PLANT OMICs

Encompassing plant and animal OMICs

   ISSN: 1836-3644 (online) | ISSN: 1836-0661 (print)












Plant 
           
          OMICS





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 ARTICLES 2022




ARTICLES 2021

 


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New Articles Published in 2022



Effect of surfactant and different spray volumes on the efficacy of acetic acid based natural herbicide for controlling Imperata cylindrica and Sporobolus indicus 

Chuah Tse-Seng*, Akmal Ruzaini Mohd Nasarrudin, Dilipkumar Masilamany, Ken Chai, Lee Byung-Woo, Muhammad Firdaus Arifin, Lim Sang-Sun

Faculty of Plantatation and Agrotechnology, Universiti Teknologi MARA, Perlis Branch 02600 Arau, Perlis, Malaysia
Inbred Rice Program, Rice Research Center, Malaysian Agricultural Research and Development Institute (MARDI), 13200 Kepala Batas, Pulau Pinang, Malaysia
CJ Bio Malaysia Sdn. Bhd, Lot Q, Bio Polymer Park, Phase 2, Mukim Kerteh, 24300 Kerteh, Malaysia

Abstract
Weed-outTM is a contact post-emergence herbicide that contains the active component acetic acid. Our prior research showed that it was ineffective against grassy weeds with thick cuticle, small, and upright leaves. This study aims to determine different spray volumes of Weed-outTM applied with or without surfactant for controlling grassy weeds Imperata cylindrica and Sporobolus indicus in a ten-year-old mango farm. At the inter rows of mango trees, Weed-outTM was applied at spray volumes of 0, 2000, 4000, 6000, and 8000 L/ha with or without non-ionic surfactant (NIS). The efficacy of each treatment was assessed based on percentage of weed killed (0 to 100%) weekly for one month. Weed-outTM combined with NIS did not significantly increase weed control (p<0.05). After one week of treatment (WAT), application of Weed-outTM at 6000 and 8000 L/ha spray volumes produced excellent control (93-100 %) of I. cylindrica and S. indicus. At 4 WAT, the spray volumes still provided adequate weed control, although control was reduced to 63-75 %. At 1 WAT, Weed-outTM applied at 2000 and 4000 L/ha produced 75-91 % control of the weeds, but at 4 WAT, the efficacy of Weed-outTM was reduced to 22-56 % control. When Weed-outTM was applied at 2000 L/ha, S. indicus regrew at 3 WAT, but I. cylindrica recovered at 2 WAT. These findings suggested that application of Weed-outTM at 6000 and 8000 L/ha without NIS could effectively control I. cylindrica and S. indicus within 4 weeks.

Pages 1-5 | Full Text PDF| doi: 10.21475/POJ.15.01.22.p3371
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Efficacy of virus elimination from Rehmannia glutinosa using simultaneous thermotherapy, chemotherapy, and meristem culture


Young Hee Kwon*, Won Il Choi, Hee Kyu Kim, Kyung Ok Kim, Ju hyung Kim, Yoon Sun Huh, Woo Tae Park

Chungcheongbuk-do Agricultural Research and Extension Services, Cheongju 28130, Republic of Korea
Department of Herbal Crop Research, NIHHS, RDA, Eumseong 27709, Korea

Abstract
Rehmannia glutinosa Libosch. is considered a valuable medicinal plant in Asia owing to its antianemic, antipyretic, anti-inflammatory, and antisenescence effects. Propagating the seeds of R. glutinosa is difficult; therefore, the plants are propagated vegetatively. However, this method increases the incidence of viral infection in commercial production. Experiments were conducted to determine the optimal micropropagation conditions for the production of healthy and virus-free R. glutinosa plants using thermotherapy, chemotherapy, and meristem tip culture. Thermotherapy (heat treatment at 37°C for 4 weeks), chemotherapy (addition of an antiviral agent into the growth medium), and meristem tip culture (0.3–0.5 mm) were separately performed. Reverse transcription-polymerase chain reaction tests were used to detect five viruses, namely, Rehmannia mosaic virus, Youcai mosaic virus, Broad bean wilt virus 2, Plantago asiatica mosaic virus, and Rehmannia virus 1. The virus elimination rate reached 55% with chemotherapy (60 mgL 1 ribavirin) and 10% with thermotherapy and 37% with meristem culture, respectively. The survival rates were high with thermotherapy (67.9%) and chemotherapy (55.2%) but low with meristem culture (29.4%). Complete inactivation of the viruses was challenging using these treatments; therefore, the treatments were combined. After the application of meristem culture followed by thermotherapy (37°C for 6 weeks) and chemotherapy (60 mgL 1 ribavirin), a high virus elimination rate (73%) and vigorous growth were observed. Furthermore, we obtained virus-free plants. Meristem culture followed by thermotherapy and chemotherapy may be effective for the elimination of major viruses from infected R. glutinosa plants.

Pages 6-12 | Full Text PDF| doi: 10.21475/POJ.15.01.22.p3527

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Oxophytodienoic acid reductase 1 (HvOPR1) is differentially expressed during spike development of barley

Bayan Al-Momany, Hazem Hasan, Saeid Abu-Romman*

Department of Biotechnology, Faculty of Agricultural Technology, Al-Balqa Applied University, Al-Salt 19117, Jordan
Department of Plant Production and Protection, Faculty of Agricultural Technology, Al-Balqa Applied University, Al-Salt 19117, Jordan
Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman 11733, Jordan

Abstract
Interest is increasing towards revealing genes network underlying cereals developmental stages. Pattern of HvOPR1 gene expression during spike developmental stages has remained unknown. In this study, the relationship between HvOPR1 and spike development in barley was identified. Transcriptomic levels of HvOPR1 gene were quantified using qRT-PCR. Expression analysis revealed that HvOPR1 was differentially regulated during spike development. The lowest expression levels were scored for Milk Development and Dough Development stages. One the other hand, the highest expression of HvOPR1 was noticed during Heading. Our data showed an evidence of a possible regulatory role of HvOPR1 during booting, heading and pollination stages.

Pages 13-16 | Full Text PDF| doi: 10.21475/POJ.15.01.22.p3466
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Development and characterization of EST-SSR derived functional domain marker (FDM) in Phaseolus vulgaris (common bean)

Shatabdi Basu and Saurav Bhattacharya*

Department of Biotechnology, Techno India University West Bengal-700091

Abstract
EST-SSR markers have been increasingly useful in crop improvement studies owing to their rapid and less expensive development, better chances of association with protein-coding regions and cross-taxon transferability. In the present study, SSR sequences were mined from 117,596 EST sequences of Phaseolus vulgaris (common bean) (from NCBI) representing expressed cDNA data from different plant tissues (leaves, roots) grown under variable growth conditions. A total 1481, perfect non redundant SSR containing contig sequences were assembled that showed highest percentages of mononucleotide (44.8%) followed by trinucleotide (30.4%) di-nucleotide (14.0%), tetra-nucleotide (7.0%) and hexanucleotide (3.6%) repeat sequences. Among the distribution pattern, trinucleotide SSR sequences (65.4%) were found to be relatively frequent in the coding regions, the mononucleotide (25.6%) and dinucleotide (38.4%) SSRs were found to be highly frequent in the UTR region. Assembled SSR sequences were assigned to 2700 unique functional domain markers using the InterproScan program, the most significant were heat shock protein DnaJ, a cysteine-rich domain, RNA binding domain, S-adenosyl methionine decarboxylase, Brassinosteroid (BES1/BZR1) plant transcription factor, B3 DNA binding domain. Functional annotation results of selected 949 blasted EST-SSR sequences using BLAST2GO revealed its association with several important molecular functions (MF), biological processes (BP) and cellular components (CC) in P. vulgaris. Our results also showed a relatively higher density of SSR (1SSR/0.2kb) that were used to design 146 SSR primer pairs from 280 annotated sequences (52.1%) using Primer3 and successfully amplified in silico using FastPCR. The present findings report a new array of SSR markers with significant association with diverse functional domains that could be used in future studies on genetic diversity of common bean cultivars as well as in marker-assisted breeding.

Pages 17-24 | Full Text PDF| doi: 10.21475/POJ.15.01.22.p3580
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The role of anthocyanins in activating antioxidant enzymes during postharvest degradation of (Hibiscus sabdariffa L.) Roselle calyx

Abubakar Abdullahi Lema, Nor Hasima Mahmod*, Mohammad Moneruzzaman Khandake, Mahmoud Dogara Abdulrahman

Department of Plant Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin (UniSZA), Besut Campus, 22200, Terengganu, Malaysia
Biology Department, College of Natural and Applied Sciences Al-Qalam University Katsina, 2137, Katsina state Nigeria
Department of Biology, Faculty of Education, Tishk International University Erbil, Iraq

Abstract
The perishable roselle, calyx, and anthocyanin can swiftly degrade and become brown. The pH, temperature, light, and postharvest enzymes affect anthocyanin stability. The calyx is damaged when the seed was removed, causing stress and microbial decay. Despite this, anthocyanins benefit plants under stress, including drought, high salinity, excessive light, and damage. This study evaluates the role of anthocyanins in activating antioxidant enzymes during deterioration. Total anthocyanin content, Total phenolic content, and Total flavonoids content were assessed, as well as H2O2, antioxidant enzymes, polyphenol oxidase (PPO), and phenylalanine ammonia lyase (PAL). The findings revealed that the TAC, TPC, and TFC were significantly higher at (p ≤ 0.05), from 0 hours to 4days. Both Catalase (CAT), Guaiacol Peroxidase (POD), and Ascorbate Peroxidase (APX) were expressed at significantly higher concentrations after 1 hour and 1 day, leading to a reduction in H2O2 concentration. Still, at 3-5-days post deterioration induction, the enzyme activity significantly decreased drastically or depleted. This indicates that anthocyanins play a role in activating antioxidant enzymes in response to stress during roselle calyx deterioration. We have also reported the biochemical changes during deterioration of roselle calyx for the first time. Therefore, anthocyanins might be a potential deterioration biomarker in roselle.

Pages 25-36 | Full Text PDF| doi: 10.21475/POJ.15.01.22.p3627
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Proteomic analysis of rubber trees uncovers a systemic response to white root rot disease

Julalak Janket, Ashara Pengnoo, Panida Kongsawadworakul, Unchera Viboonjun*

Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai Campus, Songkhla, 90110, Thailand
Natural Biological Control Research Center, National Research Council of Thailand, 196 Phahonyothin Road, Lat Yao, Chatuchak, Bangkok, 10900 Thailand

Abstract
White root rot disease caused by Rigidoporus microporus (Sw.) Overeem is a disastrous root disease found in rubber trees (Hevea brasiliensis). It significantly reduces natural rubber production and triggers plant death. In the early stages of infection, the aboveground parts of the diseased plant are still healthy. However, by the time that disease symptoms are apparent, it is too late for the plant to recover. Thus, this study aims to understand the systemic response of rubber trees during root infection by using 2D-PAGE coupled with LC-MS/MS. The root system of rubber tree clone RRIM600 was inoculated with R. microporus for 50 days and the stems were then collected for analysis. The results indicate that fungal infection of underground rubber tree parts can trigger changes in the proteome profile of asymptomatic aboveground parts. Fifteen protein spots were found to be differentially expressed between pathogen-inoculated and mock-inoculated plants. Nine spots were significantly changed after infection (p < 0.05). Small heat shock proteins were the major group of stress-related proteins that were significantly down-regulated after infection. Moreover, the hydrogen cyanide releasing enzymes, antioxidant enzymes and photosynthesis associated proteins were down-regulated in the stems of infected trees. The down-regulation of several proteins that are involved in the stress defense response contributed to white root rot disease susceptibility of the RRIM600 clone. This research contributes to a better understanding of the mechanisms behind rubber tree systemic responses to white root rot disease, and the candidate proteins that may be useful in rubber trees breeding programs.

Pages 37-47 | Full Text PDF| doi: 10.21475/POJ.15.01.22.p3756