Abiotic Stress-Mediated Sensing and Signaling in Plants: An Omics Perspective

Abiotic Stress-Mediated Sensing and Signaling in Plants: An Omics Perspective
Author: Sajad Majeed Zargar
Publisher: Springer
Total Pages: 358
Release: 2018-02-20
Genre: Science
ISBN: 9811074798
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The natural environment for plants is composed of a complex set of abiotic and biotic stresses; plant responses to these stresses are equally complex. Systems biology allows us to identify regulatory hubs in complex networks. It also examines the molecular “parts” (transcripts, proteins and metabolites) of an organism and attempts to combine them into functional networks or models that effectively describe and predict the dynamic activities of that organism in different environments. This book focuses on research advances regarding plant responses to abiotic stresses, from the physiological level to the molecular level. It highlights new insights gained from the integration of omics datasets and identifies remaining gaps in our knowledge, outlining additional focus areas for future crop improvement research. Plants have evolved a wide range of mechanisms for coping with various abiotic stresses. In many crop plants, the molecular mechanisms involved in a single type of stress tolerance have since been identified; however, in order to arrive at a holistic understanding of major and common events concerning abiotic stresses, the signaling pathways involved must also be elucidated. To date several molecules, like transcription factors and kinases, have been identified as promising candidates that are involved in crosstalk between stress signalling pathways. However, there is a need to better understand the tolerance mechanisms for different abiotic stresses by thoroughly grasping the signalling and sensing mechanisms involved. Accordingly, this book covers a range of topics, including the impacts of different abiotic stresses on plants, the molecular mechanisms leading to tolerance for different abiotic stresses, signaling cascades revealing cross-talk among various abiotic stresses, and elucidation of major candidate molecules that may provide abiotic stress tolerance in plants.

The Applications of New Multi-Locus GWAS Methodologies in the Genetic Dissection of Complex Traits

The Applications of New Multi-Locus GWAS Methodologies in the Genetic Dissection of Complex Traits
Author: Yuan-Ming Zhang
Publisher: Frontiers Media SA
Total Pages: 236
Release: 2019-06-19
Genre:
ISBN: 2889458342
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Genome-Wide Association Studies (GWAS) are widely used in the genetic dissection of complex traits. Most existing methods are based on single-marker association in genome-wide scans with population structure and polygenic background controls. To control the false positive rate, the Bonferroni correction for multiple tests is frequently adopted. This stringent correction results in the exclusion of important loci, especially for GWAS in crop genetics. To address this issue, multi-locus GWAS methodologies have been recommended, i.e., FASTmrEMMA, ISIS EM-BLASSO, mrMLM, FASTmrMLM, pLARmEB, pKWmEB and FarmCPU. In this Research Topic, our purpose is to clarify some important issues in the application of multi-locus GWAS methods. Here we discuss the following subjects: First, we discuss the advantages of new multi-locus GWAS methods over the widely-used single-locus GWAS methods in the genetic dissection of complex traits, metabolites and gene expression levels. Secondly, large experiment error in the field measurement of phenotypic values for complex traits in crop genetics results in relatively large P-values in GWAS, indicating the existence of small number of significantly associated SNPs. To solve this issue, a less stringent P-value critical value is often adopted, i.e., 0.001, 0.0001 and 1/m (m is the number of markers). Although lowering the stringency with which an association is made could identify more hits, confidence in these hits would significantly drop. In this Research Topic we propose a new threshold of significant QTN (LOD=3.0 or P-value=2.0e-4) in multi-locus GWAS to balance high power and low false positive rate. Thirdly, heritability missing in GWAS is a common phenomenon, and a series of scientists have explained the reasons why the heritability is missing. In this Research Topic, we also add one additional reason and propose the joint use of several GWAS methodologies to capture more QTNs. Thus, overall estimated heritability would be increased. Finally, we discuss how to select and use these multi-locus GWAS methods.

Plant Receptor-Like Kinases

Plant Receptor-Like Kinases
Author: Santosh Kumar Upadhyay
Publisher: Academic Press
Total Pages: 429
Release: 2022-09-27
Genre: Science
ISBN: 0323907172
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Plant Receptor-like Kinases: Role in Development and Stress presents the latest research in receptor-like kinases (RLKs), a class of development and defense-response proteins in plants. As one of the largest protein families, with roles ranging from growth and development to stress response, RLKs are involved in every aspect of the plant life cycle, including growth and development, reproduction, and immunity. Development of high throughput sequencing technology has improved the identification and characterization of numerous gene families in plants in the recent years, allowing researchers to identify and characterize numerous RLK sub-families in model plant species and agro-economically important crop plants like rice, wheat, sorghum, tomatoes, and more. This book provides foundational knowledge on the classification of RLKs, their mechanism of action and their roles in the plant life cycle, as well as the most up-to-date advances in the applications of RLKs. It is an essential read for researchers interested in plant signaling and plant genomics. - Presents detailed information on receptor like kinases (RLKs), including their mechanism of action and classification - Analyzes numerous sub-families of RLKs and their roles in plant development and stress management - Highlights the function of RLKs in plant innate immunity

Advances in Rice Research for Abiotic Stress Tolerance

Advances in Rice Research for Abiotic Stress Tolerance
Author: Mirza Hasanuzzaman
Publisher: Woodhead Publishing
Total Pages: 988
Release: 2018-11-12
Genre: Science
ISBN: 0128143339
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Advances in Rice Research for Abiotic Stress Tolerance provides an important guide to recognizing, assessing and addressing the broad range of environmental factors that can inhibit rice yield. As a staple food for nearly half of the world's population, and in light of projected population growth, improving and increasing rice yield is imperative. This book presents current research on abiotic stresses including extreme temperature variance, drought, hypoxia, salinity, heavy metal, nutrient deficiency and toxicity stresses. Going further, it identifies a variety of approaches to alleviate the damaging effects and improving the stress tolerance of rice. Advances in Rice Research for Abiotic Stress Tolerance provides an important reference for those ensuring optimal yields from this globally important food crop. - Covers aspects of abiotic stress, from research, history, practical field problems faced by rice, and the possible remedies to the adverse effects of abiotic stresses - Provides practical insights into a wide range of management and crop improvement practices - Presents a valuable, single-volume sourcebook for rice scientists dealing with agronomy, physiology, molecular biology and biotechnology

Genetic advancements for improving the plant tolerance to biotic and abiotic stresses

Genetic advancements for improving the plant tolerance to biotic and abiotic stresses
Author: Krishnanand P. Kulkarni
Publisher: Frontiers Media SA
Total Pages: 204
Release: 2024-05-31
Genre: Science
ISBN: 283254990X
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Crop plants are constantly exposed to multiple abiotic (such as drought, salinity, cold, flooding, heavy metal, and heat) and/or biotic (bacterial/fungal/viral) stress factors that hinder their growth and development, subsequently leading to decreases in quality and yield. During the last two decades, many classical genetic and breeding approaches have been used to develop stress-tolerant and climate-adaptable plants that can provide a better yield to meet food demands. Climate change poses a major risk to food security as the world faces frequent floods, droughts, heat waves, and the emergence of new invasive pests and diseases. Novel genomic and genetic approaches look promising to improve plant resilience under stress conditions and achieve sustainable crop improvements. Recent advances in sequencing technologies have facilitated the generation of a plethora of genomic resources in a variety of crop and plant species. With the increased availability of genomic and transcriptomic data, an increasing number of quantitative trait loci and candidate genes are being identified for their application in improving plant tolerance to abiotic and biotic stresses. New approaches such as genomic selection and genomic-assisted breeding have been utilized to develop stress-tolerant cultivars in a variety of plant species. Furthermore, transgenics and rapidly evolving CRISPR technology offer great potential for plant improvement. This Research Topic aims to provide insights into the molecular and genetic factors involved in imparting abiotic and biotic stress tolerance in plants and their application in enhancing plant adaptation to these stress conditions. To review the progress in this research category, we invite manuscripts related to the plant responses to abiotic/biotic stresses and trait improvement through genomic selection, and transgenic or gene-editing approaches. Studies including physiological, biochemical, and molecular genetic analyses revealing the mechanisms involved in plant response to abiotic/biotic stresses are welcome. Topic editor Dr. Balaji Aravindhan Pandian is employed by Enko Chem Inc. All other Topic Editors declare no competing interests with regard to the Research Topic subject.

Applied Plant Genomics and Biotechnology

Applied Plant Genomics and Biotechnology
Author: Palmiro Poltronieri
Publisher: Woodhead Publishing
Total Pages: 354
Release: 2015-01-27
Genre: Science
ISBN: 0081000715
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Applied plant genomics and biotechnology reviews the recent advancements in the post-genomic era, discussing how different varieties respond to abiotic and biotic stresses, investigating epigenetic modifications and epigenetic memory through analysis of DNA methylation states, applicative uses of RNA silencing and RNA interference in plant physiology and in experimental transgenics, and plants modified to produce high-value pharmaceutical proteins. The book provides an overview of research advances in application of RNA silencing and RNA interference, through Virus-based transient gene expression systems, Virus induced gene complementation (VIGC), Virus induced gene silencing (Sir VIGS, Mr VIGS) Virus-based microRNA silencing (VbMS) and Virus-based RNA mobility assays (VRMA); RNA based vaccines and expression of virus proteins or RNA, and virus-like particles in plants, the potential of virus vaccines and therapeutics, and exploring plants as factories for useful products and pharmaceuticals are topics wholly deepened. The book reviews and discuss Plant Functional Genomic studies discussing the technologies supporting the genetic improvement of plants and the production of plant varieties more resistant to biotic and abiotic stresses. Several important crops are analysed providing a glimpse on the most up-to-date methods and topics of investigation. The book presents a review on current state of GMO, the cisgenesis-derived plants and novel plant products devoid of transgene elements, discuss their regulation and the production of desired traits such as resistance to viruses and disease also in fruit trees and wood trees with long vegetative periods. Several chapters cover aspects of plant physiology related to plant improvement: cytokinin metabolism and hormone signaling pathways are discussed in barley; PARP-domain proteins involved in Stress-Induced Morphogenetic Response, regulation of NAD signaling and ROS dependent synthesis of anthocyanins. Apple allergen isoforms and the various content in different varieties are discussed and approaches to reduce their presence. Euphorbiaceae, castor bean, cassava and Jathropa are discussed at genomic structure, their diseases and viruses, and methods of transformation. Rice genomics and agricultural traits are discussed, and biotechnology for engineering and improve rice varieties. Mango topics are presented with an overview of molecular methods for variety differentiation, and aspects of fruit improvement by traditional and biotechnology methods. Oilseed rape is presented, discussing the genetic diversity, quality traits, genetic maps, genomic selection and comparative genomics for improvement of varieties. Tomato studies are presented, with an overview on the knowledge of the regulatory networks involved in flowering, methods applied to study the tomato genome-wide DNA methylation, its regulation by small RNAs, microRNA-dependent control of transcription factors expression, the development and ripening processes in tomato, genomic studies and fruit modelling to establish fleshy fruit traits of interest; the gene reprogramming during fruit ripening, and the ethylene dependent and independent DNA methylation changes. - provides an overview on the ongoing projects and activities in the field of applied biotechnology - includes examples of different crops and applications to be exploited - reviews and discusses Plant Functional Genomic studies and the future developments in the field - explores the new technologies supporting the genetic improvement of plants

Marker-Assisted Selection (MAS) in Crop Plants, volume II

Marker-Assisted Selection (MAS) in Crop Plants, volume II
Author: Ting Peng
Publisher: Frontiers Media SA
Total Pages: 307
Release: 2024-06-13
Genre: Science
ISBN: 2832550355
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Global climate change, reductions in arable land, and food security demands that plant breeding will continue to play an imperative role in feeding 9 billion people sustainably by 2050. In order to face this challenge, modern plant breeding will necessitate the adoption of new technologies and practices to boost production of cultivated plants by capturing or generating more favorable genetic diversity. In crop plants, the majority of agronomically important traits are quantitatively inherited, controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). The most common approach to pre-breeding is to use genetic mapping to identify QTLs for key phenotypic variation followed by introgressing those QTLs into the elite gene pool with marker-assisted selection (MAS), which can enhance the selection criteria of phenotypes comparing to conventional breeding with the selection of genes. As the cost of genotyping continues to decline, the use of genotyping-by-sequencing (GBS) technologies or whole genome re-sequencing, coupled with the release of the genome sequences of plant species have permitted the development of dense arrays of single nucleotide polymorphisms (SNPs) covering the entire genome, which have in turn paved the way to genome-wide association studies (GWAS). Meanwhile, fine mapping guided by genome sequences of many plant species have facilitated the exploration of functional genes; in addition, pan-genomes constructed from various available resources such as the reference sequence and its variants, raw reads and haplotype reference panels provide a new perspective on QTL locations and potential molecular targets for plant breeding. Similarly, new approaches to marker-trait association analyses such as quantitative trait locus sequencing (QTL-seq) and quantitative trait gene sequencing (QTG-seq) that are based on bulked-segregant analysis (BSA) and whole-genome resequencing will help accelerate QTL fine-mapping and identification of the causal genes. In conclusion, the tools and strategies for MAS in modern plant breeding have been expanding in recent years. By embracing a broad array of conventional and new molecular techniques, modern plant breeding has a bright future in delivering new crop cultivars to keep our food, fiber and biobased economy diverse and safe.

Mapping Abiotic Stress-Tolerance Genes in Plants

Mapping Abiotic Stress-Tolerance Genes in Plants
Author: Richard R.-C. Wang
Publisher: MDPI
Total Pages: 450
Release: 2020-12-02
Genre: Science
ISBN: 3039361147
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This book presents the latest research results on plant genes controlling tolerance to abiotic stresses including heat, cold, drought, salt, nitrogen, metals, irradiation, and exogenous phytohormones. The authors report the expression profiles, function/roles in physiological pathways, and chromosomal locations of tolerance genes. The studies involve cytogenetics, genomics, proteomics, and bioinformatics. The information is critical for food security in an environment experiencing global climate changes. Therefore, this book provides a useful reference to students and professionals in plant sciences encompassing genetics, physiology, chemistry, and breeding.