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Recent Trends in Genomics and Transcriptomics of Field Crops
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Recent Trends in Genomics and Transcriptomics of Field Crops

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (15 June 2022) | Viewed by 18740

Special Issue Editors

Dr. Muhammud Qasim Shahid

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Guest Editor
College of Agriculture, South China Agricultural University, Guangzhou 510642, China
Interests: plant breeding and genetics; agronomy; molecular biology; polyploidy; plant reproduction
Special Issues, Collections and Topics in MDPI journals
Dr. Faheem Shehzad Baloch

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Guest Editor
Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
Interests: genetic diversity; plant responses to abiotic stress; molecular markers; plant breeding; food security
Special Issues, Collections and Topics in MDPI journals
Dr. Ephrem Habyarimana

E-Mail Website
Guest Editor
CREA Research Center for Cereal and Industrial Crops, 40128 Bologna, Italy
Interests: cereals; molecular breeding; high-throughput phenotyping; GWAS; big data analysis and genomic selection
Special Issues, Collections and Topics in MDPI journals
Dr. Muhammad Azhar Nadeem

E-Mail Website
Guest Editor
Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Turkey
Interests: legumes; germplasm characterization; molecular breeding; molecular genetics; genetic diversity; molecular markers; genome-wide association studies (GWAS); marker-assisted breeding; QTL mapping; DNA studies
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It is well known that there are more than 600 cultivated plant species, from which about 100–200 species play an important role in world trade and serve as a source of food for human beings. Field crops are considered to be the main pillar of agriculture production systems as they provide commodities essential for the survival of human beings on this planet. Field crops include cereals, legumes, oilseed, industrial crops, medicinal plants and other minor crops that are cultivated all over the world.

Currently, human society is at a turning point of its time due to climate change, which is becoming increasingly more real and inevitable. The world is facing various unprecedented scenarios such as rising temperature to melting glaciers and resulting various biotic and abiotic stresses, ultimately leading to food scarcity. Under such circumstances, there is the utmost requirement to unlock the repository of genetic basis and extensive utilization of germplasm to develop “Climate Resilient Cultivars” through the application of plant breeding and biotechnological tools.

Recent advancement in molecular markers, transcriptomics, gene expression, genome sequencing, and genome editing technologies has revolutionized the field of plant breeding. Now, efforts are ongoing with rapid pace using various plant breeding and biotechnological tools to develop cultivars with better adaptation to the changing climatic conditions. Therefore, this Special Issue of Plants journal will provide a platform to the scientific and breeding community to share their research and review studies regarding the genomic, transcriptomic and biotechnological aspects of field crops. This Special Issue will cover a wide variety of areas including:

  • Germplasm characterization of field crops;
  • Genomic and genetic advancement in field crops;
  • Identifiction of genomic regions for trait of interest in field crops;
  • Transcriptomics and RNAseq of field crops;
  • Gene expression and genome editing of field crops for trait of interest;
  • Tissue culture and gene transformation in field crops;
  • Genomic prediction and marker-assisted breeding for trait of interest;
  • High-throughput phenotyping and big data analysis in field crops.

Dr. Muhammud Qasim Shahid
Dr. Faheem Shehzad Baloch
Dr. Ephrem Habyarimana
Dr. Muhammad Azhar Nadeem
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. Plants is an international peer-reviewed open access semimonthly 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 2700 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

  • Cereals
  • Legumes
  • Oilseed
  • Industrial crops
  • Medicinal plants
  • Genetic diversity
  • Genomics
  • Marker-assisted selection
  • Genomic selection
  • Big data analysis
  • KASP
  • CRISPR-Cas9

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Published Papers (5 papers)

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Research

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16 pages, 26681 KiB  
Article
High-Throughput RNA Sequencing of Mosaic Infected and Non-Infected Apple (Malus × domestica Borkh.) Cultivars: From Detection to the Reconstruction of Whole Genome of Viruses and Viroid
by Sajad U. Nabi, Virendra K. Baranwal, Govind P. Rao, Sheikh Mansoor, Carmen Vladulescu, Wasim H. Raja, Basit L. Jan and Saleh Alansi
Plants 2022, 11(5), 675; https://doi.org/10.3390/plants11050675 - 1 Mar 2022
Cited by 16 | Viewed by 3552
Abstract
Many viruses have been found associated with apple mosaic disease in different parts of the world. In order to reveal and characterize the viruses and viroids in symptomatic apple plants, next-generation sequencing (RNA seq.) of rRNA-depleted total RNA using Illumina Hiseq2500 was applied [...] Read more.
Many viruses have been found associated with apple mosaic disease in different parts of the world. In order to reveal and characterize the viruses and viroids in symptomatic apple plants, next-generation sequencing (RNA seq.) of rRNA-depleted total RNA using Illumina Hiseq2500 was applied to two cultivars, Oregon Spur and Golden Delicious, with symptoms of mosaic and necrosis and one cultivar, Red Fuji, which was asymptomatic. The RNA sequencing detected five viruses, viz., apple necrotic mosaic virus (ApNMV), apple mosaic virus (ApMV), apple stem grooving virus (ASGV) and apple stem pitting virus (ASPV), apple chlorotic leaf spot virus (ACLSV), and one viroid i.e., apple hammerhead viroid (AHVd). RT-PCR amplification and sequencing also confirmed the presence of all these five viruses and viroids detected in HTS of total RNA. The complete genomes of five viruses and AHVd were reconstructed. The phylogenetic analysis of these viruses and AHVd revealed genetic diversity by forming subclusters with isolates from other countries. Recombination events were observed in all five viruses while single-nucleotide variants were detected only in ApMV and ApNMV. The absence of ApMV and ApNMV in asymptomatic samples from the same cultivars in an RT-PCR assay indicated that these two viruses are associated with mosaic disease of apples in India. This is the first viral genome analysis of symptomatic and asymptomatic apple plants and the first report of genome characterization of viruses associated with apple mosaic disease from India. High-throughput RNA sequencing is a powerful tool to characterize the genome of viruses and viroids in plants previously undetected by conventional methods. This would also help in the indexing and certification of large-scale germplasm. Full article
(This article belongs to the Special Issue Recent Trends in Genomics and Transcriptomics of Field Crops)
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21 pages, 2594 KiB  
Article
Genome-Wide Identification and Expression Profiling of Potassium Transport-Related Genes in Vigna radiata under Abiotic Stresses
by Farrukh Azeem, Usman Ijaz, Muhammad Amjad Ali, Sabir Hussain, Muhammad Zubair, Hamid Manzoor, Muhammad Abid, Roshan Zameer, Dong-Seon Kim, Kirill S. Golokhvast, Gyuhwa Chung, Sangmi Sun and Muhammad Amjad Nawaz
Plants 2022, 11(1), 2; https://doi.org/10.3390/plants11010002 - 21 Dec 2021
Cited by 17 | Viewed by 4402
Abstract
Potassium (K+) is one of the most important cations that plays a significant role in plants and constitutes up to 10% of plants’ dry weight. Plants exhibit complex systems of transporters and channels for the distribution of K+ from soil [...] Read more.
Potassium (K+) is one of the most important cations that plays a significant role in plants and constitutes up to 10% of plants’ dry weight. Plants exhibit complex systems of transporters and channels for the distribution of K+ from soil to numerous parts of plants. In this study, we have identified 39 genes encoding putative K+ transport-related genes in Vigna radiata. Chromosomal mapping of these genes indicated an uneven distribution across eight out of 11 chromosomes. Comparative phylogenetic analysis of different plant species, i.e., V. radiata, Glycine max, Cicer arietinum, Oryza sativa, and Arabidopsis thaliana, showed their strong conservation in different plant species. Evolutionary analysis of these genes suggests that gene duplication is a major route of expansion for this family in V. radiata. Comprehensive promoter analysis identified several abiotic stresses related to cis-elements in the promoter regions of these genes, suggesting their role in abiotic stress tolerance. Our additional analyses indicated that abiotic stresses adversely affected the chlorophyll concentration, carotenoids, catalase, total soluble protein concentration, and the activities of superoxide and peroxidase in V. radiata. It also disturbs the ionic balance by decreasing the uptake of K+ content and increasing the uptake of Na+. Expression analysis from high-throughput sequencing data and quantitative real-time PCR experiments revealed that several K+ transport genes were expressed in different tissues (seed, flower, and pod) and in abiotic stress-responsive manners. A highly significant variation of expression was observed for VrHKT (1.1 and 1.2), VrKAT (1 and 2) VrAKT1.1, VrAKT2, VrSKOR, VrKEA5, VrTPK3, and VrKUP/HAK/KT (4, 5, and 8.1) in response to drought, heat or salinity stress. It reflected their potential roles in plant growth, development, or stress adaptations. The present study gives an in-depth understanding of K+ transport system genes in V. radiata and will serve as a basis for a functional analysis of these genes. Full article
(This article belongs to the Special Issue Recent Trends in Genomics and Transcriptomics of Field Crops)
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20 pages, 3239 KiB  
Article
Genome-Wide Identification, Genomic Organization, and Characterization of Potassium Transport-Related Genes in Cajanus cajan and Their Role in Abiotic Stress
by Muhammad Hussnain Siddique, Naeem Iqbal Babar, Roshan Zameer, Saima Muzammil, Nazia Nahid, Usman Ijaz, Ashir Masroor, Majid Nadeem, Muhammad Abdul Rehman Rashid, Abeer Hashem, Farrukh Azeem and Elsayed Fathi Abd_Allah
Plants 2021, 10(11), 2238; https://doi.org/10.3390/plants10112238 - 20 Oct 2021
Cited by 14 | Viewed by 3218
Abstract
Potassium is the most important and abundant inorganic cation in plants and it can comprise up to 10% of a plant’s dry weight. Plants possess complex systems of transporters and channels for the transport of K+ from soil to numerous parts of [...] Read more.
Potassium is the most important and abundant inorganic cation in plants and it can comprise up to 10% of a plant’s dry weight. Plants possess complex systems of transporters and channels for the transport of K+ from soil to numerous parts of plants. Cajanus cajan is cultivated in different regions of the world as an economical source of carbohydrates, fiber, proteins, and fodder for animals. In the current study, 39 K+ transport genes were identified in C. cajan, including 25 K+ transporters (17 carrier-like K+ transporters (KUP/HAK/KTs), 2 high-affinity potassium transporters (HKTs), and 6 K+ efflux transporters (KEAs) and 14 K+ channels (9 shakers and 5 tandem-pore K+ channels (TPKs). Chromosomal mapping indicated that these genes were randomly distributed among 10 chromosomes. A comparative phylogenetic analysis including protein sequences from Glycine max, Arabidopsis thaliana, Oryza sativa, Medicago truncatula Cicer arietinum, and C. cajan suggested vital conservation of K+ transport genes. Gene structure analysis showed that the intron/exon organization of K+ transporter and channel genes is highly conserved in a family-specific manner. In the promoter region, many cis-regulatory elements were identified related to abiotic stress, suggesting their role in abiotic stress response. Abiotic stresses (salt, heat, and drought) adversely affect chlorophyll, carotenoids contents, and total soluble proteins. Furthermore, the activities of catalase, superoxide, and peroxidase were altered in C. cajan leaves under applied stresses. Expression analysis (RNA-seq data and quantitative real-time PCR) revealed that several K+ transport genes were expressed in abiotic stress-responsive manners. The present study provides an in-depth understanding of K+ transport system genes in C. cajan and serves as a basis for further characterization of these genes. Full article
(This article belongs to the Special Issue Recent Trends in Genomics and Transcriptomics of Field Crops)
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11 pages, 2505 KiB  
Article
Over-Expression of Endogenous SUGARWIN Genes Exalted Tolerance against Colletotrichum Infection in Sugarcane
by Aqsa Parvaiz, Ghulam Mustafa, Muhammad Sarwar Khan and Muhammad Amjad Ali
Plants 2021, 10(5), 869; https://doi.org/10.3390/plants10050869 - 26 Apr 2021
Cited by 4 | Viewed by 2301
Abstract
Sugarcane being the major contributor of sugar and potential source of biofuel around the globe, occupies significant commercial importance. Red rot is the most devastating disease of sugarcane, severely affecting its quality as well as yield. Here we report the overexpression of SUGARWIN1 [...] Read more.
Sugarcane being the major contributor of sugar and potential source of biofuel around the globe, occupies significant commercial importance. Red rot is the most devastating disease of sugarcane, severely affecting its quality as well as yield. Here we report the overexpression of SUGARWIN1 and SUGARWIN2 genes in any field crop for the first time. For this purpose, SUGAWIN1 and SUGARWIN2 were cloned downstream of maize ubiquitin (Ubi-1) promoter to construct two independent expression cassettes. The bar gene conferring resistance against phosphinothricin was used as selectable marker. Embryogenic calli of sugarcane were bombarded with both expression cassettes and selected on regeneration medium supplemented with phosphinothricin. The phosphinothricin-resistant shoots were rooted and then, analyzed using molecular tools at the genomic as well as transcriptomic levels. The transcriptomic analysis, using real time qPCR, showed that expression of SUGARWIN1 (SWO) and SUGARWIN2 (SWT) was higher in transgenic plants as compared to untransformed plants. Our results further demonstrated that over expression of these genes under maize ubiquitin (Ubi-1) promoter causes significant restriction in proliferation of red rot causal agent, Colletotrichum falcatum in sugarcane transgenic plants, under in vitro conditions. This report may open up exciting possibilities to extend this technology to other monocots for the development of crops with better ability to withstand fungal pathogens. Full article
(This article belongs to the Special Issue Recent Trends in Genomics and Transcriptomics of Field Crops)
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Review

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21 pages, 3064 KiB  
Review
An Insight into Animal Glutamate Receptors Homolog of Arabidopsis thaliana and Their Potential Applications—A Review
by Ruphi Naz, Andleeb Khan, Badrah S. Alghamdi, Ghulam Md Ashraf, Maimonah Alghanmi, Altaf Ahmad, Sheikh Shanawaz Bashir and Qazi Mohd Rizwanul Haq
Plants 2022, 11(19), 2580; https://doi.org/10.3390/plants11192580 - 30 Sep 2022
Cited by 8 | Viewed by 2699
Abstract
Most excitatory impulses received by neurons are mediated by ionotropic glutamate receptors (iGluRs). These receptors are located at the apex and play an important role in memory, neuronal development, and synaptic plasticity. These receptors are ligand-dependent ion channels that allow a wide range [...] Read more.
Most excitatory impulses received by neurons are mediated by ionotropic glutamate receptors (iGluRs). These receptors are located at the apex and play an important role in memory, neuronal development, and synaptic plasticity. These receptors are ligand-dependent ion channels that allow a wide range of cations to pass through. Glutamate, a neurotransmitter, activates three central ionotropic receptors: N-methyl-D-aspartic acid (NMDA), -amino-3-hydroxy-5-methylisoxazole-4-propionate (AMPA), and kainic acid (KA). According to the available research, excessive glutamate release causes neuronal cell death and promotes neurodegenerative disorders. Arabidopsis thaliana contains 20 glutamate receptor genes (AtGluR) comparable to the human ionotropic glutamate (iGluRs) receptor. Many studies have proved that AtGL-rec genes are involved in a number of plant growth and physiological activities, such as in the germination of seeds, roots, abiotic and biotic stress, and cell signaling, which clarify the place of these genes in plant biology. In spite of these, the iGluRs, Arabidopsis glutamate receptors (AtGluR), is associated with the ligand binding activity, which confirms the evolutionary relationship between animal and plant glutamate receptors. Along with the above activities, the impact of mammalian agonists and antagonists on Arabidopsis suggests a correlation between plant and animal glutamate receptors. In addition, these glutamate receptors (plant/animal) are being utilized for the early detection of neurogenerative diseases using the fluorescence resonance energy transfer (FRET) approach. However, a number of scientific laboratories and institutes are consistently working on glutamate receptors with different aspects. Currently, we are also focusing on Arabidopsis glutamate receptors. The current review is focused on updating knowledge on AtGluR genes, their evolution, functions, and expression, and as well as in comparison with iGluRs. Furthermore, a high throughput approach based on FRET nanosensors developed for understanding neurotransmitter signaling in animals and plants via glutamate receptors has been discussed. The updated information will aid in the future comprehension of the complex molecular dynamics of glutamate receptors and the exploration of new facts in plant/animal biology. Full article
(This article belongs to the Special Issue Recent Trends in Genomics and Transcriptomics of Field Crops)
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