PLANT OMICs

Encompassing plant and animal OMICs

Drought sensitive maize inbred shows more oxidative damage and higher ROS scavenging enzymes, but not glyoxalases than a tolerant one at seedling stage

Md. Motiar Rohman*, Shahnewaz Begum, M.Z.A. Talukder,  Afsana Hoque Akhi, M. Amiruzzaman, A. F. M. S. Ahsan and Zakir Hossain


Molecular Breeding Laboratory, Bangladesh Agricultural Research Institute, Gazipur-1701, Bangladesh

Research Biologist, Swift Current Research and Development Centre, Agriculture and Agri-Food Canada

Abstract

This study was undertaken to unveil the oxidative stress tolerance mechanism in maize seedlings under drought.  The level of oxidative stress and involvement of antioxidant and glyoxalase systems were investigated in seedlings of two maize inbreds: P134, a relatively drought tolerant, and P142, a drought susceptible inbred subjected to water deficit for 7 days and then rewatered to reveal the mechanism of oxidative stress tolerance under drought. Water content, chlorophyll (Chl), reactive oxygen species (ROS), lipid peroxidation, methylglyoxal (MG), lipoxygenase (LOX) activity, enzymatic and non-enzymatic antioxidants and glyoxalases status were investigated in the uppermost fully expanded leaves. The superoxide (O2•-) generation rate, hydrogen peroxide (H2O2), lipid peroxidationand methylglyoxal (MG) contents as well as lipoxygenase (LOX) activity were higher in P142 throughout the drought period. Conversely, relative water content (RWC), Chl, carotenoid (Car) and proline contents were remarkably higher in P134. However, in rewatering, recovery of Chl and Car were higher in P142. The reduced glutathione (GSH), ascorbic acid (ASA) and their redox homeostasis indicated more oxidative damage in P142. The ROS scavenging enzymes like superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX) and dehydroascorbate reductase (DHAR) activities were comparatively higher in P142 under drought, while catalase (CAT), monodehydroasacorbate reductase (MDHAR) and glutathione reductase (GR) activities were higher in P134. Though the activity of GST increased in both inbreds, activities of glyoxalase-I (Gly-I) and glyoxalse-II (Gly-II) increased only in P134. In rewatering, activities of most of the enzymes decreased in both inbreds. Taken together, the non-enzymatic antioxidant system was stronger in P134, but the higher SOD, POD, APX, GPX and DHAR activities in P142 suggesting that these enzymes might involve in cellular protection through reducing oxidative damage.

Pages 220-232 | DOI: 10.21475/poj.16.09.04.pne31 |   Full Text PDF 

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Different tobacco cultivation regions lead to variations in tobacco leaf gene expression profiles involved in carbonhydrate metabolism and ion transportation

LiMing Lu, WenShan Xu, Yong Chen, ZongXiang Tang, Lei Liu and LiQin Li*

Agronomy College, Sichuan Agricultural University, Huimin Road 211#, Wenjiang, Chengdu, Sichuan Province, 611130, People’s Republic of China

Abstract

Tobacco is an important crop economically in China, and tobacco quality varies across its cultivated regions. To unveil the mechanisms that result in such varied tobacco leaf qualities, we have analyzed the tobacco leaf gene expression profiles of four areas in Sichuan province, China. Tobacco leaves in the 12th position were collected from plants in four different regions, namely Huili, Miyi, Xingwen and Jiange, and submitted for microarray analysis. Gene expression levels from Miyi group were used as control, and that from Jiange, Xingwen and Huili were compared to Miyi group respectively. A total of 5154 differentially expressed genes (DEGs) were detected, among which 2731 genes were up-regulated and 2423 genes were down-regulated. Based on gene ontology (GO) analysis, significant DEGs were classified into 15 categories (P0.05) based on properties pertaining to transferase activity, transmembrane transporter activity, binding, transcription regulator activity, metabolic processes, secondary metabolic processes, etc. Our results also show that these DEGs were significantly enriched in 11 pathways, including metabolic pathways, starch and sucrose metabolism, photosynthesis, etc. Our study suggests that many of the genes involved in various plant physiological and biochemical processes significantly differed across these four different regions, which may explain their differences in tobacco leaf quality.  

Pages 233-239 | DOI: 10.21475/poj.16.09.04.pne32 |   Full Text PDF   

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Gas exchange, photosystem II photochemistry, and the antioxidant system of longan plant (Dimocarpus longan Lour.) leaves in response to lead (Pb) stress

Yanna Wang, Yongyu Li, Cuilan Ma, Dongliang Qiu*

College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

Abstract

Longan is one of the most important subtropical fruit trees and a famous special product in south China. Increased fruit demand brings longan cultivation to Pb-affected regions. Seedlings of longan (cv. Wulongling) in pots with sands were irrigated daily for 30 d with a freshly prepared nutrient solution containing different concentrations of Pb(NO3)2 (0, 100 , 200 , 400 , 600 , 800  and 1000 mg L-1) to determine physiological and biochemical responses of longan seedlings to various levels of lead (Pb). The results indicated that Pb stress substantially inhibited the growth of longan plants and markedly declined in their dry biomass. However, when the plants were grown at 100 mg L-1 Pb, the growth and dry biomass of the plants showed no significant difference from control. In addition, the chlorophyll a fluorescence and gas exchange parameters were correlated with the growth and yield response. Pb treatments increased the minimum fluorescence (Fo) and caused a decrease in maximum fluorescence (Fm), variable fluorescence (Fv), the maximum quantum efficiency of PSII photochemistry (Fv/Fm), trapped energy flux per cross section (CS) at t=0 (TRo/CSo), electron transport flux per CS at t=0 (ETo/CSo), dissipated energy flux per CS at t=0(DIo/CSo), and the amount of active PSII reaction centers (RCs) per CS at t = 0 (RC/CSo). Furthermore, Pb stress led to decreases in the protein contents, the activity of peroxidase (POD, EC 1.11.1.7) and the accumulation of proline and malondialdehyde (MDA), and enhanced superoxide dismutase activity (SOD, EC 1.15.1.1), whereas catalase (CAT, EC 1.11.1.6) and ascorbate peroxidase (APX,EC 1.11.1.11) were enhanced at low Pb levels and decreased under high Pb stress. Nonetheless, these changes were closely related to the severity of the Pb stress.

Pages 240-247 | DOI: 10.21475/poj.16.09.04.pne95 |   Full Text PDF 

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A computational study on genetic diversity of shatterproof1 (shp1) and shatterproof2 (shp2) genes in some members of Oleraceae and its molecular implications

Shachi Gahoi, Neetesh Pandey, B.V. Suresh, Monendra Grover*, S.S. Marla and Anil Rai

National Bureau of Plant Genetic Resources, New Delhi-110012, India

Centre for Agricultural Bioinformatics, ICAR-IASRI, Library Avenue, Pusa, New Delhi -110012, India

Abstract

Dispersal and maturation of seed is a complex event in flowering plants. The genes shatterproof1 (shp1) and shatterproof2 (shp2) are essential for fruit dehiscence in Arabidopsis. In this study, we have analyzed the diversity in these two genes and their molecular implications in some members of Oleraceae. We have studied the gene organization of these two genes and various biochemical and biophysical parameters of the proteins encoded by these two genes. Though there are some similarities, there also exist some notable differences. These differences could be exploited for creating a library of synthetic alleles (neutral or advantageous) to be used for genetic engineering, thus ensuring a wide genetic base. This diversity analysis may be significant to create diversity in the transgenic plants for shattering resistance using genetic engineered methods. This analysis explores the possible correlation of results of this study with the phenotypic data to derive functional significance of the diversity in SHP genes.

Pages 248-260 | DOI: 10.21475/poj.16.09.04.pne103 |   Full Text PDF 

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Review Article

Plant gene co-suppression; basis of the molecular machinery of interfering RNA

Jorge Ricaño-Rodríguez*, Jacel Adame-García, Carolina I. Patlas-Martínez, Enrique Hipólito-Romero, José M. Ramos-Prado

Center for Eco-Literacy and Dialogue of Knowledge, University of Veracruz, Campus USBI, Veracruz Cultures Avenue 1. Col. Emiliano Zapata, P.C. 91060. Xalapa, Veracruz, México

Cell Biology Laboratory, Technologic Institute of Úrsulo Galván, Cardel-Chachalacas Road Km. 4.5 P.C. 91667, Úrsulo Galván, Veracruz, México

Abstract

RNA interference (RNAi), also known as post-transcriptional gene silencing (PTGS) co-suppression, is considered one of the most significant discoveries in molecular biology during the last several years. First recognized in plants, the starting point for its historical overview begins in the late 1980s and early 1990s when researchers used genetic engineering to alter flower color. RNAi is considered a gene down-regulation mechanism demonstrated to exist in all eukaryotes, where small RNAs (of approximately 21-24 nucleotides in size) function to guide specific effector proteins (Argonaute protein family) to a target nucleotide sequence by complementary base pairing. Subsequently, the effector protein complex down-regulates the expression of a RNA or DNA target. Although the small RNAi-directed gene regulation system was independently discovered in plants, fungi, worms and mammalian cells, scientific attention has been focused mainly on the regulation of development, biotic and abiotic stress responses and genome stability through controlling plant gene expression. On the other hand, the small interfering (si) RNA-mediated RNA silencing also functions as a neutral antiviral defense mechanism. The purpose of this review is to provide an overview of the discovery and molecular characterization of RNAi in plants.

Pages 261-269 | DOI: 10.21475/poj.16.09.04.p7802 |   Full Text PDF 

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De novo transcriptome sequencing and analysis of Hydrilla verticillata (L.f.) Royle

Etika Goyal, Singh Amit Kumar, Ravi Shankar Singh, Ajay Kumar Mahato, Kumar Kanika*

Biotechnology and Climate Change Laboratory, ICAR-National Research Centre on Plant Biotechnology, New Delhi, India

Current address: Department of Plant Breeding and Genetics, Bihar Agricultural University, Sabour, Bihar, India

Abstract

Hydrilla verticillata (L.f.) Royle, an aquatic plant, best documented example of an inducible C4 photosynthetic system, which concentrates CO2 in the chloroplasts without enzymatic compartmentation in mesophyll and bundle sheath cells. H. verticillata is a facultative C4 plant, which shifts from C3 to C4 photosynthesis under certain conditions, but lacks Kranz anatomy. Little is known about the molecular changes required for the transition to the C4 carbon concentrating mechanism (CCM). To gain insight into the processes that are involved in the C3 to the C4 transition, high throughput transcriptome sequencing and analysis were carried out using 454-GS FLX Titanium technology. A total of 533,595 reads were obtained after quality filtering. From these reads, 1,813 “Expressed sequence tags (ESTs)” were generated yielding 1,538 unigenes. Almost 95% of these unigenes aligned to the “Non-redundant (nr)” database, whereas 4.88% did not show homology to any other known gene. “Reads per kilobase per million sequenced reads (RPKM)” analysis indicated that 283 unigenes were up-regulated and 383 unigenes were down-regulated in the C4 state as compared to the C3 state. A number of transcription factors found in our study were involved in photosynthesis. These consisted of, HAP3/NF-YB, AP/EREBP and C2H2 family. GO, COG and KEGG analysis indicated that many genes were involved in energy metabolism, nucleotide metabolism, photosynthesis, signal transduction, stress responses and are worthy of further investigation. This transcriptome analysis is an important first step towards understanding the molecular changes underpinning the transition from the C3 to the C4 photosynthesis in H. verticillata. It could also be a useful genomic resource for engineering C4 photosynthetic CCM in C3 crops.

Pages 270-280 | DOI: 10.21475/poj.16.09.04.p7882 |    Full Text PDF Supplementary Data PDF Supplementary Data xls 

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Establishing an association between molecular markers and sheath blight (Rhizoctonia solani Kuhn) resistance in rice

Megha Joshi, Pawan K. Singh*, Showkat A. Waza, Vineeta Singh, Sanjay Goswami, Pallavi, Sujit Kumar, Anil K. Singh, Najam W. Zaidi, Uma S. Singh

Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi- 221005, India

Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi- 221005, India

Department of Botany, Faculty of Science, Banaras Hindu University, Varanasi- 221005, India

Uttar Pradesh Research Council, Lucknow (UP), India

IRRI-STRASA India Office, 9th Floor Agrawal Corporate Tower, Plot No. 23, Rajendra Place, New Delhi, 110 012, India

Abstract

The use of multiple regression analysis to validate molecular markers associated with sheath blight resistance was carried out in 73 germplasm accessions of rice. Data on disease reaction was recorded as lesion size and used for calculation of AUDPC (Area Under Disease Progress Curve) and Percent Disease Index (PDI). A variation in AUDPC ranging from 217.78 to 793.33 with a mean value of 532.51 was recorded for the genotypes infected with sclerotia. PDI ranged from 28.89 to 84.44 with the mean values of 55.40 for infected lines. The AUDPC and PDI values for resistant check Tetep were found to be 432.70 and 45.22, respectively. Higher AUDPC and PDI values serve as an indication for susceptibility towards the disease reaction. The PIC value for the SSR loci varied from 0.225 to 0.743 with an average value of 0.47. Markers RM336, RM209, RM251 and RM224 were most informative on the basis of their high PIC values. UPGMA clustering based on molecular data and AUDPC were found to be in good agreement with each other. Twenty five germplasm accessions were grouped as common in cluster I of dendrogram generated by all alleles, cluster I of dendrogram constructed by Tetep specific alleles, and clusters I and II of the AUDPC dendrogram. Multiple regression analysis revealed that the two markers RM251175 and RM257150 may be considered as markers for association with low disease index (resistance to sheath blight) in rice. Amongst the germplasm accessions, IC383396 and IC426017 behaved as potentially resistant to sheath blight.

Pages 281-288 | DOI: 10.21475/poj.16.09.04.p7887 |   Full Text PDF Supplementary Data PDF   

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GC-MS/Olfactometric characterisation and aroma extraction dilution analysis of aroma active compounds in Polygonum minus essential oil

Nor Azizun Rusdi, Hoe-Han Goh, Syarul Nataqain Baharum*

Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia

Abstract

Polygonum minus Huds. is an aromatic plant with potential anti-inflammatory, antiulcer and diuretic properties. Although the volatile compounds from the essential oil of P. minus have been extensively studied, knowledge of the aroma-active compounds is still incomplete. Hence, the aim of this study is to investigate and to characterise the aroma-active compounds that contribute to the potent odour of P. minus. Essential oil was extracted from the leaves of kesum (P. minus) using hydrodistillation and was analysed by gas chromatography-mass spectrometry (GC-MS) to identify the volatile constituents. The important aroma-active compounds were further analysed by GC-MS/Olfactometry (GC-MS/O) and aroma extraction dilution analysis (AEDA). The GC-MS analysis using Kováts retention indices detected 39 volatile compounds in the essential oil. Aldehydes represented the major class of compounds, encompassing 75.43% of the total peak area, followed by sesquiterpenes (13.19%), alcohols (8.07%) and organic acids (0.83%). The dominant components of the kesum essential oil were dodecanal (54.25%) and decanal (18.27%) in the aldehyde group. The sesquiterpenes that were detected include β-farnesene (1.74%), α-caryophyllene (1.72%), β-caryophyllene oxide (1.51%) and β-selinene (1.36%). In this study, GC-MS/O and AEDA analysis identified dodecanal, decanal, farnesol, 1-nonanal and α-bergamotene as the main contributors to the characteristic fragrance of this plant. This is the first olfactometric study on the essential oil of P. minus, and it is important for our understanding of the biosynthesis of volatile compounds in this medicinal herb. Moreover, the characterisation of aromatic compounds that contributed to the potent odour of P. minus can be further applied in the flavour and fragrance industries.

Pages 289-294 | DOI: 10.21475/poj.16.09.04.p7901 |   Full Text PDF