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Plant Bioengineering and Omics for Improving Crop Productivity, Stress Tolerance, and Industrial Applications

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A special issue of Bioengineering (ISSN 2306-5354).

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 25581

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Special Issue Editors

Dr. Mohammad Irfan

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Guest Editor

Plant Biology Section, School of Integrative Plant Science, College of Agriculture and Life Science, Cornell University, Ithaca, NY 14853, USA
Interests: plant bioengineering; plant molecular biology; plant biochemistry; plant specialized metabolism; plant glycobiology
Special Issues, Collections and Topics in MDPI journals

Dr. Ali Raza

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Guest Editor

Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
Interests: Crop genetics and breeding; plant biotechnology; crop stress physiology; genetic diversity; abiotic stress responses and tolerance mechanisms; transcription factors; multi-omics; RNA-seq; genomics; transcriptomics; metabolomics; proteomics; metabolic pathways; plant hormones; gene functional analysis; transgenic plants; oilseed crops

Dr. Mohammed Wasim Siddiqui

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Guest Editor

Department of Food Science and Postharvest Technology, Bihar Agricultural University, Sabour, Bihar, India
Interests: food technologies; food science; food processing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plants affect human life both directly and indirectly every day, providing food, fiber, energy, shelter, and medicine. Therefore, it is essential to achieve sustainable cultivation of plants to meet society’s current and future needs. However, crop production and food safety have been challenged worldwide due to climate change, overpopulation, crop establishment failure, and new patterns of biotic and abiotic stresses. Climate change (abiotic and biotic stresses) in particular has a significant impact on crop productivity, creating food security problems. For instance, fruits and vegetables, which are important dietary component, have high rate of wastage among food crops, mainly at post-harvest level. The post-harvest deterioration of perishable fruits and vegetables limits transportation and storage, causing post-harvest losses of up to 50% of the total produce. To overcome these challenges, modern biotechnological and multi-omics tools can be useful for crop improvement programs in more sustainable and rational ways. Further, plants themselves are excellent hosts for producing various pharmaceuticals and high-value compounds. Therefore, taking advantage of plant biotechnological and omics tools, the capability of these systems can be drastically increased in more economical ways to ensure a food-secure world.

This Special Issue aims to address the recent developments in the above areas. We welcome original research, review articles, mini reviews, methods, and opinions within—but not limited to—the framework of the following research areas:

Transcriptomics, proteomics, and metabolomics of crop and medicinal plants.
Plant genetic and genome engineering for crop improvement.
Crop adaptation to climate change and tools for improving plant stress tolerance.
Tools to reduce post-harvest loss of fruits, vegetables, and cereals.
Plant biotechnology for medicinal and industrial applications.

Dr. Mohammad Irfan
Dr. Ali Raza
Dr. Mohammed Wasim Siddiqui
Guest Editors

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Bioengineering is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

abiotic and biotic stress
biotechnology
climate change
transgenic plants
fruits and vegetables
post-harvest loss
genome editing
plant molecular farming
food security
medicinal plants
metabolic engineering
multi-omics

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Published Papers (9 papers)

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Research

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15 pages, 4986 KiB

Open AccessArticle

Bioinformatics Analysis, Expression Profiling, and Functional Characterization of Heat Shock Proteins in Wolfi-poria cocos

by Xin Hu, Xue Tang, Yumei Zhou, Bilal ahmad, Deli Zhang, Yue Zeng, Jingyi Wei, Liling Deng, Shijiang Chen and Yu Pan

Bioengineering 2023, 10(3), 390; https://doi.org/10.3390/bioengineering10030390 - 22 Mar 2023

Cited by 5 | Viewed by 2163

Abstract

Heat shock proteins (HSPs) play critical roles in regulating different mechanisms under high-temperature conditions. HSPs have been identified and well-studied in different plants. However, there is a lack of information about their genomic organization and roles in medicinal plants and fungi, especially in Wolfi-poria cocos (W. cocos). We identified sixteen heat shock proteins (HSPs) in W. cocos and analyzed in terms of phylogenetic analysis, gene structure, motif distribution patterns, physiochemical properties, and expression comparison in different strains. Based on phylogenetic analysis, HSPs were divided into five subgroups (WcHSP100, WcHSP90, WcHSP70, WcHSP60, and WcsHSP). Subgroups WcHSP100s, WcHSP90s, WcHSP70s, WcHSP60, and WcsHSPs were further divided into 3, 2, 3, 1, and 6 subfamilies, respectively. Moreover, the expression profiling of all HSP genes in five strains of W. cocos under different temperature extremes revealed that expression of most HSPs were induced by high temperature. However, every subfamily showed different expression suggesting distinctive role in heat stress tolerance. WcHSP70-4, WcHSP90-1, and WcHSP100-1 showed the highest response to high temperature stress. Heterologous expression of WcHSP70-4, WcHSP90-1, and WcHSP100-1 genes in Escherichia coli enhanced survival rate of E. coli during heat stress. These findings suggest the role of W. cocos heat shock genes in the high temperature stress tolerance. Full article

(This article belongs to the Special Issue Plant Bioengineering and Omics for Improving Crop Productivity, Stress Tolerance, and Industrial Applications)

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13 pages, 2156 KiB

Open AccessArticle

Exserohilum turcicum (Passerini) Leonard and Suggs: Race Population Distribution in Bihar, India

by Ram Niwas, Md Arshad Anwer, Tushar Ranjan, Abhijeet Ghatak, Khushbu Jain, Jitesh Kumar, Aditya Bharti, Neha Kumari and Jitendra Nath Srivastava

Bioengineering 2023, 10(1), 7; https://doi.org/10.3390/bioengineering10010007 - 21 Dec 2022

Cited by 2 | Viewed by 1987

Abstract

Northern corn leaf blight (NCLB) of maize, caused by Exserohilum turcicum (Pass.) Leonard and Suggs., is an important foliar disease common across maize-producing areas of the world, including Bihar, India. In this study, virulence and distribution of races were observed against Ht-resistant genes and also identified the E. turcicum race population distribution in Bihar. For that, 45 E. turcicum isolates were collected from maize fields in Bhagalpur, Begusarai, Khagaria, Katihar and Samastipur districts between 2020 and 2022. These isolates were screened on maize differential lines containing Ht1, Ht2, Ht3 and HtN1 resistance genes. Five different physiological races were observed based on the symptoms response of the differential maize lines. These races are race 0, race 1, race 3, race 23N and race 123N. E. turcicum race 3 was the most prevalent race having 26.6% frequency followed by race 0 (24.4%) and race 1 (22.2%) and the least prevalent races were race 23N and 123N having 13.3% each. Varied resistance response of different isolates was observed on differential lines having different resistant genes. Despite the fact that virulence was seen against all Ht resistance genes, NCLB control might be increased by combining qualitative Ht resistance genes with quantitative resistance. Full article

(This article belongs to the Special Issue Plant Bioengineering and Omics for Improving Crop Productivity, Stress Tolerance, and Industrial Applications)

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22 pages, 3906 KiB

Open AccessArticle

Proteo-Molecular Investigation of Cultivated Rice, Wild Rice, and Barley Provides Clues of Defense Responses against Rhizoctonia solani Infection

by Md. Shamim, Divakar Sharma, Deepa Bisht, Rashmi Maurya, Mayank Kaashyap, Deepti Srivastava, Anurag Mishra, Deepak Kumar, Mahesh Kumar, Vijaya Naresh Juturu, N. A. Khan, Sameer Chaudhary, Raja Hussain and K. N. Singh

Bioengineering 2022, 9(10), 589; https://doi.org/10.3390/bioengineering9100589 - 20 Oct 2022

Cited by 2 | Viewed by 2540

Abstract

Rhizoctonia solani is a soil-borne fungus causing sheath blight disease in cereal crops including rice. Genetic resistance to sheath blight disease in cereal crops is not well understood in most of the host(s). Aside from this, a comparative study on the different hosts at the biochemical and proteomic level upon R. solani infection was not reported earlier. Here, we performed proteomic based analysis and studied defense pathways among cultivated rice (cv. Pusa Basmati-1), wild rice accession (Oryza grandiglumis), and barley (cv. NDB-1445) after inoculation with R. solani. Increased levels of phenol, peroxidase, and β-1, 3-glucanase were observed in infected tissue as compared to the control in all of the hosts. Wild rice accession O. grandiglumis showed a higher level of biochemical signals than barley cv. NDB 1445 and cultivated rice cv. Pusa Basmati-1. Using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS), differently expressed proteins were also studied in control and after inoculation with R. solani. Wild rice accession O. grandiglumis induced a cysteine protease inhibitor and zinc finger proteins, which have defense functions and resistance against fungal pathogens. On the other hand, barley cv. NDB-1445 and cultivated rice cv. Pusa Basmati-1 mainly induce energy metabolism-related proteins/signals after inoculation with R. solani in comparison to wild rice accession O. grandiglumis. The present comprehensive study of R. solani interaction using three hosts, namely, Pusa Basmati-1 (cultivated rice), O. grandiglumis (wild rice), and NDB-1445 (barley) would interpret wider possibilities in the dissection of the protein(s) induced during the infection process. These proteins may further be correlated to the gene(s) and other related molecular tools that will help for the marker-assisted breeding and/or gene editing for this distressing disease among the major cereal crops. Full article

(This article belongs to the Special Issue Plant Bioengineering and Omics for Improving Crop Productivity, Stress Tolerance, and Industrial Applications)

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20 pages, 7119 KiB

Open AccessArticle

Transcriptome-Wide Analysis Revealed the Potential of the High-Affinity Potassium Transporter (HKT) Gene Family in Rice Salinity Tolerance via Ion Homeostasis

by Shahid Hussain, Rui Zhang, Shuli Liu, Rongkai Li, Yicheng Zhou, Yinglong Chen, Hongyan Hou and Qigen Dai

Bioengineering 2022, 9(9), 410; https://doi.org/10.3390/bioengineering9090410 - 23 Aug 2022

Cited by 9 | Viewed by 2525

Abstract

The high-affinity potassium transporter (HKT) genes are key ions transporters, regulating the plant response to salt stress via sodium (Na⁺) and potassium (K⁺) homeostasis. The main goal of this research was to find and understand the HKT genes in rice and their potential biological activities in response to brassinosteroids (BRs), jasmonic acid (JA), seawater, and NaCl stress. The in silico analyses of seven OsHKT genes involved their evolutionary tree, gene structures, conserved motifs, and chemical properties, highlighting the key aspects of OsHKT genes. The Gene Ontology (GO) analysis of HKT genes revealed their roles in growth and stress responses. Promoter analysis showed that the majority of the HKT genes participate in abiotic stress responses. Tissue-specific expression analysis showed higher transcriptional activity of OsHKT genes in roots and leaves. Under NaCl, BR, and JA application, OsHKT1 was expressed differentially in roots and shoots. Similarly, the induced expression pattern of OsHKT1 was recorded in the seawater resistant (SWR) cultivar. Additionally, the Na⁺ to K⁺ ratio under different concentrations of NaCl stress has been evaluated. Our data highlighted the important role of the OsHKT gene family in regulating the JA and BR mediated rice salinity tolerance and could be useful for rice future breeding programs. Full article

(This article belongs to the Special Issue Plant Bioengineering and Omics for Improving Crop Productivity, Stress Tolerance, and Industrial Applications)

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18 pages, 3896 KiB

Open AccessArticle

Molecular and Morphological Characterization of Exserohilum turcicum (Passerini) Leonard and Suggs Causing Northern Corn Leaf Blight of Maize in Bihar

by Md Arshad Anwer, Ram Niwas, Tushar Ranjan, Shyam Sundar Mandal, Mohammad Ansar, Jitendra Nath Srivastava, Jitesh Kumar, Khushbu Jain, Neha Kumari and Aditya Bharti

Bioengineering 2022, 9(8), 403; https://doi.org/10.3390/bioengineering9080403 - 19 Aug 2022

Cited by 7 | Viewed by 3819 | Correction

Abstract

Maize is considered the third most important cereal crop in Asia after rice and wheat. Many diseases affect this crop due to the cultivation of various hybrids. This research aimed to characterize the causative agent of northern corn leaf blight disease in Bihar, India, caused by Exserohilum turcicum (Passerini) Leonard and Suggs. Leaf samples were collected from infected fields in five maize growing districts of Bihar in 2020–2022. A total of 45 fungal isolates from 135 samples were examined for cultural, morphological, and molecular characteristics and were identified as E. turcicum. The isolates were grouped into four groups based on colony color, i.e., olivaceous brown, blackish brown, whitish black, and grayish, and into two groups based on regular and irregular margins. The conidial shapes were observed to be elongated and spindle-shaped with protruding hilum, with conidial septa ranging from 2–12. Similarly, conidial length varied from 52.94 μm to 144.12 μm. β-tubulin gene sequences analysis made it possible to verify the identities of fungal strains and the phylogenetic relationships of all isolates, which were clustered in the same clade. The β-tubulin gene sequences of all the isolates showed a high level of similarity (100%) with reference isolates from GenBank accession numbers KU670342.1, KU670344.1, KU670343.1, KU670341.1, and KU670340.1. The findings of this study will serve as a baseline for future studies and will help to minimize yield losses. Full article

(This article belongs to the Special Issue Plant Bioengineering and Omics for Improving Crop Productivity, Stress Tolerance, and Industrial Applications)

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25 pages, 11121 KiB

Open AccessArticle

The Homeodomain-Leucine Zipper Genes Family Regulates the Jinggangmycin Mediated Immune Response of Oryza sativa to Nilaparvata lugens, and Laodelphax striatellus

by Sheraz Ahmad, Yu Chen, Amir Zaman Shah, Huaiqi Wang, Chuanyuan Xi, Haowen Zhu and Linquan Ge

Bioengineering 2022, 9(8), 398; https://doi.org/10.3390/bioengineering9080398 - 17 Aug 2022

Cited by 20 | Viewed by 2340

Abstract

The homeodomain-leucine zipper (HDZIP) is an important transcription factor family, instrumental not only in growth but in finetuning plant responses to environmental adversaries. Despite the plethora of literature available, the role of HDZIP genes under chewing and sucking insects remains elusive. Herein, we identified 40 OsHDZIP genes from the rice genome database. The evolutionary relationship, gene structure, conserved motifs, and chemical properties highlight the key aspects of OsHDZIP genes in rice. The OsHDZIP family is divided into a further four subfamilies (i.e., HDZIP I, HDZIP II, HDZIP III, and HDZIP IV). Moreover, the protein–protein interaction and Gene Ontology (GO) analysis showed that OsHDZIP genes regulate plant growth and response to various environmental stimuli. Various microRNA (miRNA) families targeted HDZIP III subfamily genes. The microarray data analysis showed that OsHDZIP was expressed in almost all tested tissues. Additionally, the differential expression patterns of the OsHDZIP genes were found under salinity stress and hormonal treatments, whereas under brown planthopper (BPH), striped stem borer (SSB), and rice leaf folder (RLF), only OsHDZIP3, OsHDZIP4, OsHDZIP40, OsHDZIP10, and OsHDZIP20 displayed expression. The qRT-PCR analysis further validated the expression of OsHDZIP20, OsHDZIP40, and OsHDZIP10 under BPH, small brown planthopper (SBPH) infestations, and jinggangmycin (JGM) spraying applications. Our results provide detailed knowledge of the OsHDZIP gene family resistance in rice plants and will facilitate the development of stress-resilient cultivars, particularly against chewing and sucking insect pests. Full article

(This article belongs to the Special Issue Plant Bioengineering and Omics for Improving Crop Productivity, Stress Tolerance, and Industrial Applications)

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Review

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15 pages, 2806 KiB

Open AccessReview

The Role of Calmodulin Binding Transcription Activator in Plants under Different Stressors: Physiological, Biochemical, Molecular Mechanisms of Camellia sinensis and Its Current Progress of CAMTAs

by Shah Zaman, Syed Shams ul Hassan and Zhaotang Ding

Bioengineering 2022, 9(12), 759; https://doi.org/10.3390/bioengineering9120759 - 2 Dec 2022

Cited by 3 | Viewed by 2024

Abstract

Low temperatures have a negative effect on plant development. Plants that are exposed to cold temperatures undergo a cascade of physiological, biochemical, and molecular changes that activate several genes, transcription factors, and regulatory pathways. In this review, the physiological, biochemical, and molecular mechanisms of Camellia sinensis have been discussed. Calmodulin binding transcription activator (CAMTAs) by molecular means including transcription is one of the novel genes for plants’ adaptation to different abiotic stresses, including low temperatures. Therefore, the role of CAMTAs in different plants has been discussed. The number of CAMTAs genes discussed here are playing a significant role in plants’ adaptation to abiotic stress. The illustrated diagrams representing the mode of action of calcium (Ca²⁺) with CAMTAs have also been discussed. In short, Ca²⁺ channels or Ca²⁺ pumps trigger and induce the Ca²⁺ signatures in plant cells during abiotic stressors, including low temperatures. Ca²⁺ signatures act with CAMTAs in plant cells and are ultimately decoded by Ca²⁺sensors. To the best of our knowledge, this is the first review reporting CAMAT’s current progress and potential role in C. sinensis, and this study opens a new road for researchers adapting tea plants to abiotic stress. Full article

(This article belongs to the Special Issue Plant Bioengineering and Omics for Improving Crop Productivity, Stress Tolerance, and Industrial Applications)

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22 pages, 3779 KiB

Open AccessReview

Molecular Tools and Their Applications in Developing Salt-Tolerant Soybean (Glycine max L.) Cultivars

by Adnan Rasheed, Ali Raza, Hongdong Jie, Athar Mahmood, Yushen Ma, Long Zhao, Hucheng Xing, Linlin Li, Muhammad Umair Hassan, Sameer H. Qari and Yucheng Jie

Bioengineering 2022, 9(10), 495; https://doi.org/10.3390/bioengineering9100495 - 22 Sep 2022

Cited by 21 | Viewed by 4405

Abstract

Abiotic stresses are one of the significant threats to soybean (Glycine max L.) growth and yields worldwide. Soybean has a crucial role in the global food supply chain and food security and contributes the main protein share compared to other crops. Hence, there is a vast scientific saddle on soybean researchers to develop tolerant genotypes to meet the growing need of food for the huge population. A large portion of cultivated land is damaged by salinity stress, and the situation worsens yearly. In past years, many attempts have increased soybean resilience to salinity stress. Different molecular techniques such as quantitative trait loci mapping (QTL), genetic engineering, transcriptome, transcription factor analysis (TFs), CRISPR/Cas9, as well as other conventional methods are used for the breeding of salt-tolerant cultivars of soybean to safeguard its yield under changing environments. These powerful genetic tools ensure sustainable soybean yields, preserving genetic variability for future use. Only a few reports about a detailed overview of soybean salinity tolerance have been published. Therefore, this review focuses on a detailed overview of several molecular techniques for soybean salinity tolerance and draws a future research direction. Thus, the updated review will provide complete guidelines for researchers working on the genetic mechanism of salinity tolerance in soybean. Full article

(This article belongs to the Special Issue Plant Bioengineering and Omics for Improving Crop Productivity, Stress Tolerance, and Industrial Applications)

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