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A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Genotype Evaluation and Breeding".

Deadline for manuscript submissions: closed (25 March 2023) | Viewed by 7664

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Special Issue Editors

Dr. Santosh Kumar Upadhyay

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Guest Editor

Department of Botany, Panjab University, Chandigarh 160014, India
Interests: agriculture biotechnology; transgenic; functional genomics; gene expression; genome engineering
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Kashmir Singh

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Guest Editor

Department of Biotechnology, Panjab University, Chandigarh 160014, India
Interests: biotechnology; gene expression; transgenics; bioinformatics; plants stress

Dr. Prashant Misra

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Guest Editor

Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu 180001, India
Interests: agriculture biotechnology; metabolomics; secondary metabolites

Special Issue Information

Dear Colleagues,

In recent years, several advancements in functional genomic approaches and tools, especially related to genome editing, have been attained. These tools have been utilized or are being utilized for numerous purposes, including nutritional improvement and stress tolerance in several agricultural and horticultural crop species, including rice, wheat, potato, tomato, oil seed crops, bananas, etc. In this context, advancements in the use of functional genomics and genome engineering tools for crop biofortification for nutritional improvement, nutraceuticals improvement, flavonoid enrichment, yield improvement, disease resistance, virus resistance, abiotic stress tolerance, etc. should be covered in this field. Moreover, the applications of these tools in oil seed crops, vegetables, ornamental plants, etc., should also be included. Furthermore, their application in reducing post-harvest loss in various crops and the biosafety measures and regulatory mechanisms suggested by various regulatory authorities around the world along with their importance and shortcomings should also be discussed.

This Special Issue focuses on the application of advances in functional genomics approaches for the nutritional, quality, and yield improvements in various agricultural and horticultural crops. For this reason, it welcomes highly interdisciplinary quality studies from disparate research fields, including agriculture, horticulture, functional genomics, plant biotechnology, gene cloning, characterization, etc. Original research articles and reviews are accepted.

Dr. Santosh Kumar Upadhyay
Prof. Dr. Kashmir Singh
Dr. Prashant Misra
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Agriculture is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

agriculture
horticulture
functional genomics
genome engineering
gene cloning

Published Papers (6 papers)

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Research

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Open AccessArticle

Exploration of Piezo Channels in Bread Wheat (Triticum aestivum L.)

and

Santosh Kumar Upadhyay

Agriculture 2023, 13(4), 783; https://doi.org/10.3390/agriculture13040783 - 29 Mar 2023

Cited by 1 | Viewed by 668

Abstract

Piezo channels belong to an important class of cell membrane-bound, Ca²⁺-permeable, mechanosensitive channels consisting of a pore and multiple transmembrane helices. In plants, the functional aspects of Piezo channels have been less studied than other mechanosensitive channels. However, a few studies that have been carried out indicate the involvement of Piezo channels in stress response and developmental processes. In our analysis, we identified a total of three Piezo genes in the Triticum aestivum genome. The phylogenetic analysis revealed the monocot and dicot-specific clustering of Piezo proteins. The gene and protein structure analysis indicated their conserved architecture. The promoter region of each of the three Piezo genes contained light-, growth-and development-, hormone-, and stress-responsive cis-regulatory elements. Moreover, the differential expression of Piezo genes in tissue developmental stages and under abiotic and biotic stress conditions indicated their probable role in plant growth and development and various stresses. The quantitative real-time polymerase chain reaction (qRT-PCR) analysis suggested that TaPiezo1-D might be involved in Ca²⁺ homeostasis. In addition, protein–protein interaction indicated their precise role in glucose, hormone and stress responses. The miRNA interaction analysis further suggested their participation in signaling cascades and biological processes. The present study will extend our understanding about Piezo channels in Ca²⁺ mediated signaling in plants under various stresses and provide a path for the functional validation of TaPiezo genes in future research. Full article

(This article belongs to the Special Issue Advances in Functional Genomics for Crop Improvement)

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Open AccessArticle

Transcriptional Plasticity and Cell Wall Characterization in High-Methanol-Producing Transgenic Tobacco Plants

Sameer Dixit

Krishnappa Chandrashekar

Santosh Kumar Upadhyay

and

Praveen Chandra Verma

Agriculture 2023, 13(3), 521; https://doi.org/10.3390/agriculture13030521 - 22 Feb 2023

Viewed by 830

Abstract

Volatile organic compounds emanating from plant surfaces serve as a sustainable natural solution to combat biotic stresses in plants. Leaf methanol is the simplest and second major volatile organic compound after isoprene emitted through the leaf surface. Methanol has been neglected as a by-product of other secondary metabolites for a long time, but recent studies have suggested its importance in development and stress responses. In our previous findings, we had revealed that transgenic plants over-expressing PME, enhanced methanol production providing resistance against a broad spectrum of insects. In the current study, we extended our previous work to provide new insights by performing differential transcriptomics of high-methanol-producing insect-resistant transgenic lines. We found that 2262 genes were differentially expressed in the transgenics plants, including transcription factors, cell wall modulating, phytohormones signaling and development-related genes. Our results demonstrated that the expression levels of transcription factors associated with development and biotic stress were altered in the transgenic lines. In addition, phytohormones ABA and gibberellin signalling genes were upregulated, whereas ethylene and auxin signalling genes were downregulated. Moreover, biochemical characteristics of cell walls in both transgenic tobacco plants were comparable to the control plants. Full article

(This article belongs to the Special Issue Advances in Functional Genomics for Crop Improvement)

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Open AccessArticle

Cold Tolerance Mechanisms in Mungbean (Vigna radiata L.) Genotypes during Germination

Lekshmi S. Manasa

Madhusmita Panigrahy

Kishore Chandra Panigrahi

Gayatri Mishra

Sanjib Kumar Panda

and

Gyana Ranjan Rout

Agriculture 2023, 13(2), 315; https://doi.org/10.3390/agriculture13020315 - 28 Jan 2023

Viewed by 1470

Abstract

Mungbean or greengram (Vigna radiata) is an important legume crop well known for its high protein with nitrogen-fixing abilities. However, the severe yield loss in mungbean occurs due to susceptibility to low temperatures at all stages of plant growth including germination and is a serious concern for its cultivation and productivity. To select cold-tolerant genotypes, a germination-based screening at 10 °C was performed in a total of 204 germplasms. The study showed that cold stress of the initial 8-days during seedling establishment imposed a negative impact throughout the life of mungbean genotypes, which were reflected in the vegetative and reproductive phase (plant height, days to 50% flowering and pods/plant, seeds/pod, yield/plant, and 100-seed weight). The biplot analysis showed that parameters such as germination rate index, Timson’s index, mean germination time, and coefficient of the velocity of germination are the key influential germination parameters for identifying cold tolerance in the seedling stage. Identified cold-tolerant genotype (PAU911) retained higher rootlet number, leaf area, and increased chlorophyll, carotenoid, and malondialdehyde (MDA) content at 10 °C. Based on the confocal microscopic study, it is noticed that the stomatal density, open pore percentage, and trichome density were significant differences in seedlings exposed to cold stress as compared to non-stress. On the basis of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) analysis, it is observed that a new protein identified as TETRATRICOPEPTIDE-REPEAT THIOREDOXIN-LIKE1 (TTL1) (UNIPROT Identifier: LOC106762419) which highly correlated with the cold stress response of in the cold-tolerant genotype. Our study identifies a noble member, TTL1, whose expression has a positive role in cold tolerance response at the protein level in V. radiata. This study will help breeding programs with regard to the sustainable growth of mungbean. Full article

(This article belongs to the Special Issue Advances in Functional Genomics for Crop Improvement)

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Open AccessArticle

Genome-Wide Identification of BTB Domain-Containing Gene Family in Grapevine (Vitis vinifera L.)

and

Agriculture 2023, 13(2), 252; https://doi.org/10.3390/agriculture13020252 - 20 Jan 2023

Viewed by 868

Abstract

BTB (broad-complex, tram track and bric-a-brac) proteins have broad functions in different growth processes and biotic and abiotic stresses. However, the biological role of these proteins has not yet been explored in grapevine, which draws our attention towards the BTB gene family. Herein, we identified 69 BTB genes (VvBTB) in the Vitis vinifera genome and performed comprehensive in silico analysis. Phylogenetic analysis classified VvBTB proteins into five groups, and further domain analysis revealed the presence of other additional functional domains. The majority of BTB proteins were localized in the nucleus. We also performed differential expression analysis by harnessing RNA- seq data of 10 developmental stages and different biotic and abiotic stresses. Our findings revealed the plausible roles of the BTB gene family in developmental stages; Fifty VvBTB were differentially expressed at different developmental stages. In addition, 47 and 16 VvBTB were responsive towards abiotic and biotic stresses, respectively. Interestingly, 13 VvBTB genes exhibited differential expression in at least one of the developmental stages and biotic and abiotic stresses. Further, miRNA target prediction of 13 VvBTB genes revealed that vvi-miR482 targets VvBTB56, and multiple miRNAs, such as vvi-miR172, vvi-miR169 and vvi-miR399, target VvBTB24, which provides an insight into the essential role of the BTB family in the grapevine. Our study provides the first comprehensive analysis and essential information that can potentially be used for further functional investigation of BTB genes in this economically important fruit crop. Full article

(This article belongs to the Special Issue Advances in Functional Genomics for Crop Improvement)

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Review

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Open AccessReview

Plant Synthetic Promoters: Advancement and Prospective

Santosh Kumar Upadhyay

Lini Sethi

and

Nrisingha Dey

Agriculture 2023, 13(2), 298; https://doi.org/10.3390/agriculture13020298 - 26 Jan 2023

Cited by 1 | Viewed by 1167

Abstract

Native/endogenous promoters have several fundamental limitations in terms of their size, Cis-elements distribution/patterning, and mode of induction, which is ultimately reflected in their insufficient transcriptional activity. Several customized synthetic promoters were designed and tested in plants during the past decade to circumvent such constraints. Such synthetic promoters have a built-in capacity to drive the expression of the foreign genes at their maximum amplitude in plant orthologous systems. The basic structure and function of the promoter has been discussed in this review, with emphasis on the role of the Cis-element in regulating gene expression. In addition to this, the necessity of synthetic promoters in the arena of plant biology has been highlighted. This review also provides explicit information on the two major approaches for developing plant-based synthetic promoters: the conventional approach (by utilizing the basic knowledge of promoter structure and Cis-trans interaction) and the advancement in gene editing technology. The success of plant genetic manipulation relies on the promoter efficiency and the expression level of the transgene. Therefore, advancements in the field of synthetic promoters has enormous potential in genetic engineering-mediated crop improvement. Full article

(This article belongs to the Special Issue Advances in Functional Genomics for Crop Improvement)

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Open AccessReview

CRISPR/Cas9 for Insect Pests Management: A Comprehensive Review of Advances and Applications

Santosh Kumar Upadhyay

Geetanjali Mishra

and

Praveen C. Verma

Agriculture 2022, 12(11), 1896; https://doi.org/10.3390/agriculture12111896 - 10 Nov 2022

Cited by 1 | Viewed by 1913

Abstract

Insect pests impose a serious threat to agricultural productivity. Initially, for pest management, several breeding approaches were applied which have now been gradually replaced by genome editing (GE) strategies as they are more efficient and less laborious. CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-associated system) was discovered as an adaptive immune system of bacteria and with the scientific advancements, it has been improvised into a revolutionary genome editing technique. Due to its specificity and easy handling, CRISPR/Cas9-based genome editing has been applied to a wide range of organisms for various research purposes. For pest control, diverse approaches have been applied utilizing CRISPR/Cas9-like systems, thereby making the pests susceptible to various insecticides, compromising the reproductive fitness of the pest, hindering the metamorphosis of the pest, and there have been many other benefits. This article reviews the efficiency of CRISPR/Cas9 and proposes potential research ideas for CRISPR/Cas9-based integrated pest management. CRISPR/Cas9 technology has been successfully applied to several insect pest species. However, there is no review available which thoroughly summarizes the application of the technique in insect genome editing for pest control. Further, authors have highlighted the advancements in CRISPR/Cas9 research and have discussed its future possibilities in pest management. Full article

(This article belongs to the Special Issue Advances in Functional Genomics for Crop Improvement)

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