PLANT OMICS


Differential and developmental stage specific abundance of Zmdreb2a mRNA transcripts under drought stress and root development in Zea mays (L.)

Rakesh Sharma, Manan Azad, Vandana Nunia, S.L. Kothari, Sumita Kachhwaha*

Bioinformatics Infrastructure Facility (DBT-BIF), University of Rajasthan, Jaipur- 302004, Rajasthan, India
Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur- 303002, Rajasthan, India
Departement of Botany, University of Rajasthan, Jaipur- 302004, Rajasthan, India


Abstract
Environmental stress constraints like temperature, drought and salinity affect plant growth, development and productivity negatively. In maize (Zea mays L.) water-deficiency affects flowering, pollination and embryo development. Transgenic plants having drought tolerance is a priority target in maize breeding programs worldwide. Various transcription factors play a key role in plant development and stress management. DRE-Binding Protein 2A (DREB2A) has been shown to play a central role in drought tolerance in Arabidopsis thaliana. The homologue of dreb2a in Zea mays is Zmdreb2a, a well-known transcription factor regulating genes induced under stress conditions. Studies indicated that Zmdreb2a transgenic plants show not only stress tolerance but also growth retardation. It is a major targeted gene for transgenesis to produce drought-tolerant plants. However, to make construct for transgenic plants, there is need to consider functional transcripts and regulating mechanism of Zmdreb2a mRNAs under drought condition. We have analyzed publicly available RNASeq data of leaf meristem, ovary and developing root and used a host of FastQC, Tophat, Cufflinks, Cuffmerge, Cuffdiff and ‘R’ packages to functionally characterize the differentially expressed genes (DEGs). In addition, prediction of protein structure, nuclear localization signals and transactivation domain were performed using cNLS mapper and 9aaTAD prediction tools. Alternative splicing of Zmdreb2a pre-mRNA was shown to be strongly associated with developmental stage and isoforms show fluctuating expression under stress. This study provides putative functional transcripts of Zmdreb2a, and NMD as a regulating mechanism to control their abundance.

Pages 78-86 | Full Text PDF| Supplementary File PDF| doi: 10.21475/POJ.12.02.19.p1763
.........................................................................................................................................................................................................................................

Phytoremediation of some heavy metals using Prosopis juli flora and Conocarpus lancifolius– Soil analysis

Ghalia Saleem Aljeddani

Faculty of Science, University of Jeddah, PO Box 80327, Jeddah 21589, Saudi Arabia

Abstract
Environmental pollution is causing damage to the flora and fauna, resulting in a number of negative impacts on the environment. The present study aims towards evaluation of soil heavy metals (chromium, lead, and nickel) from different locations of Jeddah using leaves of two plant species. Two naturally grown plant species, Prosopis juli flora and Conocarpus lancifolius were collected from four different sites. The soil samples were collected near the factories, main roads, and branch roads in Jeddah. The soil samples were dried and sieved through a 2mm plastic sieve to remove large gravel-sized materials. Soil texture, pH, and EC evaluation were conducted. The amount of Cr, Pb, and Ni was determined using Atomic Absorption Spectrophotometer Model Inductivity coupled plasma emission spectrometer ICP (PARKIN ELEMER). SPSS, ANOVA, and Post-Hoc Test were used to analyze the data. The results showed that the amount of heavy metal in the soil of Prosopis juli flora were between 0.74-54.0μg/g D.wt. for Cr, 0.31-4.64 μg/g D.wt. for Pb and 1.22-24.5 μg/g D.wt. for Ni. The range of Cr, Pb and Ni in the leaves were between 0.04-13.3.0μg/g D.wt. for Cr, 0.06-20.0 μg/g D.wt. for Pb and 0.16-9.0μg/g D.wt. for Ni. For the soil of Prosopis juli flora, the EC ranged between 0.27- 1.05 mS/cm; whereas, pH ranged from 7.29-7.55 and 78.5-96.5% for sand, 1.0-16.5% for silt, and 1.0-6.0 for clay. There was a significant correlation between the soil textures, clay, and silt at selected sites. Phytoremediation is an effective strategy to overcome the effects of heavy metals including Cr, Pb, and Ni that are being absorbed in plants.

Pages 87-92 | Full Text PDF| doi: 10.21475/POJ.12.02.19.p1896
...........................................................................................................................................................................................................................................

Screening of beneficial bacteria associated with Calophyllum brasiliense Cambess so as to develop microbial inoculants for agriculture

Bruno Rogério de Souza*, Lílian Estrela Borges Baldotto, Alessandra Monteiro de Paula, Fabrício Souza Campos, Klever Cristiano Silveira, Pabline Marinho Vieira, Fernando Fabriz Sodré, Jader Galba Busato

University of Brasília, Institute of Chemistry, Darcy Ribeiro University Campus, PO Box 4478, CEP 70910-970, Brasília / DF, Brazil
Federal University of Viçosa, Forest Campus, Rodovia LMG 818, Km 6, CEP 35690-000, Florestal / MG, Brazil
University of Brasília, Faculty of Agronomy and Veterinary Medicine, Darcy Ribeiro University Campus, PO Box 4508, CEP 70910-970, Brasília / DF, Brazil
Federal University of Tocantins, University Campus of Gurupi, PO Box 66, CEP 77402-970, Gurupi / TO, Brazil
Institute Federal Goiano, Department of Biological Sciences, highway Geraldo Silva Nascimento Km-12.5 - Rural Area, CEP 75790-000, Urutaí / GO, Brazil


Abstract
Beneficial bacteria belong to a group of microorganisms that are able to enhance plant growth by several mechanisms. In this study, phosphorus and zinc solubilizing, nitrogen-fixing and indole acetic acid (IAA) producing bacteria associated with C. brasiliensis were screened to develop microbial inoculants (MI) for use in agriculture. Characterization and identification of screened bacteria were also performed. A total of thirty-one nitrogen-fixing bacteria isolates were obtained, of which 28 showed the ability to solubilize phosphorus and 25 to solubilize zinc. The isolate AP-JNFb-3-2, belonging to the genus Pseudomonas, presented the highest value of solubilized phosphorus (100.4 µg mL-1). The isolates AP-JNFb-3-2 and RHI-JMVL-3-1, associated with the genera Pseudomonas and Enterobacter, respectively, showed the highest values for zinc solubilization (147.8 and 147.7 µg mL-1). Isolate RO-LGI.P-3-2, belonging to the genus Pseudomonas, was the most promising for IAA production (0.52 µg mL-1). The results obtained showed the presence of a large diversity of beneficial bacteria associated with C. brasiliensis, which may be explored as MI in agriculture.

Pages 93-101 | Full Text PDF| doi: 10.21475/POJ.12.02.19.p2025
.........................................................................................................................................................................................................................................

Expression analysis of key enzymes involved in the accumulation of iridoid in Rehmannia glutinosa

Hongying Duan, Wenxiao Liu, Yunpeng Zeng, Wenjing Jia, Huihui Wang, Yanqing Zhou*

College of Life Sciences, Henan Normal University, Xinxiang 453007, P. R. China

Abstract
As the traditional Chinese herb, Rehmannia glutinosa (R. glutinosa) has significant effects, and the main active ingredient of R. glutinosa is iridoid. In this study, root, stem and leaf of R. glutinosa at five different growth stages were used, the content of iridoid in R. glutinosa was determinated, and the expression of key enzymes in R. glutinosa was analyzed by quantitative real-time PCR (q-PCR). It was found that the content of iridoid increased continuously during the first three growth stages (Ⅰ- Ⅲ) of R. glutinosa, reached the maximum value in root and leaf at Ⅲ growth stage of R. glutinosa, and the content of iridoid in leaf was not lower as compared with that in root. 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), Geranyl pyrophosphate synthase (GPPS), Geraniol 10-hydroxylase (G10H) and 10-hydroxygeraniol oxidoreductase (10HGO) are key enzymes involved in the synthesis of iridoid in plant, but their expression pattern or level was different in various tissues and stages of R. glutinosa, all appeared tissue specificity, and their expression was related to the accumulation of iridoid in R. glutinosa. Thus, DXR, GPPS, G10H and 10HGO might take part in the synthesis of iridoid in R. glutinosa and could be differently regulated during the growth and development of R. glutinosa, which would provide theoretical basis for the research on secondary metabolism of iridoid in R. glutinosa.

Pages 102-108 | Full Text PDF| doi: 10.21475/POJ.12.02.19.p2221


.........................................................................................................................................................................................................................................


Genome-wide characterization and expression patterns of chitinase genes in the pigeonpea (Cajanus cajan (L.) Millsp.) genome

Ajay Kumar Mahato, Ajay Kumar Sharm, Nagendra Kumar Singh

ICAR-National Research Centre on Plant Biotechnology (NRCPB), IARI, Pusa Campus, New Delhi 110012, India
Meerut Institute of Engineering and Technology, A.P.J. Abdul Kalam Technical
University (APJAKTU), Meerut, Uttar Pradesh 226031, India


Abstract
Plant chitinases are involved in defense as well as a wide range of physiological functions in plants, including germination, embryogenesis, flowering, and senescence. This study was conducted to identify and annotate the chitinase-related genes from the pigeonpea genome version 2.0, their chromosomal localization and phylogenetic relationship with chitinase genes from 13 different plant species. Here, we report the identification of 34 putative chitinase genes in the pigeonpea genome. These 34 genes encode proteins belonging to two functional domain families, and are subdivided into four classes matching four of the five chitinase classes in Arabidopsis. These chitinase genes are present in clusters on the chromosome. We investigated the expression patterns of these chitinases in 29 different tissues at five developmental stages. There was clear clustering of the chitinase genes into three groups based on their expression patterns in tissues. We identified two chitinase genes C_caj-24 and C_caj-25 that were highly expressed in all tissues as well as other chitinase genes with tissue-specific expression, which suggests that they play important roles in plant defense at specific developmental stages. This information on pigeonpea chitinases could be useful for the development of pigeonpea varieties that are resistant to insect pests and fungal diseases.

Pages 109-119 | Full Text PDF| Supplementary Data| doi: 10.21475/POJ.12.02.19.p1825