Developing Climate-Resilient Crops

Improving Global Food Security and Safety

Shah Fahad, Osman Sonmez, Shah Saud, Depeng Wang, Chao Wu, Muhammad Adnan, Veysel Turan, Shah Fahad, Osman Sonmez, Shah Saud, Depeng Wang, Chao Wu, Muhammad Adnan, Veysel Turan

• Publisher: CRC Press
• Year: 2021
• ISBN:
  9781000380965
• Edition: 1
• Topic: Scienze biologiche
• Subtopic: Botanica

Developing Climate-Resilient Crops: Improving Global Food Security and Safety is timely, as the world is gradually waking up to the fact that a global food crisis of enormous proportions is brewing. Climate change is creating immense problems for agricultural productivity worldwide, resulting in higher food prices. This book elucidates the causative aspects of climate modification related to agriculture, soil, and plants, and discusses the relevant resulting mitigation process and also how new tools and resources can be used to develop climate-resilient crops.

Features:

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• Addresses the limits of the anthropogenic global warming theory advocated by the Intergovernmental Panel on Climate Change

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• Presents the main characters (drought tolerance, heat tolerance, water-use efficiency, disease resistance, nitrogen-use efficiency, nitrogen fixation, and carbon sequestration) necessary for climate-resilient agriculture

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• Delivers both theoretical and practical aspects, and serves as baseline information for future research

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• Provides valuable resource for those students engaged in the field of environmental sciences, soil sciences, agricultural microbiology, plant pathology, and agronomy

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• Highlights factors that are threatening future food production

1

Bimolecular Invention in Understanding Plant Adaptation to Climate Change

Nahid Hazrati and Mohammad Hassanzadeh

Moghan Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran

1.1 Introduction

Increasing innovation in technologies that promote mitigation and adaptation is essential for encountering climate change. Such innovation may decline the costs of policy measures and improve more effectively responses to the complexities of climate changes. A great many literatures have examined the impact of innovation in climate policy (Popp 2010; Saud et al. 2013; Shah et al. 2013; Saud et al. 2014; Hafiz et al. 2016; Saud et al. 2016; Aziz et al. 2017a,b; Habib ur Rahman et al. 2017; Kamarn et al. 2017; Uz Zaman et al. 2017; Saud et al. 2017; Wajid et al. 2017; Yang et al. 2017; Zahida et al. 2017; Adnan et al. 2018a,b; Akram et al. 2018a,b; Depeng et al. 2018; Hafiz et al. 2018; Tariq et al. 2018; Adnan et al. 2019; Ahmad et al. 2019; Baseer et al. 2019; Hafiz et al. 2019; Muhammad et al. 2019; Sajjad et al. 2019; Wu et al. 2019; Adnan et al. 2020; Farhana et al. 2020; Farhat et al. 2020; Hafiz 2020; Hussain et al. 2020; Ilyas et al. 2020; Jan et al. 2019; Mubeen et al. 2020; Rehman et al. 2020; Saleem et al. 2020a,b,c; Shafi et al. 2020; Subhan et al. 2020; Wahid et al. 2020; Wu et al. 2020; Zafar-ul-Hye et al. 2020a,b).

Due to large number of fundamental and applied researches, significant progress has been made so far in understanding the mechanisms and processes of abiotic stress adaptation and defence in various plant species (Fraire-Velázquez et al. 2011; Fahad and Bano 2012; Fahad et al. 2013; Fahad et al. 2014a,b; Fahad et al. 2015a,b; Fahad et al. 2016a,b,c,d; Fahad et al. 2017; Fahad et al. 2018; Fahad et al. 2019a,b; Hesham and Fahad 2020). The sensing of abiotic or biotic stress circumstances induces signalling cascades that activate ion channels; kinase cascades; accumulation of hormones such as salicylic acid (SA), ethylene, jasmonic acid (JA), and abscisic acid; and production of reactive oxygen species (ROS). These signals ultimately induce expression of specific subsets of genes relating to defence that results in the assembly of the overall defence reaction (Jaspers and Kangasjärvi 2010; Pérez-Clemente et al. 2013).

In recent years, Omics technologies have been extensively used in the study of biotic and abiotic stress responses in plants. Omics enables a system biology approach towards understanding the complex interactions between genes, proteins, and metabolites within the resulting phenotype. This approach relies mainly on chemical analytical methods, bioinformatics and computational analysis, and many other disciplines of biology that lead to product conservation and improvement (Van Emon 2016).

Recent advances in genetics are expected to increase crop resilience to climate change by increasing the efficiency of plant breeding to improve agriculture under environmental constraints. It will be particularly useful for efficient exploitation of adaptation traits present in germplasm accessions (Huang and Han 2014) and to expand the gene pool for crop improvement (Brozynska et al. 2016).

In recent years, genomics knowledge based on next-generation sequencing (NGS), gene editing systems, gene silencing, and overexpression methods hasvesuggested a large amount of genetic information to help understanding the mechanisms of biotic and abiotic stress responses in plants (Luan et al. 2015; Ibraheem et al. 2018).

Proteomics is able to successfully distinguish and characterize many proteins in legumes and cereals responsible for stress responses and their regulations (Silva-Sanchez et al. 2015). Metabolomics focuses on the global profile of the metabolites with low molecular weight (<1000 Da) that are the end products of metabolisms in tissues and even whole organisms that are produced in response to abiotic stresses such as heavy metal toxicity, salinity, drought, and so on (Brosche et al. 2005; Ibraheem et al. 2018).

1.2 Genomics

1.2.1 Molecular Marker Resources

Although we have available tools, understanding of the genetic basis of adaptation is still an interesting task. We only have a basic understanding of most important traits, and the number of genes controlling each of these traits is large; therefore, the entire (and objective) approach would be understanding correlation between genes with phenotypes by scanning the whole genome with molecular markers (Howe and Brunner 2005). Molecular makers are used to detect the genetic variation caused by DNA polymorphisms in the DNA. The whole genome sequencing (WGS) provided the basis for the development of thousands of simple sequence repeat (SSR) markers and millions of single-nucleotide polymorphism (SNP) markers. The main method for the development of plant adaptation is molecular mapping and marker-assisted selection. In different species, amplified fragment length polymorphism (AFLPs), restriction fragment length polymorphism (RFLPs), RAPDs, microsatellites or simple sequence repeat (SSR), and SNPs are used for mapping of interesting traits (Iqbal 2019).

Since commercial SNP-genotyping platforms, such as Taqman, SNPlex, KASPar, Axiom Biobank, Infinium II, BioMark HD, GoldenGate, and iPlex, have been developed, the cost per data point for SNP-based genotyping has become cheaper than that for SSRs. However, the SNP information for target organisms is essential for commercial SNP-genotyping platforms, causing the increased costs and a longer experimental time (Kim et al. 2016; Chung et al. 2017).

Appearance of the next-generation sequencing (NGS) technologies has provided new opportunities for potent genotyping in various plant species. Recent improvements in high-throughput sequencing have enabled sequences to be used to detect and score single-nucleotide polymorphisms (SNPs) by shortening of the time-consuming process needed for marker development (Chung et al. 2017). Three main complexity reduction methods, namely reduced representation libraries (RRLs), restriction site associated DNA (RAD) sequencing, and genotyping-by-sequencing (GBS), are routinely used. Among these, GBS is a simple, robust, and affordable procedure for SNP distinguishing and mapping. Totally, this approach decreases complexity of genome with restriction enzymes (REs) in high diversity, and large genome species for efficient, high-throughput, and highly multiplexed sequencing. By using appropriate REs, repetitive regions of genomes can be inhibited and lower copy regions can be targeted, which decrease problems of alignments in genetically diverse species. This method was first explained by Elshire Robert et al. (2011). However, sequencing-based genotyping methods require computational expertise and a lot of time for analysing of data. This inhibits its use in marker-assisted breeding where timely selection is very crucial (Deshmukh et al. 2014).

Genome-wide association study (GWAS) is an observational study of a genome-wide set of genetic variants in different individuals to observe association of any variant with a trait. GWAS assesses the entire genome, opposite to methods that specifically test a small number of prespecified genetic regions. GWAS typically concentrates on correlations between single-nucleotide polymorphisms (SNPs) and traits. In general, where natural selection is acting and fixing the allele (eliminating other variants) of the SNPs, that constitutes the most favourable genetic adaptation (Barreiro et al. 2008).

Integrative investigations including GWAS, functional studies, selection scans, and fitness measurements in this regard have successfully distinguished loci for adaptation, demonstrated the molecular basis of genetic trade-offs, and showed that fitness can be predicted by polygenic effects of a number of loci related to local climate (Bamba et al. 2019).

1.2.2 QTL Mapping

Candidate genes can also be distinguished based on their positions on quantitative trait locus (QTL) maps or patterns of gene expression. Mapping quantitative trait loci (QTL) has become a routine tool for complex traits in functional genomic studies. Functional genomics is an important tool to find the correlation between phenotype and genome of an organism subjected to various environmental conditions (Soda et al. 2015; Ahmad et al. 2018). However, the construction of a high-density genetic linkage map is essential for genetic investigation of a target trait through quantitative trait locus (QTL) analysis. Moreover, high-resolution genetic linkage map is a crucial and powerful tool for positional cloning of genes, comparative genomic analysis, and scaffold sequence anchoring and genome assembly (Jones et al. 2009; Tang et al. 2019).

QTL analysis is complicated by the fact that one QTL region can have pleiotropic effects on a wide range of traits or consists of multiple QTLs. In addition, QTLs are frequently subjected to epistatic interactions, and their traits can be significantly influenced by the environment (Dixit et al. 2014; Tsaneva et al. 2019), so it is important to identify specific genes from new germplasm resources that are tolerant to multiple stresses. Exploit of the functions of genes that are responsible for drought will enable the plant biologists to use them in plant breeding programs to obtain cultivars resistant to drought stress (Ahmed et al. 2011). Realizing that mechanism of drought tolerance is quantitatively inherited and controlled by various genetic loci has led to the development of several drought-related QTLs (Sayed et al. 2012; Kalladan et al. 2013). Ahmad et al. (2018) have collected QTLs for different traits related to the ada...