7(2) 2014 issue
March 2014 issue
Southern Cross Publishing Group©2014

Plant Omics | March 2014
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Molecular characterization of a WRKY gene from Oryza sativa indica cultivar UKMRC9

Kalaivani Nadarajah1*, Nurfarahana Syuhada Omar1 and Tan Yun Thing2

1School of Environmental Sciences and Natural Resources, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Malaysia
2School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Malaysia

It has been almost two decades since the work was initiated on characterization and function of the WRKY gene. This gene has been implicated in various biological and other developmental processes. It is involved in systemic acquired resistance (SAR) and has the potential to contribute to a wide spectrum resistance in plants. The aim of this study is to isolate, sequence and analyze the WRKY gene from a local Malaysian rice cultivar, UKMRC9. The nucleotide sequence was translated and the 410 amino acid WRKY protein was subjected to physico-chemical, structural and phylogenetic analysis. The results showed that the protein had low level homology with other WRKY proteins. It only showed conservative sequence within the signature WRKY domains. The physico-chemical characteristics predicted the protein as a globular intracellular protein that is hydrophilic with borderline stability and a predicted molecular weight and isoelectric point of 45.1 kDa, and 4.91, respectively. The resolved 3D protein structure of WRKY consisted of four ß-sheet strands with the zinc ion bound by two Cysteine and two Histidine residues, forming a zinc-binding pocket, where the WRKYGQK residues exist. This corresponds to the most N-terminal ß-strand and is the interactive domain of this transcriptional factor.

Pages 63-71 | Full Text PDF | Supplementary data
Marker-assisted verification of Kinggrass (Pennisetum purpureum Schumach. x Pennisetum glaucum [L.] R. Br.)

Charlie D. Dowling1, Byron L. Burson2, and Russell W. Jessup1

1Department of Soil and Crop Sciences, Texas A&M University, College Station, USA
2USDA-ARS, Crop Germplasm Research Unit, Texas A&M University, College Station, USA         

Perennial grasses currently targeted for large-scale deployment as biofuel feedstocks have not been definitively characterized regarding their potential weediness from either or both seed- and rhizome-derived propagules. Kinggrass (napiergrass [Pennisetum purpureum Schumach.] x pearl millet [Pennisetum glaucum {L.} R. Br.]) is unique as a seed-sterile, non-rhizomatous, perennial crop that is capable of high biomass production during the establishment year.  For this study, controlled crosses were made between napiergrass and pearl millet to produce novel Kinggrass genotypes for potential biofuel crop production. Hybrids could not be confirmed by observing morphological traits because all progeny resemble napiergrass.  Consequently, a DNA marker survey of napiergrass and pearl millet was conducted to validate purported napiergrass x pearl millet interspecific hybrids with Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR).  Three paternal, pearl millet-specific markers, as well as six codominant markers, were identified and used to screen putative Kinggrass hybrids.  All paternal-specific EST-SSRs were present in each of the F1 individuals, and the codominant EST-SSR markers fit within the expected transmission ratios.  These EST-SSRs confirmed that all individuals analyzed were true Kinggrass hybrids, and they provide valuable molecular tools towards more rapid development of elite biofuel Kinggrass feedstocks.

Pages 72-79 | Full Text PDF
Wine quality of grapevine ‘Cheongsoo’ and the related metabolites on proton nuclear magnetic resonance (NMR) spectroscopy at the different harvest times

Eun-Ha Chang1, Sung-Min Jung1*, Seo-Jun Park2, Jeong-Ho Noh1, Youn-Young Hur1, Jong Chul Nam, Kyo Sun Park1

1Fruit Research Division National Institute of Horticultural & Herbal Science, RDA, Suwon 440-310, Korea

2Horticulture & Herbal Crop Division, Extension Service Bureau, RDA Suwon 441-707, Korea

Harvest time is major factor of affecting fruit and wine quality of grape. But quantify evaluation of wine quality according to harvest time is too difficult. We conducted this study to identify the metabolites, affecting the sensory, quality and fruit characters of grapevine cv. ‘Cheongsoo’ at the different harvest times, using proton nuclear magnetic resonance (NMR) spectroscopy. Our results showed that there was a clear separation of the spectrum data on the PCA plot at each harvest time. In addition, the S-plot of OPLS-DA was useful to identify the essential metabolites across the harvest times. Tartaric acid (d4.47) was a main factor responsible for the titratable acidity and the acidity of the wine on the sensory test. In addition, both proline (d2.37) and arginine (d3.25) are nitrogen source during wine fermentation, and they were closely associated with the body and balance of the wine on the sensory test. The relative concentration of proline was increased across the harvest times, and it was a positive factor that is associated with changes in the body and balance of the wine. In conclusion, our results indicate that the metabolic profiling based on proton NMR spectroscopy, combined with a multivariate analysis, is useful in identifying the metabolites that are responsible for the quality of grape and wine.

Pages 80-86 | Full Text PDF
Genome-wide analysis of the mildew resistance locus o (MLO) gene family in tomato (Solanum lycopersicum L.)

Yongbing Chen*, Yan Wang*, Haili Zhang

Wenzhou Vocational College of Science and Technology, Wenzhou, Zhejiang, 325006, People’s Republic of China

Mildew resistance locus o (MLO), a plant-specific gene family, plays an important role in plant resistance to powdery mildew (PM). In tomato, a MLO gene associated with PM has been identified. The recently available tomato genome provides an opportunity to conduct a comprehensive overview of the MLO gene family. In the present study, identification and analysis of the MLO gene family was conducted by bioinformatic methods. Results demonstrated that there were at least 17 MLO gene members with encoded protein lengths between 270 and 591 amino acids. Multiple-sequence alignments showed they had seven highly conserved transmembrane domains (TMs), a calmodulin-binding domain, peptide domains I and II, and 30 important amino acid residues for MLO function. Chromosome location results revealed that MLO genes were unevenly distributed in each chromosome. By phylogenetic analysis, the MLO genes from tomato and other plant species were divided into seven groups, some of which contained members from Arabidopsis thaliana, rice, sorghum, grape, poplar, and tomato, indicating that these genes may have evolved prior to the divergence of monocots and dicots. These findings will facilitate the functional characterization and evolutionary relationship of the MLO genes in tomato.

Pages 87-93 | Full Text PDF
Stress-inducible expression of a gene encoding C-repeat binding factor 4 (CBF4) from Arabidopsis improved performance of transgenic maize under drought condition

Huawen Zou1,3†, Xiaohan Wang1, 2†, Conglin Huang1, Jinsong Chen1,2, Xiuhai Zhang1, Chang Luo1, RongYu2, Zhongyi Wu1

1Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
2College of Life Sciences, Capital Normal University, Beijing 10048, China
3College of Agriculture, Yangtze University, Jingzhou 434023, China

Drought is one of the significant limiting factors affecting crops yields in the world. AtCBF4 (C-repeat binding factor 4) is a homolog of the CBF/DREB1 (dehydration-responsive element-binding protein 1) transcription factors that plays important roles during drought tolerance. Here, we report the functional characterization of transgenic maize (inbred line Mo17) expressing AtCBF4 under the control of RD29A (responsive to dehydration 29A) promoter from Arabidopsis. Some morphological and physiological traits related to drought tolerance such as relative water content (RWC), proline and MDA (malondialdehyde) content, etc. were measured. The results show that expression of AtCBF4 in maize significantly enhanced drought tolerance. Under dehydration stress, AtCBF4 transgenic plants L3, L4 and L8 showed lower cell membrane damage (decreased 21-24%), higher relative water content (increased 7-12%), higher total soluble sugars (increased 7-29%), higher proline content (increased 23-37%), better growth and development, greater biomass and higher grain yield (increased 20-25%), compared to wild type. Furthermore, the transgenic lines kept significantly higher germination index and drought tolerance index under PEG condition. These results strongly indicate that expression of AtCBF4 could increase drought tolerances in maize.

Pages 94-101 | Full Text PDF
Nucleotide based validation of the endangered plant Diospyros mespiliformis (Ebenaceae) by evaluating short sequence region of plastid rbcL gene

Abdullah Alaklabi1, Ibrahim A. Arif 2,3,  Sameera O. Bafeel4, Ahmad H. Alfarhan2,3, Anis Ahamed2,3, Jacob Thomas2 and Mohammad A. Bakir2,3*

1Department of Biology, College of Arts and Science, Al-Baha University (BU), Baljurashi, Saudi Arabia
2Department of Botany and Microbiology, College of Science, King Saud University (KSU), Riyadh, Saudi Arabia
3Saudi Biological Society and Prince Sultan Research Chair for Environment and Wildlife, King Saud University
4Department of Biology, King Abdulaziz University (KAU), Jeddah, Saudi Arabia

Diospyros mespiliformis (Hochst. ex A.DC.; Ebenaceae) is a large deciduous medicinal plant. This plant species is currently listed as endangered in Saudi Arabia. Molecular identification of this plant species based on short sequence regions (571 and 664 bp) of plastid rbcL (ribulose-1, 5-biphosphate carboxylase) gene was investigated in this study. The endangered plant specimens were collected from Al-Baha, Saudi Arabia (GPS coordinate: 19.8543987, 41.3059349). Phylogenetic tree inferred from the rbcL gene sequences showed that this species is very closely related with D. brandisiana. Close relationship was also observed among D. bejaudii, D. Philippinensis and D. releyi (=99.7% sequence homology). The partial rbcL gene sequence region (571 bp) that was amplified by rbcL primer-pair rbcLaF-rbcLaR failed to discriminate D. mespiliformis from the closely related plant species, D. brandisiana. In contrast, primer-pair rbcL1F-rbcL724R yielded longer amplicon, discriminated the species from D. brandisiana and demonstrated nucleotide variations in 3 different sites (645G>T; 663A>C; 710C>G). Although D. mespiliformis (EU980712) and D. brandisiana (EU980656) are very closely related species (99.4%); however, studied specimen showed 100% sequence homology with D. mespiliformis and 99.6% with D. brandisiana.  The present findings showed that rbcL short sequence region (664 bp) of plastid rbcL gene, amplified by primer-pair rbcL1F-rbcL724R, can be used for authenticating samples of D. mespiliforformis and may provide help in authentic identification and management process of this medicinally valuable endangered plant species.

Pages 102-107 | Full Text PDF
Bioinformatic characterization and expression analysis of miRNAs in Solanum lycopersicum

Ehsan Valiollahi*1, Mohammad Farsi1, Pedro Fevereiro**2,3, Amin Mirshamsi Kakhki1

1Department of Biotechnology and Plant Breeding, College of Agriculture Ferdowsi University of Mashhad, Mashhad, Iran
2Instituto de Tecnologia Química e Biológica, Laboratório de Biotecnologia de Células Vegetais, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
3Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal

MicroRNAs (miRNAs) are a class of small endogenous non-coding RNAs that modulate gene expression in both plants and animals and are involved in several biological processes, ranging from organ differentiation to biotic and abiotic stress responses. The comparative analysis of the target genes for miRNAs families may augment our understanding of conserved regulatory mechanisms in the plant kingdom. Here, we used a high throughput sequencing and computational approach to identify new miRNAs in S. lycopersicum. Using this approach 18 miRNAs were identified in S.lycopersicum leaf samples. We found a closely related mature sequence for Sly-miR319 that derived from distinct precursor sequences and genomic loci. Furthermore, a qRT-PCR-based assay was performed to validate the prediction of five identified miRNAs. Identification of miRNA targets showed that most of the identified miRNAs such as Sly-miR156a, Sly-miR164, Sly-miR166a, Sly-miR172a, Sly-miR319a and Sly-miR482c, modulate the expression of transcription factors that regulate plant development, signaling and metabolism. In brief, our reliable computational analysis of miRNAs and their targets suggests that many important miRNA-targets circuits are also conserved in S.lycopersicum and fulfill critical roles in growth and development. These findings provide valuable information for functional characterization of miRNAs in S.lycopersicum

Pages 108-116 | Full Text PDF | Supplementary data
Comparative ecophysiological analysis of photosynthesis, biomass allocation, polysaccharide and alkaloid content in three Dendrobium candidum cultivars

Wu Jiang1,2, Bo Jiang3, Nitin Mantri4, Zhigang Wu1, Lingzhi Mao2, Hongfei Lu2,*, Zhengming Tao1,*

1Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005 China
2College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, China
3Department of Biological and Food Engineering, Changshu Institute of Technology, Changshu 215500, China

4School of Applied Sciences, Health Innovations Research Institute, RMIT University, Melbourne, Victoria, Australia

The photosynthesis, plant biomass, alkaloid and polysaccharide contents of three Dendrobium candidum cultivars were compared in order to investigate the differences between their ecophysiological characteristics and provide recommendations for cultivation of Dendrobium candidum. The results demonstrate that leaf perimeter and leaf length in Kuanye was significantly higher (P < 0.05) than the other two cultivars. Compared to Zhaiye and Qingeng, Kuanye had the highest PN value (0.346 µmol m-2 s-1) at PAR of 70 to 90 µmol m-2 s-1
. Further, Kuanye had the highest (P < 0.05) stem polysaccharide content in autumn. On the other hand, stem alkaloid content of one-year old Qingeng was higher than that of Kuanye and Zhaiye in autumn, while two-year old stem of Zhaiye had higher alkaloid content than Kuanye and Qingeng. Interestingly, three-year old Kuanye had higher (P < 0.05) stem alkaloid content than the other two cultivars. These results suggest that the Kuanye cultivar has has superior ecophysiology than the other two cultivars and it can be recommended for cultivation in southeastern China.

Pages 117-122 | Full Text PDF