessions at local population level. The reason for greater amount of diversity in cultivars could be due to bulking and mixing of cultivated gene pool from geographically distant populations by crossbreeding under condition of artificial domestication, while, gene flow was difficult in natural habitats between wild populations.

Pages 415-423 | Full Text PDF | Supplementary Data PDF


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Enhancement of antioxidant activity and biomass by mineral water in rehmannia root (Rehmannia glutinosa L. purpurea Makino)

Eun Soo Seong, In Seong Hwang
, Nam Jun Kim, Ji Hye Yoo, Jae Geun Lee, Hee Young Kim, Seon-Kang Choi, Soon-Sung Kwon, Hyun Young Kil, 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
University-Industry Cooperation Foundation, Kangwon National University, Chuncheon 200-701, South Korea
Seolmeui Co., Ltd., Gangneung, South Korea
Gangneung Science Industry Foundation, South Korea

Summary
We investigated the functional mechanisms of brine mineral water (BMW) in plants. Antioxidant activities were determined by DPPH free radical-scavenging analysis of crude extracts of Rehmannia glutinosa treated with BMW. The DPPH was measured by value for the density of antioxidant required to absorbance equal to 50% that of a control containing no antioxidant. Plants treated with 0.05-0.1% BMW showed weak antioxidant activity. The concentrations of the principal mineral components, Mg2+, K+, and Sr2+ were increased in samples treated with 1% BMW. Antimicrobial activities of BMW-treated R. glutinosa were determined. The greatest inhibition was against Salmonella typhimurium and Klebsiella pneumoniae.


Pages 424-429 | Full Text PDF

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Comparative analysis of phenolic acid profiles of rice grown under different regions using multivariate analysis

Soo-Yun Park, Jae Kwang Kim, So Young Lee, Sung-Dug Oh, Si Myung Lee, Jae-Seon Jang, Chang-Ihn Yang, Yong-Jae Won, Yunsoo Yeo*

National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea
Division of Life Sciences, Incheon National University, Yeonsu-gu, Incheon 406-772, Republic of Korea
Department of Food & Nutrition, Gachon University, Yeonsu-gu, Incheon 406-799, Republic of Korea
National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea

Summary
This study was conducted to determine the content of phenolic acids in various rice cultivars and to evaluate the impact of genotype versus environmental influence on the phenolic acid profiles of rice grains. Three forms of phenolic acids (free, esterified, and insoluble-bound forms) were identified using gas chromatography-time-of-flight mass spectrometry (GC-TOFMS) in samples of eight Korean rice cultivars (Oryza sativa L.) grown together at two different locations. The phenolic acid profiles were subjected to data mining processes, including principal components analysis (PCA), partial least-squares discriminant analysis (PLS-DA), and orthogonal PLS-DA (OPLS-DA). The results of OPLS-DA showed clear discrimination between the rice samples based on their growing locations rather than by their genotypes. The major components that contributed to the separation between the two regions were sinapic and ferulic acids in both free and bound forms.


Pages 430-437 | Full Text PDF

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Stress-inducible expression of a Cleistogenes songorica ALDH gene enhanced drought tolerance in transgenic Arabidopsis thaliana

Jiyu Zhang, Zhen Duan, Zulfi Jahufer, Shijing An, Yanrong Wang*

State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
Grasslands Research Centre, AgResearch Ltd., Palmerston North 4442, New Zealand

Summary
Aldehyde dehydrogenases (ALDHs) have been considered as general detoxifying enzymes which eliminate abiotic stress in a variety of organisms. The ALDH12A participates in preventing proline toxicity. To targeted mining drought responsive genes from Cleistogenes songorica, a xerophytic grass distributed in the arid-desert grasslands of Inner Mongolia China, cDNA libraries from leaves and roots of drought-stressed seedlings were constructed. Here, we cloned an ALDH12A homologue, CsALDH12A1 (GenBank No. FJ972824). The CsALDH12A1 cDNA is 2,016 bp and encodes a deduced polypeptide of 551 amino acids, approximately 93% identical to the Sorghum bicolor homologue. Quantitative RT-PCR was conducted to examine the expression pattern. The results showed that CsALDH12A1 transcripts accumulated a six-fold abundance in response to drought stress.

Pages 438-444 | Full Text PDF | Supplementary Data PDF


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Genome-wide discovery and analysis of single nucleotide polymorphisms and insertions/ deletions in Juglans regia L. by high-throughput pyrosequencing

Zhuoyi Liao, Kai Feng, Yingnan Chen, Xiaogang Dai, Shuxian Li*, Tongming Yin

The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing 210037, China

Summary
Walnut (Juglans regia L.) is one of the most widespread economic trees in the world. In this study, genome sequencing of J. regia was performed with Roche 454 GS-FLX sequencer. A total of 541,176 high-quality reads were produced with an average read length of 359 bp. We obtained 31,362 contigs (=100 bp) after assembling with the Roche Newbler de novo Assembler (Version 2.8); the total length of the assembly was 15.1 Mb. We then mapped all the sequence reads against the J. regia genome assembly. Totally, 49,202 nucleotide variations were detected including 48,165 single nucleotide polymorphisms (SNPs) and 1,037 insertions/deletions (InDels).

Pages 445-449 | Full Text PDF

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Features of transcriptome in trioecious papaya revealed by a large-scale sequencing of ESTs and comparative analysis in higher plants

Fanchang Zeng, Qingyi Yu, Shaobin Hou, Paul H. Moore, Maqsudel Alam, Ray Ming*

State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China 271018, China
Department of Plant Biology, University of Illinois at Urbana-Champaign, Illinois 61801 USA
Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, Dallas, TX 75252, USA
Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI 96822, USA
Hawaii Agriculture Research Center, Kunia, HI 96759, USA
FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China


Summary
Although the papaya genome has been sequenced, a systematic transcriptome analysis has not been performed. We report the generation of 75,847 raw sequences from Sanger sequencing of normalized cDNA libraries of the papaya cultivar SunUp prepared from 8 tissues collected from 14 developmental stages and the 3 sex types male, female and hermaphrodite. After trimming, processing and analysis, 16,362 unique sequences were obtained. Functional classification and domain analysis of the collection of unique ESTs indicates there are several protein families with functional domain, gene regulatory network and signal transduction that are involved in a variety of developmental processes including sex differentiation. Comparison of the trioecious papaya transcriptome with that of monoecious plants revealed a unique sex related transcriptome profile.

Pages 450-460 | Full Text PDF | Supplementary Data PDF | Supplementary Data Excel

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Growth, dendrobine content and photosynthetic characteristics of Dendrobium nobile under different solar irradiances

Ximin Zhang, Lili Hao, Kun Hong, Yin Yi*

School of Life Science, Guizhou Normal University, Guiyang 550001, China
Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal niversity, Guiyang 550001, China

Summary
Dendrobium nobile is an ornamental and endangered traditional Chinese medicinal plant, which grows naturally on shaded rocks on high mountains or on shaded tree trunks. The aim of this study was to investigate how the seedlings of D. nobile acclimate to different light levels and to obtain an optimal light level for artificial planting and cultivation. The seedlings of D. nobile were grown at four light levels (15, 30, and 58% of solar irradiance, and as a control with 100% of solar irradiance): the plant growth, dendrobine content, photosynthesis, and chlorophyll fluorescence of these seedlings were investigated. The results indicated that plant height, stem diameter, leaf dry mass per unit area (LMA), and light-saturation point (LSP) were higher at 58% of solar irradiance than all other light levels. Meanwhile, net photosynthetic rate (PN) and stomatal conductance (gs) showed their highest (P = 0.05) values at midday (MM) and they were also higher at 58% of solar irradiance.

Pages 461-467 | Full Text PDF

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A eukaryotic translation initiation factor 5A from Tamarix androssowii (Tamarisk), TaeIF5A1, can form a homodimer and interact with other proteins

Liuqiang Wang, Chenxi Xu, Chao Wang, Yucheng Wang*

State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin 150040, China
Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China

Summary
Eukaryotic translation initiation factor 5A (eIF5A) proteins, a highly conserved protein family found in all eukaryotic organisms, are involved in translation elongation, mRNA turnover and decay, cell proliferation, programmed cell death, and abiotic stress responses. However, the precise cellular functions of eIF5A proteins are still not fully known, and especially little is known about their interaction partners. In the present study, we report that an eIF5A protein from T. androssowii, TaeIF5A1, can form homodimers with itself, but cannot form heterodimers with other eIF5A proteins. In addition, TaeIF5A1 can specifically interact with xyloglucan endotransglucosylase/hydrolase (XTH) and ADP-ribosylation factor GTPase activator (Arf GAP), suggesting that TaeIF5A1 may share similar functions with these proteins.

Pages 468-473 | Full Text PDF


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Adaptive traits associated with tolerance to flash flooding during emergence and early seedling growth stages in rice

Salah El-Hendawy*, Nasser Al-Suhaibani, Urs Schmidhalter, Jun-Ichi Sakagami

Plant Production Department, College of Food and Agriculture Sciences, King Saud University, 11451  Riyadh, Saudi Arabia
Agronomy Department, Faculty of Agriculture, Suez Canal University, 41522 Ismailia, Egypt
Department of Plant Sciences, Technische Universität München, Emil-Ramann-Str. 2, D-85350 Freising-Weihenstephan, Germany
Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan

Summary
Dry seeds of 53 contrasting genotypes were sown in soil and watered normally (control) or submerged with 10 cm of water for 17 days. Subsequently, the plants kept under normal rice cultivation conditions for a further 7 days. Among these genotypes, nine lines had been  developed  for  anaerobic  germination  and  submergence  tolerance  (AG + Sub1)  by  IRRI. The length of coleoptile and mesocotyl were measured at different times of submergence period. Length and dry weight of shoot and root were measured during submergence and recovery periods. Emergence date and percentage of plants reaching the floodwater surface were monitored during submergence period. The results showed that tested genotypes were classified into four clusters based on coleoptile and mesocotyl lengths at different times of submergence period using Ward’s method. The coleoptile and mesocotyl of IR06F561 genotype that placed individually in cluster 4 and AG + Sub1 lines in cluster 2 elongated more rapidly than other genotypes under control and submerged treatments.


Pages 474-489 | Full Text PDF

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Little impacts on transcriptome and secondary metabolites of transgenic rice by resveratrol synthase gene

Yang Qin, Soon-Jong Kweon, Soo-Yun Park, Jin-Hyoung Lee, Hee-Jong Woo, Kong-Sik Shin, Hyun-Suk Cho, Soon-Ki Park, and Myung-Ho Lim*

Biosafety Division, National Academy of Agricultural Science, RDA, Jeonju-si, Jeollabuk-do 560-500, Republic of Korea

Summary
In this study, the microarray-based transcriptome profiles of two transgenic resveratrol rice lines, Iksan515 (I515) and Iksan526 (I526) were compared with those of the isogenic DJ variety and a non-transgenic common variety Nagdong (ND) as a reference strain, in order to identify the unpredictable effects of gene insertion
. Only five genes were differentially expressed in both transgenic lines, suggesting that the impact of insertion of RS on the transcriptome was minimal. No gene up- or down-stream from the RS insertion showed more than 2-fold change in expression, implying that overexpression of RS could occur without causing activation of any unexpected gene networks in secondary metabolic pathways.

Pages 490-498 | Full Text PDF | Supplementary Data PDF

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The interaction of arsenic (As) and chromium (Cr) influences growth and antioxidant status in tossa jute (Corchorus olitorius)

Muhammad Kamrul Islam, Mst. Salma Khanam, Si Young Lee, Iftekhar Alam4, 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
Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju 660-701, Korea
National Institute of Biotechnology, Ganakbari, Savar, Dhaka 1349, Bangladesh

Abstract

Co-occurrence of arsenic (As) and chromium (Cr) is observed worldwide. However, their combined effects on plant physiology are not well documented. This experiment was designed to study both individual and combined phytotoxicity of arsenic (As) and chromium (Cr) in jute in terms of plant growth, net photosynthesis, chlorophyll content, oxidative stress and antioxidant enzyme activities. As or Cr stress significantly decreased plant growth, chlorophyll content, chlorophyll florescence (Fv/Fm), photosynthetic rate (Pn) and caused oxidative damage compared to control, indicated by increased MDA and H2O2 contents. The activities of superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), glutathione reductase (GR) and catalase (CAT), were dramatically increased in both varieties compared to control. Moreover, less severe inhibition of plant growth and oxidative damage was observed in O-795 than in O-9897 indicating variety O-795 had more efficient defense system to mitigate heavy metal induced oxidative stress.


Pages 499-509 | Full Text PDF

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Variation in bioactive principles of Korean black raspberry (Rubus coreanus Miquel) during ripening

Tae Kyung Hyun, Yeonggil Rim, Ekyune Kim, Ju-Sung Kim*

Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
College of Pharmacy, Catholic University of Daegu, Gyeongsan 712-702, Republic of Korea

Majors in Plant Resource and Environment, College of Agriculture & Life Sciences, SARI, Jeju National University, Jeju 690-756, Korea
The Research Institute for Subtropical Agriculture and Biotechnology, Jeju National University, Jeju 690-756, Korea

Summary
The present investigation was carried out to appraise the variation in antioxidant and antidiabetic potential of Korean black raspberry during its ripening process. Bioactive principles of Korean black raspberry were evaluated by in vitro antioxidant and antidiabetic assays including free radical scavenging activity, reducing power by Fe3+-Fe2+ transformation and a-glucosidase inhibitory activity. Overall, an extract of unripe fruit contained the highest levels of total phenolic and flavonoid contents, radical scavenging activity, reducing power, and a-glucosidase inhibitory activity, compared with extracts of fruit at other stages of ripening. On the other hand, total anthocyanin content increased with the progression of fruit ripening, indicating that the metabolic shift from proanthocyanidins to anthocyanins in the flavonoid biosynthesis pathways influenced the antioxidant and antidiabetic activities of Korean black raspberry.

Pages 510-516 | Full Text PDF

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Exogenous spermidine improves water stress tolerance of white clover (Trifolium repens L.) involved in antioxidant defence, gene expression and proline metabolism

Zhou Li, Yan Peng*, Xin-Quan Zhang, Ming-Hong Pan, Xiao Ma, Lin-Kai Huang and Yan-Hong Yan

College of Animal Science and Technology, Sichuan Agricultural University, Ya’an 625014, China

Summary
The objectives of the study were to identify the physiological effect and elucidate the possible mechanism caused by exogenous Spd (0.05 mM) in white clover under water stress induced by 20% polyethylene glycol 6000 for 12 days. Water stress elevated significantly the accumulation of reactive oxygen species and malonaldehyde, and resulted in the decrease of cell membrane stability, relative water content and relative growth rate. Spd effectively alleviated the damage effect from water stress. Spd-treated plants showed a promoted the ascorbate-glutathione cycle and maintained greater antioxidant enzyme activities (superoxide dismutase, peroxidase and catalase), as well as higher transcript level of genes encoding antioxidant enzymes than untreated plants. Additionally, the plants treated with Spd under water stress exhibited more accumulated organic solutes including soluble sugar, reducing sugar, betaine and free proline.

Pages 517-526 | Full Text PDF


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Comparison of transcriptomes of chilling- and drought-tolerant and intolerant Nicotiana tabacum varieties and identification of genes associated with stress tolerance

Dahai Hao, Wenguang Ma, Yelong Sheng, Jianbo Zhang, Yunfeng Jin, Huiqin Yang, Zhongguang Li, Shasha Wang, Ming Gong*

School of Life Sciences, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Key Laboratory of Biomass Energy and Environmental Biotechnology of Yunnan Province, Yunnan Normal University, Kunming 650500, China
Root and Tuber Crop Research Institute, Yunnan Normal University
Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China

Summary
The transcriptome changes during chilling or drought stress in model plant tobacco is not clear yet. In this study, transcriptomes of two Nicotiana tabacum cultivars, one from MSK326 (tolerance to chilling and drought) and the other from Yunyan203 (intolerance to chilling and drought) were investigated by Illumina HiseqTM 2000 next-generation sequencing platform. Fourteen digital gene expression (DGE) libraries were sequenced by the same platform. From the sequencing results, 106 million 90-bp quality-reads were obtained from two transcriptomes. The reads were assembled as reference sequences into 97,921 non-redundant unigenes with mean length of 653 nt. After annotation to noted databank, all unigenes were used as references to annotate DGE sequences. Comparing expressed genes of these two cultivars, we found that 4,320 genes were up-regulated and 1,091 genes down-regulated in MSK326.

Pages 527-539 | Full Text PDF | Supplementary Data PDF | Supplementary Data Excel

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Identification and network construction of zinc finger protein (ZFP) genes involved in the rice-Magnaporthe oryzae interaction

Wei-Tao Li, Wei-Lan Chen, Chao Yang, Jing Wang, Lian Yang, Min He, Ji-Chun Wang, Peng Qin, Yu-Ping Wang, Bing-Tian Ma, Shi-Gui Li, Xue-Wei Chen*

Rice research institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China

Summary
Previous studies have shown that some rice ZFP genes from the WRKY, RING, C2H2 and LSD1 families are associated with defense against Magnaporthe oryzae (M. oryzae). However, it remains unknown whether other ZFP families are involved in the rice-M. oryzae interaction. Here, we reported the global characterization of rice ZFP genes involved in the rice-M. oryzae interaction based on bioinfromatics analysis of important rice databases. By analyzing the data obtained from the microarray database, we found that 241 ZFP genes belonging to 27 families were expression-responsive to M. oryzae. Among these ZFP families, a total of 23 ZFP families were newly identified to be involved into the rice-M. oryzae interaction. The expression patterns of the ZFP genes with expression responsiveness to M. oryzae in each family were similar, suggesting that each family might play similar roles in the rice-M. oryzae interaction.

Pages 540-548 | Full Text PDF | Supplementary Data Excel