Articles
8(4) 2015 issue
8(4) 2015 issue
July 2015 issue
Southern Cross Publishing Group©2015
Australia
Australia
Plant Biology Research
Allelopathic effect of Arundo donax, a mediterranean invasive grass
Saeid Abu-Romman*, Tarek Ammari
Department of Biotechnology, Faculty of Agricultural Technology, Al-Balqa Applied University, Al-Salt 19117, Jordan
Department of Water Resources and Environmental Management, Faculty of Agricultural Technology, Al-Balqa Applied University. Al-Salt 19117, Jordan
Abstract
Arundo donax often dominates plant communities by forming large stands throughout Mediterranean climate zones. The objective of this study was the investigation of allelopathic property of A. donax leaves on germination and seedling growth of lentil (Lens culinaris) under laboratory and greenhouse conditions. Four concentrations of aqueous extract (2, 4, 6, and 10%) were compared with the control (distilled water). The germination percentage of lentil seeds was significantly reduced at extract concentrations = 6%. Aqueous extracts of A. donax at concentrations of 6 and 10% significantly reduced the germination percentage of lentil with reduction percentages of 21.3% and 47.4%, respectively. Aqueous extract of A. donax significantly delays the germination process of lentil and reduces the seedling vigor index. Root and shoot growth of lentil seedlings were significantly inhibited by the extract. Root growth was more suppressed than shoot growth in response to A. donax aqueous extract. The results suggested that A. donax aqueous extracts possesses allelopathic potential which could explain in part the dominance competitiveness for this invasive species. Further, the A. donax extract or its active substances could be used for the development of bio-herbicides as alternatives of commercial herbicides.
Pages 287-291 | Full Text PDF
Overexpression of the stress-associated protein (SAP) SAPMR219 in Oryza sativa (var. MR219) increases salt tolerance in transformed Arabidopsis thaliana plants
Poya Hedayati, Hossein Hosseni Monfard, Nurulhikma Md Isa, Duk Ju Hwang, Che Radziah Che Mohd Zain, Md. Imtiaz Uddin, Ab Rahman Zuraida, Ismanizan Ismail, Zamri Zainal*
School of Biosciences and Biotechnology, Faculty Science and Technology, UKM, 43600 Bangi, Selangor, Malaysia
Institute of Systems Biology (INBIOSIS), UKM, 43600 Bangi, Selangor Malaysia
National Academy of Agricultural Science, RDA, Suwon 441-857, Korea
Biotechnology Research Centre, MARDI Headquarters, Persiaran MARDI-UPM, 43400 Serdang, Selangor, Malaysia
Abstract
The stress-associated protein (SAP) family provides salinity stress tolerance in plants. We performed functional studies of SAP MR219, which is a member of the SAP family that is induced after salinity stresses. Computational analysis of the SAP MR219 cDNA clone that was isolated from rice root and shoot revealed significant homology with the SAP gene families from rice (89% to 36% ) and Arabidopsis (44% to 32%). This clone has a 516-bp coding region encoding a 171 amino acid protein with a predicted molecular mass of 18.31 kDa. In silico analysis demonstrated that the SAP MR219 gene product encoded a cytoplasmic zinc finger protein that might perform its functions via protein-protein interactions aided by its AN1 and A20 zinc finger domains. The SAP MR219 gene was isolated, cloned and introduced into Arabidopsis thaliana under the control of the CaMV35S promoter. Five transgenic Arabidopsis lines were obtained by the floral-dip transformation method using Agrobacterium tumefaciens strain GV3101. The survivability of the transgenic lines under salinity stress was evaluated at 100, 150, 200 and 250 mM NaCl. At 250 mM NaCl, the germination rates of transgenic lines were approximately 50%, whereas the wild-type plants did not grow. Our results indicate that SAP MR219 may play a significant role in the response to salt stress tolerance in plants.
Pages 292-299 | Full Text PDF
Genome-wide analysis of the cation/proton antiporter (CPA) super family genes in grapevine (Vitis vinifera L.)
Yuanchun Ma, Jiaoyang Wang, Yan Zhong, Grant R. Cramer, Zong-Ming (Max) Cheng*
The Laboratory of Fruit Crop Systems Biology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu province 210095, The Peoples Republic of China
Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
Abstract
Grapevine (Vitis vinifera L.) is sensitive to salinity. Cation/proton antiporter genes function in regulating ions and pH homeostasis in organisms, enhance salt resistance/tolerance of plants through the vacuolar compartmentalization of Na+, Na+ efflux from the cell, and affecting K+ concentrations. Two previous general bioinformatics studies on CPA gene families, including that of grapevine, showed different numbers of grapevine CPA genes because of using different genome assemblies. In this report, we employed comprehensive bioinformatics and annotation analysis and carefully re-evaluated the previous studies characterizing the CPA proteins. We resolved the discordance of CPA family genes in grapevine, and revealed that duplications contribute contributing to expansion of CPA family genes in grapevine. Furthermore, we identified motifs between grapevine and Arabidopsis and found some motifs are subgroup subgroup-specific motifs. In addition, we investigated the gene structure among the CPA1 subfamily genes in six species. In our analysis 29 CPA genes were identified in the grapevine reference genome. This detailed information on the CPA superfamily in the physiological responses to salinity and osmotic stress and for potential development of salt resistant cultivars.
Pages 300-311 | Full Text PDF | Supplementary Data PDF
Characteristics of photo-oxidation in phosphoenolpyruvate carboxylase-transgenic pollen lines of rice
Zhang Bianjiang*, Zhou Feng, Chen Quanzhan, Hua Chun, Tang Ning, and Jiao Demao
Nanjing Xiaozhuang University, Nanjing 21171, China
Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
Abstract
The JAAS45 pollen line is a new breeding line with high photosynthetic efficiency and high yield. The aim of this study was to elucidate the photo-oxidative characteristics and other inherited physiological traits of the JAAS45 pollen line of rice (Oryza sativa L.) and its parents. The photosynthetic rate, yield components, chlorophyll fluorescence parameters, and antioxidant enzyme activities were measured in leaves of the stable JAAS45 pollen line and its male parent (maize phosphoenolpyruvate carboxylase- (PEPC-) transgenic rice) and female parent (Japonica rice cv. 9516). Under photo-oxidative conditions, the net photosynthetic rate, maximum photochemical efficiency of photosystem II, and photochemical quenching showed smaller decreases in the JAAS45 pollen line than in 9516, its female parent. Non-photochemical quenching was significantly higher in JAAS45 than in 9516 under photo-oxidative conditions, indicating that JAAS45 was more tolerant to photoinhibition and photo-oxidative stress. Higher activities of superoxide dismutase and peroxidase in JAAS45 led to lower accumulation of superoxide radicals, suggesting that JAAS45 has a strong antioxidant capacity. As a result, there was a lower content of malondialdehyde, the product of membrane-lipid peroxidation, in JAAS45 than in 9516. These findings show that JAAS45 is more tolerant than its female parent to photo-oxidation, and that the PEPC gene can be transferred to common rice cultivars through germplasm transfer. The introduction of the photosynthetic PEPC gene into common rice represents a new pathway for breeding photo-oxidation-tolerant rice with high photosynthetic efficiency.
Pages 312-315 | Full Text PDF
Cloning and in silico analysis of two genes, stearoyl-ACP desaturase (PtSAD) and small heat shock protein (PtsHSP), in response to heat stress of Pinellia ternata
Yongbo Duan, Hedong Lu, Mingmei Huang, Fenglan Zhao, Jingtong Teng, Aimin Zhang, Wei Sheng, Yanfang Zhu, Jianping Xue*
Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
Abstract
High temperature has become a major deleterious factor affecting the production of Pinellia ternata. Here, we report the cloning of two genes that have been confirmed to be involved in the response of P. ternata to heat stress. The expression patterns of stearoyl-ACP desaturase gene and small heat shock protein gene of P. ternata during heat stress at 35? were investigated via real-time quantitative RT-PCR, and then the two genes were cloned employing RACE strategy by using the heat-treated materials with peaked mRNA level. The stearoyl-ACP desaturase gene, named PtSAD, was slightly down-regulated within the first four hours of heat stress and up-regulated whereafter, and reached a peak level 48 h later. The small heat shock protein gene, named PtsHSP, was up-regulated since the 4th h of heat stress, with a peaked mRNA level at the 72nd h. The full length of PtSAD gene (GenBank Accession JQ390410) was 1595 bp containing an open reading frame (ORF) of 1185 bp. The full length of PtsHSP cDNA (GenBank Accession JQ390411) was 852 bp containing an ORF of 468 bp. In silico analysis indicated that both PtSAD and PtsHSP are stable hydrophilic proteins. Our study would be helpful for uncovering the functions of PtSAD and PtsHSP, further facilitating us to understand the responses of P. ternata to heat stress.
Pages 316-321 | Full Text PDF
DNA barcoding for identification of Melicope pteleifolia and its close species based on ITS2 sequences
Guanqing Zhang, Dianyun Hou, Dongwei Xu, Sibu Ma, Shaohui Wang, Zongshen Zhang, Xiaoyin Xu, Zongwei Wang, Tongxiang Liu*, Shilin Chen*
Institute of Chinese Minority Traditional Medicine, Minzu University of China, Beijing, Peoples Republic of China
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, Peoples Republic of China
Agricultural College, Henan University of Science and Technology, Luoyang, Peoples Republic of China
Key Laboratory of Fermentation Engineering, Dalian Polytechnic University, Dalian, Peoples Republic of China
Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
Abstract
Melicope pteleifolia (Evodia lepta), named San-cha-ku in traditional Chinese medicine, is commonly used for the treatment of cold and gastropathy. Due to its wide regional distribution and a broad range of closely-related species, M. pteleifolia and its close species have been used in different regions of China. However, it is challenging to identify M. pteleifolia from other close species by only using traditional methods. Here, we report a molecular identification method based on ITS2 sequences of DNA barcoding to differentiate M. pteleifolia from its adulterants or related species. Our results showed that the ITS2 sequence length of M. pteleifolia was 221 bp. The K2P model that assesses the relative variation of the ITS2 regions was used to evaluate the genetic distance of M. pteleifolia from its closely related species. The inter-specifi distance was 0.1187, which is larger than the intra-specifi distance of 0.0116. The identification efficiency of ITS2 was 100% when evaluated with Blastn. The identification of NJ trees showed that M. pteleifolia formed into one clade, which can be distinguished successfully from its adulterants or related species. Our results suggested that M. pteleifolia can be identified stably and accurately through evaluating the ITS2 regions.
Pages 322-326 | Full Text PDF
The heat shock protein 70a from Pyropia seriata increases heat tolerance in Chlamydomonas
San Choi, Sun-Hee Kim, Sung Oh Im, Won-Joong Jeong, Mi Sook Hwang, Eun-Jeong Park, Dong-Woog Choi*
Department of Biology Education and Kumho Life Science Laboratory, Chonnam National University, Kwangju, 500-757, Korea
Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
Marine Algae Research Institute, National Fisheries Research and Development Institute, Mokpo, Korea
Abstract
The heat shock protein 70 (HSP70) molecular chaperones constitute a large family of highly conserved proteins, which are key survival components under stress and normal physiological conditions. Pyropia seriata grows on intertidal rocks, where it is exposed to environmental changes including desiccation and temperature variations. We identified five HSP70 cDNAs from P. seriata transcriptome. An amino acid sequence analysis suggested that PsHSP70a and PsHSP70d are cytosolic HSP70s, whereas PsHSP70b and PsHSP70c are in the mitochondria and PsHSP70e may be transported into the endoplasmic reticulum. Most of the PsHSP70 genes were detected under normal growth and heat stress conditions, except PsHSP70c. Among them, PsHSP70a displayed the strongest response to heat stress. PsHSP70a-transformed Chlamydomonas showed much higher survival and growth rates than those of wild-type under high temperature conditions. These results indicate that the Pyropia genome contains at least five HSP70 genes, and that cytosolic PsHSP70a is involved in high temperature stress tolerance.
Pages 327-334 | Full Text PDF
Establishment of hairy root cultures and analysis of rotenoid in Tibetan medicinal plant Mirabilis himalaica
Xiaozhong Lan, Hong Quan, Xinli Xia, Weilun Yin*
College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
TAAHC-SWU Medicinal Plant Joint R&D Centre, School of Food Sciences, Agricultural and Animal Husbandry College, Tibet University, Nyingchi of Tibet 860000, China
Institute of Plateau Ecology, Agricultural and Animal Husbandry College, Tibet University, Nyingchi of Tibet 860000, China
Abstract
Mirabilis himalaica is an endangered plant species that has been used as an herb by native Tibetan people because of its rotenoid composition. In the present study, the effects of different factors including explants, preculture time and bacterial infection time on the induction rate of hairy roots were investigated. The highest hairy root induction rates were obtained using top leaves as explants, a preculture time of 2 d for young leaves, and Agrobacterium infection of young leaves for 20 min. Genomic PCR confirmed that the rol genes were integrated into the genome of M. himalaica. Different liquid media including MS, 1/2 MS, B5 and 1/2 B5 had significantly different influences on biomass and rotenoid accumulation in hairy root cultures. The hairy root cultures grew better in 1/2 MS and 1/2 B5 than in MS and B5, while a higher level of rotenoid was obtained in hairy root cultures growing in MS and 1/2 MS liquid media. Further, the contents of rotenoid were detected by HPLC in wild roots (0.176 mg.g-1 DW), stems (0.168 mg.g-1 DW) and leaves (0.157 mg.g-1 DW) of M. himalaica. In particular, the hairy root cultures had the highest rotenoid content (0.755 mg.g-1 DW) in 1/2 MS liquid medium, which was 4.3 times higher than in wild type roots (0.176 mg.g-1 DW).
Pages 335-339 | Full Text PDF
Transcriptome analysis of potato phosphorus-tolerant variety seedlings (Atlantic) revealing the gene expression profile under low phosphorus stress
Liqin Li, Xue Zou, Jiao Li, Xiyao Wang*, Su Ni, Fan Liu, Xueli Huang
College of Agronomy, Sichuan Agricultural University, Chengdu, Peoples Republic of China
Abstract
Phosphorus (Pi) is one of several essential plant macronutrients. Potato is the fourth largest food crop in the world, and potato tuber quality is significantly affected by Pi. The potato variety Atlantic has been reported to have a strong tolerance to low Pi conditions; however, the molecular mechanism by which this tolerance occurs remains unclear. In this study, we used 454 GS FLX sequencing technology to investigate the mixed transcriptional profile of this tolerant potato variety after 3, 6, 12, and 24 h of exposure to Pi-deficient conditions. A final Pi concentration of treatment was 10 ΅M. A total of 29,563 unigenes were assembled after sequencing. Of them, 27,255 (92.2%) were annotated using multiple public protein and nucleotide databases. They were categorized into 33 GO functional groups and 220 KEGG pathways, and 5,361 unigenes were assigned to 24 COG groups. Additionally, 733 simple sequence repeats (SSRs) were identified. Real-time PCR was performed to confirm the validity of the sequencing data. Furthermore, we have found 5 most important genes that are active under Pi deficiency such as ribulose diphosphate carboxylase, ribosomal protein, photosystem I and II reaction center, elongation factor and glycolytic enzymes . Our study is the first comprehensive transcriptome analysis of a Pi-tolerant potato variety under low Pi stress. Our results provide useful information that may facilitate further research of important genes involved in plant adaptation to low Pi conditions.
Pages 340-347 | Full Text PDF | Supplementary Data xls
High resolution agarose-based system for single-tube genotyping of fgr and Waxy genes in rice: MAGE to displace PAGE?
Acga Cheng*, Festo Massawe, Ismanizan Ismail, Mohamad Osman, Habibuddin Hashim
Biotechnology Research Centre, School of Biosciences, The National University of Nottingham Malaysia Campus, 43500 Semenyih, Selangor Darul Ehsan, Malaysia
School of Biosciences and Biotechnology, The National University of Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia
Center for Plant Biotechnology, Institute of System Biology, The National University of Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia
Faculty of Plantation and Agrotechnology, MARA University of Technology, 40450 Shah Alam, Selangor Darul Ehsan, Malaysia
Agric Inov Resources, 08000 Sungai Petani, Kedah Darul Aman, Malaysia
Abstract
Aroma and amylose content are the key determinants of grain quality and commercial value in rice (Oryza sativa L.). Here, we report a novel agarose-based multiplex polymerase chain reaction (PCR)-assay for the unambiguous identification of genes controlling aroma (fgr) and amylose content (Wx) traits in rice. The multiplex assay was developed following the validation of two previously reported gene-specific primers, namely, the fgr-SNP and Wx-SSR. Twenty aromatic and non-aromatic rice genotypes with a wide range of variation in amylose content were used in this study. Optimization of primer concentration and critical parameters for thermal cycling, inclusive of cycle number and annealing temperature, were performed to obtain optimal results for the multiplex amplification. The resulting amplification products displayed well-differentiated allelic variants of both fgr and Wx genes on a 3% MetaPhor agarose gel, at the cost of less than $0.15 per sample. MetaPhor agarose gel electrophoresis (MAGE) was effectively employed as a genotyping method which offers an alternative to polyacrylamide gel electrophoresis (PAGE); a system, commonly used in rice research, that can be technically challenging and time-consuming. Without the need of expensive probes or specialized equipment, this newly developed multiplex assay is suitable for researchers, whose studies are dependent on mass genotyping, and in molecular laboratories with limited resources.
Pages 348-352 | Full Text PDF
In silico genome-wide analysis of the WRKY gene family in Salix arbutifolia
Guodong Rao, Jinkai Sui, Jianguo Zhang*
State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, Republic of China
Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Republic of China
Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, Republic of China
Abstract
The WRKY genes encode transcriptional regulators that function in response to biotic and abiotic stress in plants. Thus far, no detailed classification and expression profiles of WRKY genes are available for willow. In this study, a comprehensive computational analysis identified 89 WRKY family genes in willow (Salix arbutifolia) by the in silico cloning method. Based on the results of phylogenetic analysis and the number of WRKY motifs, the WRKY genes were classified into group I to group III. The expression profile was analyzed by the transcriptome data in different tissues. A comparative analysis of Salix, Populus trichocarpa, and Arabidopsis thaliana were performed, and the Salix WRKY family had a similar number as Populus and a larger size than the Arabidopsis. A detailed phylogenetic analysis between Salix and Populus revealed that the WRKY genes had evolved from the same genome duplication event. These results will be useful for future functional analyses of the WRKY family genes.
Pages 353-360 | Full Text PDF
Transcriptomics and comparative analysis of three Juglans species; J. regia, J. sigillata and J. cathayensis
Tao Wu, Liangjun Xiao, Shaoyu Chen, Delu Ning*
Institute of Economic Forest, Yunnan Academy of Forestry, Kunming 650201, China
Abstract
Walnut (Juglans) has been globally cultivated for its valuable nut, which has abundant polyunsaturated fatty acids and proteins. In China, only the Persian or English walnut (J. regia) and Yunnan or iron walnut (J. sigillata) are commercially cultivated for nut production, and Chinese butternut (J. cathayensis) is commonly used as rootstock and potential breeding material. Only few genomic resources are available for these non-model plants, particularly the last two species. Hence, we present the sequencing, de novo assembly and annotation of transcriptomes from fresh leaves of the three Juglans species by RNA-seq technology and bioinformatics analysis to discover a collection of SSR and SNP markers, to be used by researchers for further genetic improvements. In total, 59035134 (7.38 G bp), 43949544 (5.5 G bp) and 58609226 (7.32 G bp) high quality clean reads were generated from cDNA libraries of J. regia, J. sigillata and J. cathayensis, respectively. A total of 192360 unigenes longer than 200 bp were de novo assembled, 92858 (48.20%) unigenes were annotated, and 32110 CDSs (16.70%) were deduced. The potential function of each unigene was classified based on COG and GO database. 5683 differentially expressed genes (DEGs) were enriched in KEGG pathways. A total of 41141 SSRs and 206355 SNPs were identified as potential molecular markers. The raw reads of transcriptome from J. regia (accession number SRR1767234), J. sigillata (accession number SRR1767236) and J. cathayensis (accession number SRR1767237) were deposited in NCBI database. Our transcriptome data enrich the genomic resource of Juglans species and will be essential to accelerate the process of molecular research and breeding.
Pages 361-371 | Full Text PDF | Supplementary Data xls
Allelopathic effect of Arundo donax, a mediterranean invasive grass
Saeid Abu-Romman*, Tarek Ammari
Department of Biotechnology, Faculty of Agricultural Technology, Al-Balqa Applied University, Al-Salt 19117, Jordan
Department of Water Resources and Environmental Management, Faculty of Agricultural Technology, Al-Balqa Applied University. Al-Salt 19117, Jordan
Abstract
Arundo donax often dominates plant communities by forming large stands throughout Mediterranean climate zones. The objective of this study was the investigation of allelopathic property of A. donax leaves on germination and seedling growth of lentil (Lens culinaris) under laboratory and greenhouse conditions. Four concentrations of aqueous extract (2, 4, 6, and 10%) were compared with the control (distilled water). The germination percentage of lentil seeds was significantly reduced at extract concentrations = 6%. Aqueous extracts of A. donax at concentrations of 6 and 10% significantly reduced the germination percentage of lentil with reduction percentages of 21.3% and 47.4%, respectively. Aqueous extract of A. donax significantly delays the germination process of lentil and reduces the seedling vigor index. Root and shoot growth of lentil seedlings were significantly inhibited by the extract. Root growth was more suppressed than shoot growth in response to A. donax aqueous extract. The results suggested that A. donax aqueous extracts possesses allelopathic potential which could explain in part the dominance competitiveness for this invasive species. Further, the A. donax extract or its active substances could be used for the development of bio-herbicides as alternatives of commercial herbicides.
Pages 287-291 | Full Text PDF
Overexpression of the stress-associated protein (SAP) SAPMR219 in Oryza sativa (var. MR219) increases salt tolerance in transformed Arabidopsis thaliana plants
Poya Hedayati, Hossein Hosseni Monfard, Nurulhikma Md Isa, Duk Ju Hwang, Che Radziah Che Mohd Zain, Md. Imtiaz Uddin, Ab Rahman Zuraida, Ismanizan Ismail, Zamri Zainal*
School of Biosciences and Biotechnology, Faculty Science and Technology, UKM, 43600 Bangi, Selangor, Malaysia
Institute of Systems Biology (INBIOSIS), UKM, 43600 Bangi, Selangor Malaysia
National Academy of Agricultural Science, RDA, Suwon 441-857, Korea
Biotechnology Research Centre, MARDI Headquarters, Persiaran MARDI-UPM, 43400 Serdang, Selangor, Malaysia
Abstract
The stress-associated protein (SAP) family provides salinity stress tolerance in plants. We performed functional studies of SAP MR219, which is a member of the SAP family that is induced after salinity stresses. Computational analysis of the SAP MR219 cDNA clone that was isolated from rice root and shoot revealed significant homology with the SAP gene families from rice (89% to 36% ) and Arabidopsis (44% to 32%). This clone has a 516-bp coding region encoding a 171 amino acid protein with a predicted molecular mass of 18.31 kDa. In silico analysis demonstrated that the SAP MR219 gene product encoded a cytoplasmic zinc finger protein that might perform its functions via protein-protein interactions aided by its AN1 and A20 zinc finger domains. The SAP MR219 gene was isolated, cloned and introduced into Arabidopsis thaliana under the control of the CaMV35S promoter. Five transgenic Arabidopsis lines were obtained by the floral-dip transformation method using Agrobacterium tumefaciens strain GV3101. The survivability of the transgenic lines under salinity stress was evaluated at 100, 150, 200 and 250 mM NaCl. At 250 mM NaCl, the germination rates of transgenic lines were approximately 50%, whereas the wild-type plants did not grow. Our results indicate that SAP MR219 may play a significant role in the response to salt stress tolerance in plants.
Pages 292-299 | Full Text PDF
Genome-wide analysis of the cation/proton antiporter (CPA) super family genes in grapevine (Vitis vinifera L.)
Yuanchun Ma, Jiaoyang Wang, Yan Zhong, Grant R. Cramer, Zong-Ming (Max) Cheng*
The Laboratory of Fruit Crop Systems Biology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu province 210095, The Peoples Republic of China
Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
Abstract
Grapevine (Vitis vinifera L.) is sensitive to salinity. Cation/proton antiporter genes function in regulating ions and pH homeostasis in organisms, enhance salt resistance/tolerance of plants through the vacuolar compartmentalization of Na+, Na+ efflux from the cell, and affecting K+ concentrations. Two previous general bioinformatics studies on CPA gene families, including that of grapevine, showed different numbers of grapevine CPA genes because of using different genome assemblies. In this report, we employed comprehensive bioinformatics and annotation analysis and carefully re-evaluated the previous studies characterizing the CPA proteins. We resolved the discordance of CPA family genes in grapevine, and revealed that duplications contribute contributing to expansion of CPA family genes in grapevine. Furthermore, we identified motifs between grapevine and Arabidopsis and found some motifs are subgroup subgroup-specific motifs. In addition, we investigated the gene structure among the CPA1 subfamily genes in six species. In our analysis 29 CPA genes were identified in the grapevine reference genome. This detailed information on the CPA superfamily in the physiological responses to salinity and osmotic stress and for potential development of salt resistant cultivars.
Pages 300-311 | Full Text PDF | Supplementary Data PDF
Characteristics of photo-oxidation in phosphoenolpyruvate carboxylase-transgenic pollen lines of rice
Zhang Bianjiang*, Zhou Feng, Chen Quanzhan, Hua Chun, Tang Ning, and Jiao Demao
Nanjing Xiaozhuang University, Nanjing 21171, China
Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
Abstract
The JAAS45 pollen line is a new breeding line with high photosynthetic efficiency and high yield. The aim of this study was to elucidate the photo-oxidative characteristics and other inherited physiological traits of the JAAS45 pollen line of rice (Oryza sativa L.) and its parents. The photosynthetic rate, yield components, chlorophyll fluorescence parameters, and antioxidant enzyme activities were measured in leaves of the stable JAAS45 pollen line and its male parent (maize phosphoenolpyruvate carboxylase- (PEPC-) transgenic rice) and female parent (Japonica rice cv. 9516). Under photo-oxidative conditions, the net photosynthetic rate, maximum photochemical efficiency of photosystem II, and photochemical quenching showed smaller decreases in the JAAS45 pollen line than in 9516, its female parent. Non-photochemical quenching was significantly higher in JAAS45 than in 9516 under photo-oxidative conditions, indicating that JAAS45 was more tolerant to photoinhibition and photo-oxidative stress. Higher activities of superoxide dismutase and peroxidase in JAAS45 led to lower accumulation of superoxide radicals, suggesting that JAAS45 has a strong antioxidant capacity. As a result, there was a lower content of malondialdehyde, the product of membrane-lipid peroxidation, in JAAS45 than in 9516. These findings show that JAAS45 is more tolerant than its female parent to photo-oxidation, and that the PEPC gene can be transferred to common rice cultivars through germplasm transfer. The introduction of the photosynthetic PEPC gene into common rice represents a new pathway for breeding photo-oxidation-tolerant rice with high photosynthetic efficiency.
Pages 312-315 | Full Text PDF
Cloning and in silico analysis of two genes, stearoyl-ACP desaturase (PtSAD) and small heat shock protein (PtsHSP), in response to heat stress of Pinellia ternata
Yongbo Duan, Hedong Lu, Mingmei Huang, Fenglan Zhao, Jingtong Teng, Aimin Zhang, Wei Sheng, Yanfang Zhu, Jianping Xue*
Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
Abstract
High temperature has become a major deleterious factor affecting the production of Pinellia ternata. Here, we report the cloning of two genes that have been confirmed to be involved in the response of P. ternata to heat stress. The expression patterns of stearoyl-ACP desaturase gene and small heat shock protein gene of P. ternata during heat stress at 35? were investigated via real-time quantitative RT-PCR, and then the two genes were cloned employing RACE strategy by using the heat-treated materials with peaked mRNA level. The stearoyl-ACP desaturase gene, named PtSAD, was slightly down-regulated within the first four hours of heat stress and up-regulated whereafter, and reached a peak level 48 h later. The small heat shock protein gene, named PtsHSP, was up-regulated since the 4th h of heat stress, with a peaked mRNA level at the 72nd h. The full length of PtSAD gene (GenBank Accession JQ390410) was 1595 bp containing an open reading frame (ORF) of 1185 bp. The full length of PtsHSP cDNA (GenBank Accession JQ390411) was 852 bp containing an ORF of 468 bp. In silico analysis indicated that both PtSAD and PtsHSP are stable hydrophilic proteins. Our study would be helpful for uncovering the functions of PtSAD and PtsHSP, further facilitating us to understand the responses of P. ternata to heat stress.
Pages 316-321 | Full Text PDF
DNA barcoding for identification of Melicope pteleifolia and its close species based on ITS2 sequences
Guanqing Zhang, Dianyun Hou, Dongwei Xu, Sibu Ma, Shaohui Wang, Zongshen Zhang, Xiaoyin Xu, Zongwei Wang, Tongxiang Liu*, Shilin Chen*
Institute of Chinese Minority Traditional Medicine, Minzu University of China, Beijing, Peoples Republic of China
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, Peoples Republic of China
Agricultural College, Henan University of Science and Technology, Luoyang, Peoples Republic of China
Key Laboratory of Fermentation Engineering, Dalian Polytechnic University, Dalian, Peoples Republic of China
Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
Abstract
Melicope pteleifolia (Evodia lepta), named San-cha-ku in traditional Chinese medicine, is commonly used for the treatment of cold and gastropathy. Due to its wide regional distribution and a broad range of closely-related species, M. pteleifolia and its close species have been used in different regions of China. However, it is challenging to identify M. pteleifolia from other close species by only using traditional methods. Here, we report a molecular identification method based on ITS2 sequences of DNA barcoding to differentiate M. pteleifolia from its adulterants or related species. Our results showed that the ITS2 sequence length of M. pteleifolia was 221 bp. The K2P model that assesses the relative variation of the ITS2 regions was used to evaluate the genetic distance of M. pteleifolia from its closely related species. The inter-specifi distance was 0.1187, which is larger than the intra-specifi distance of 0.0116. The identification efficiency of ITS2 was 100% when evaluated with Blastn. The identification of NJ trees showed that M. pteleifolia formed into one clade, which can be distinguished successfully from its adulterants or related species. Our results suggested that M. pteleifolia can be identified stably and accurately through evaluating the ITS2 regions.
Pages 322-326 | Full Text PDF
The heat shock protein 70a from Pyropia seriata increases heat tolerance in Chlamydomonas
San Choi, Sun-Hee Kim, Sung Oh Im, Won-Joong Jeong, Mi Sook Hwang, Eun-Jeong Park, Dong-Woog Choi*
Department of Biology Education and Kumho Life Science Laboratory, Chonnam National University, Kwangju, 500-757, Korea
Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
Marine Algae Research Institute, National Fisheries Research and Development Institute, Mokpo, Korea
Abstract
The heat shock protein 70 (HSP70) molecular chaperones constitute a large family of highly conserved proteins, which are key survival components under stress and normal physiological conditions. Pyropia seriata grows on intertidal rocks, where it is exposed to environmental changes including desiccation and temperature variations. We identified five HSP70 cDNAs from P. seriata transcriptome. An amino acid sequence analysis suggested that PsHSP70a and PsHSP70d are cytosolic HSP70s, whereas PsHSP70b and PsHSP70c are in the mitochondria and PsHSP70e may be transported into the endoplasmic reticulum. Most of the PsHSP70 genes were detected under normal growth and heat stress conditions, except PsHSP70c. Among them, PsHSP70a displayed the strongest response to heat stress. PsHSP70a-transformed Chlamydomonas showed much higher survival and growth rates than those of wild-type under high temperature conditions. These results indicate that the Pyropia genome contains at least five HSP70 genes, and that cytosolic PsHSP70a is involved in high temperature stress tolerance.
Pages 327-334 | Full Text PDF
Establishment of hairy root cultures and analysis of rotenoid in Tibetan medicinal plant Mirabilis himalaica
Xiaozhong Lan, Hong Quan, Xinli Xia, Weilun Yin*
College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
TAAHC-SWU Medicinal Plant Joint R&D Centre, School of Food Sciences, Agricultural and Animal Husbandry College, Tibet University, Nyingchi of Tibet 860000, China
Institute of Plateau Ecology, Agricultural and Animal Husbandry College, Tibet University, Nyingchi of Tibet 860000, China
Abstract
Mirabilis himalaica is an endangered plant species that has been used as an herb by native Tibetan people because of its rotenoid composition. In the present study, the effects of different factors including explants, preculture time and bacterial infection time on the induction rate of hairy roots were investigated. The highest hairy root induction rates were obtained using top leaves as explants, a preculture time of 2 d for young leaves, and Agrobacterium infection of young leaves for 20 min. Genomic PCR confirmed that the rol genes were integrated into the genome of M. himalaica. Different liquid media including MS, 1/2 MS, B5 and 1/2 B5 had significantly different influences on biomass and rotenoid accumulation in hairy root cultures. The hairy root cultures grew better in 1/2 MS and 1/2 B5 than in MS and B5, while a higher level of rotenoid was obtained in hairy root cultures growing in MS and 1/2 MS liquid media. Further, the contents of rotenoid were detected by HPLC in wild roots (0.176 mg.g-1 DW), stems (0.168 mg.g-1 DW) and leaves (0.157 mg.g-1 DW) of M. himalaica. In particular, the hairy root cultures had the highest rotenoid content (0.755 mg.g-1 DW) in 1/2 MS liquid medium, which was 4.3 times higher than in wild type roots (0.176 mg.g-1 DW).
Pages 335-339 | Full Text PDF
Transcriptome analysis of potato phosphorus-tolerant variety seedlings (Atlantic) revealing the gene expression profile under low phosphorus stress
Liqin Li, Xue Zou, Jiao Li, Xiyao Wang*, Su Ni, Fan Liu, Xueli Huang
College of Agronomy, Sichuan Agricultural University, Chengdu, Peoples Republic of China
Abstract
Phosphorus (Pi) is one of several essential plant macronutrients. Potato is the fourth largest food crop in the world, and potato tuber quality is significantly affected by Pi. The potato variety Atlantic has been reported to have a strong tolerance to low Pi conditions; however, the molecular mechanism by which this tolerance occurs remains unclear. In this study, we used 454 GS FLX sequencing technology to investigate the mixed transcriptional profile of this tolerant potato variety after 3, 6, 12, and 24 h of exposure to Pi-deficient conditions. A final Pi concentration of treatment was 10 ΅M. A total of 29,563 unigenes were assembled after sequencing. Of them, 27,255 (92.2%) were annotated using multiple public protein and nucleotide databases. They were categorized into 33 GO functional groups and 220 KEGG pathways, and 5,361 unigenes were assigned to 24 COG groups. Additionally, 733 simple sequence repeats (SSRs) were identified. Real-time PCR was performed to confirm the validity of the sequencing data. Furthermore, we have found 5 most important genes that are active under Pi deficiency such as ribulose diphosphate carboxylase, ribosomal protein, photosystem I and II reaction center, elongation factor and glycolytic enzymes . Our study is the first comprehensive transcriptome analysis of a Pi-tolerant potato variety under low Pi stress. Our results provide useful information that may facilitate further research of important genes involved in plant adaptation to low Pi conditions.
Pages 340-347 | Full Text PDF | Supplementary Data xls
High resolution agarose-based system for single-tube genotyping of fgr and Waxy genes in rice: MAGE to displace PAGE?
Acga Cheng*, Festo Massawe, Ismanizan Ismail, Mohamad Osman, Habibuddin Hashim
Biotechnology Research Centre, School of Biosciences, The National University of Nottingham Malaysia Campus, 43500 Semenyih, Selangor Darul Ehsan, Malaysia
School of Biosciences and Biotechnology, The National University of Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia
Center for Plant Biotechnology, Institute of System Biology, The National University of Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia
Faculty of Plantation and Agrotechnology, MARA University of Technology, 40450 Shah Alam, Selangor Darul Ehsan, Malaysia
Agric Inov Resources, 08000 Sungai Petani, Kedah Darul Aman, Malaysia
Abstract
Aroma and amylose content are the key determinants of grain quality and commercial value in rice (Oryza sativa L.). Here, we report a novel agarose-based multiplex polymerase chain reaction (PCR)-assay for the unambiguous identification of genes controlling aroma (fgr) and amylose content (Wx) traits in rice. The multiplex assay was developed following the validation of two previously reported gene-specific primers, namely, the fgr-SNP and Wx-SSR. Twenty aromatic and non-aromatic rice genotypes with a wide range of variation in amylose content were used in this study. Optimization of primer concentration and critical parameters for thermal cycling, inclusive of cycle number and annealing temperature, were performed to obtain optimal results for the multiplex amplification. The resulting amplification products displayed well-differentiated allelic variants of both fgr and Wx genes on a 3% MetaPhor agarose gel, at the cost of less than $0.15 per sample. MetaPhor agarose gel electrophoresis (MAGE) was effectively employed as a genotyping method which offers an alternative to polyacrylamide gel electrophoresis (PAGE); a system, commonly used in rice research, that can be technically challenging and time-consuming. Without the need of expensive probes or specialized equipment, this newly developed multiplex assay is suitable for researchers, whose studies are dependent on mass genotyping, and in molecular laboratories with limited resources.
Pages 348-352 | Full Text PDF
In silico genome-wide analysis of the WRKY gene family in Salix arbutifolia
Guodong Rao, Jinkai Sui, Jianguo Zhang*
State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, Republic of China
Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Republic of China
Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, Republic of China
Abstract
The WRKY genes encode transcriptional regulators that function in response to biotic and abiotic stress in plants. Thus far, no detailed classification and expression profiles of WRKY genes are available for willow. In this study, a comprehensive computational analysis identified 89 WRKY family genes in willow (Salix arbutifolia) by the in silico cloning method. Based on the results of phylogenetic analysis and the number of WRKY motifs, the WRKY genes were classified into group I to group III. The expression profile was analyzed by the transcriptome data in different tissues. A comparative analysis of Salix, Populus trichocarpa, and Arabidopsis thaliana were performed, and the Salix WRKY family had a similar number as Populus and a larger size than the Arabidopsis. A detailed phylogenetic analysis between Salix and Populus revealed that the WRKY genes had evolved from the same genome duplication event. These results will be useful for future functional analyses of the WRKY family genes.
Pages 353-360 | Full Text PDF
Transcriptomics and comparative analysis of three Juglans species; J. regia, J. sigillata and J. cathayensis
Tao Wu, Liangjun Xiao, Shaoyu Chen, Delu Ning*
Institute of Economic Forest, Yunnan Academy of Forestry, Kunming 650201, China
Abstract
Walnut (Juglans) has been globally cultivated for its valuable nut, which has abundant polyunsaturated fatty acids and proteins. In China, only the Persian or English walnut (J. regia) and Yunnan or iron walnut (J. sigillata) are commercially cultivated for nut production, and Chinese butternut (J. cathayensis) is commonly used as rootstock and potential breeding material. Only few genomic resources are available for these non-model plants, particularly the last two species. Hence, we present the sequencing, de novo assembly and annotation of transcriptomes from fresh leaves of the three Juglans species by RNA-seq technology and bioinformatics analysis to discover a collection of SSR and SNP markers, to be used by researchers for further genetic improvements. In total, 59035134 (7.38 G bp), 43949544 (5.5 G bp) and 58609226 (7.32 G bp) high quality clean reads were generated from cDNA libraries of J. regia, J. sigillata and J. cathayensis, respectively. A total of 192360 unigenes longer than 200 bp were de novo assembled, 92858 (48.20%) unigenes were annotated, and 32110 CDSs (16.70%) were deduced. The potential function of each unigene was classified based on COG and GO database. 5683 differentially expressed genes (DEGs) were enriched in KEGG pathways. A total of 41141 SSRs and 206355 SNPs were identified as potential molecular markers. The raw reads of transcriptome from J. regia (accession number SRR1767234), J. sigillata (accession number SRR1767236) and J. cathayensis (accession number SRR1767237) were deposited in NCBI database. Our transcriptome data enrich the genomic resource of Juglans species and will be essential to accelerate the process of molecular research and breeding.
Pages 361-371 | Full Text PDF | Supplementary Data xls