Plant-Microbe Interactions

Harnessing Next-Generation Molecular Technologies for Sustainable Agriculture

Jagajjit Sahu, Anukool Vaishnav, Harikesh Bahadur Singh, Jagajjit Sahu, Anukool Vaishnav, Harikesh Bahadur Singh

• Publisher: CRC Press
• Year: 2022
• Print ISBN: 9780367774424
• eBook ISBN: 9781000613988
• Edition: 1
• Topic: Medicine
• Subtopic: Biology

A constant research effort to understand plant-microbe interactions makes it indispensable to keep abreast of the latest research developments. Researchers from a range of disciplines have used multiple approaches to infer this field. With the advent of next-generation techniques, both molecular and computational, the field has entered a new phase. These approaches often result in massive information, which is sometimes tangled and in need of further analysis. These types of analyses also require cutting-edge data analytics as well as efficient statistical models.

Plant-Microbe Interactions: Harnessing Next-Generation Molecular Technologies for Sustainable Agriculture provides a comprehensive picture of the modern-day analytics and approaches being used to provide insights into the interactions between plant and microbe. A wide range of technologies are explored along with practical guides toward these techniques. A detailed understanding of omics data in various areas could be obtained from this compilation.

Key Features:

• Crosstalk between plant and microbe

• Overview of advanced molecular techniques used to study plant-microbe interaction

• Practical guide to technologies such as NGS

• Omics data analysis used to study plant-microbe interaction

• Role of soil metagenomics

• Advanced technologies such as nanotechnology and CRISPR serving to study plant-microbe interaction

This book will serve as a great reference to various next-generation techniques in the field of plant-microbe interaction, thereby helping to better understand the mechanism. This will also help budding researchers to shape their research in similar areas.

1 Novel Approaches and Advanced Molecular Techniques for Crop Improvement

Dhanawantari L. Singha

CSIR-​North East Institute of Science and Technology

Debajit Das, Ricky Raj Paswan

CSIR-North East Institute of Science and Technology

Channakeshavaiah Chikkaputtaiah^*

CSIR-​North East Institute of Science and Technology

Sanjeev Kumar^*

Indian Institute of Technology Guwahati

DOI: 10.1201/9781003171416-1

CONTENTS

1. 1.1 Introduction
2. 1.2 Plant Tissue Culture in Crop Improvement
3. 1.3 Crop Improvement by Genetic Engineering
   1. 1.3.1 Mutagenesis
   2. 1.3.2 Genome Editing
   3. 1.3.3 RNA Interference (RNAi)
   4. 1.3.4 Metabolic Engineering
4. 1.4 Novel Genomics Technologies
   1. 1.4.1 Application of Next-​Generation Sequencing (NGS) Technologies to Crop Improvement
   2. 1.4.2 Implications of Different “Omics” Approaches in Crop Improvement
      1. 1.4.2.1 Genomics in Crop Improvement
      2. 1.4.2.2 Transcriptomics in Crop Improvement
      3. 1.4.2.3 Proteomics in Crop Improvement
      4. 1.4.2.4 Metabolomics in Crop Improvement
5. 1.5 Role of Bioinformatics in Crop Improvement
6. 1.6 Nanotechnology in Crop Improvement
7. 1.7 Modern Breeding Techniques for Crop Improvement
   1. 1.7.1 Allele Mining for Crop Improvement
      1. 1.7.1.1 EcoTILLING-​Based Allele Mining
      2. 1.7.1.2 Sequencing-​Based Allele Mining
      3. 1.7.1.3 Haplotype-​Based AM
   2. 1.7.2 Gene Pyramiding for Crop Improvement
      1. 1.7.2.1 Marker-​Assisted Gene Pyramiding
      2. 1.7.2.2 Marker-​Assisted Backcrossing
   3. 1.7.3 Implication of Marker-​Assisted Recurrent Selection (MARS) in Crop Improvement
   4. 1.7.4 Implication of Genome-​Wide Selection or Genomic Selection (GWS or GS) in Crop Improvement
8. 1.8 Summary and Future Prospects
9. Abbreviations
10. References

^* Corresponding author’s email: [email protected] & [email protected]

1.1 Introduction

Food is utmost necessity for sustainability of human life on earth. Varieties of crops have been harvested since greater than thousands of years. With the continuously increasing global population, which is expected to increase from 7.4 billion in 2016 to more than 9–​9.3 billion by 2050, the demand of food will rise up to 70% and henceforth the need to produce more food. Our agriculture will face enormous challenges to feed the global population, which will be fulfilled by developing climate-​resilient crops with higher yields and improved quality (Tilman, 2012). However, currently, conventional breeding approaches are most widely used for crop improvement, which is more labor intensive and takes several years to develop commercial varieties. Unfortunately, the conventional methods are no more serviceable toward the current needs. To fulfill the global population’s food demand in the present scenario, new methods need to be introduced for better production, improved nutrient content, and enhanced disease resistance. Although, since last five decades, global food grain production is continuously growing proportionate to increasing population, still more than 2 billion people of the world suffer hidden hunger or malnutrition caused by the deficiency of micronutrients and proteins (Ruel‐Bergeron et al., 2015). Recent studies on global food security focus on probable solutions to provide a future balance between consumption and supply of food, which is a reductionist perspective of food security (Calzadilla et al., 2011). It has been assumed that the production of food grain worldwide must be increased by ~60%–​70% by the year 2050 to fulfill the demand of expanding population and growing consumption of food (Godfray et al., 2010; Bruinsma, 2009; FAO, 2015).

In this age of technology, modern biotechnology has opened up new horizons in the field of science, which can provide improved genotypes in several of domesticated crops that can survive under climate change. Recent advancements in the fields of genetic engineering, genomics, and bioinformatics can help in the development of stress-​ and climate-​resilient crops, which can sustain in adverse conditions. In this chapter, we mainly focus on advanced molecular biology applications for crop improvement, such as plant tissue culture, mutagenesis, RNA interference, metabolic engineering, genome editing, various transformation methods, next-​generation sequencing (NGS), and omics approaches. We also highlight advanced bioinformatics tools, role of nanotechnology in crop improvement, allele mining, gene pyramiding, linkage and association mapping, molecular breeding (MB), marker-​assisted backcrossing (MABC), marker-​assisted recurrent selection (MARS), and genome-​wide selection (GWS) for crop improvement.

1.2 Plant Tissue Culture in Crop Improvement

Plant tissue culture (PTC) is an in vitro technology, which has been well recognized and extensively used to regenerate various plant parts and seeds in a nutrient medium (Reddy et al., 2013) and sterile conditions. PTC has become advanced in the recent past to regenerate any kind of plant materials in an artificial nutrient medium with plant hormones and growth regulators with favorable conditions through an in vitro technique such as micropropagation. These techniques are widely adapted to improve a variety of crops with desired characters. The major things required for the plant tissue culture are various plant tissues (explants), suitable medium containing both organic and inorganic compounds as nutrient supplements on which the plantlets could grow and develop further, and various kinds of plant growth hormones, particularly auxin, cytokinin, and gibberellin. PTC method has widely been adapted to create genetic variability from which crop plants can be improved. By associating advanced molecular biology techniques with plant tissue culture, the transfer of desirable trait into crop plants becomes easier. The various ornamental and clonally propagated plant industries are massively working to improve crop cultivars. The genetic variation induced at chromosomal level and transposable variations have widely been seen by tissue culture, which is beneficial for crop improvement. In the recent past, various attempts have been made to produce crops by introducing somaclonal variations. Therefore, a large number of cytoplasmic and nuclear genetic alterations have been made to introduce phenotypic variations. PTC has been considered the safest technique to produce plants with desired traits. The major advantages of PTC on crop improvement are the following: (i) The improved crops from this technology can facilitate the interspecific and intergeneric crosses to overcome physiological barriers-​based self-​incompatibility (Brown and Thorpe, 1995); (ii) a large number of crop varieties have been recovered through pollination of pistils and ovules through either self-​pollination or cross-​pollination; (iii) various agricultural crops such as corn, canola, and cotton tobacco have been developed by implying haploidy; (iv) various economically important plants such as orchids, roses, and bananas have been developed through embryo culture; (v) by using plant tissue culture techniques, micropropagation of ornamental, horticultural plants, secondary metabolites production, and conservation of some endangered medicinal crops can be done; (vi) salinity tolerance has been developed through in vitro selection in tobacco cell lines; (vii) various other varieties with resistance to drought and heat have been developed; (viii) in vitro propagation via cell, tissue, meristem, and organ culture, organogenesis, and somatic embryogenesis have been done in the recent past; (ix) by adapting bio-​farming of some economically important plants, a vast variety of recombinant proteins and number of crucial drugs could be produced; (x) yield and quality of the crops are getting massively increased by using this technology; (xi) various methods of PTC played a dominant role in the second green revolution, in which plant biotechnology was considered to make desirable crops. Various important PTC techniques widely used for crop improvement are wide hybridization, haploidy, somaclonal variation, micropropagation, synthetic seed, pathogen eradication, and germplasm preservation.

1.3 Crop Improvement by Genetic Engineering

1.3.1 Mutagenesis

Mutagenesis is defined as the phenomenon in which sudden heritable changes occur within the genome of an organism. Its occurrence can be spontaneous or can be on exposure to different chemical, physical, or biological agents (Oladosu et al., 2016). In plant science, it has been considered a powerful strategy for bordering genetic variability in various species (Kumawat et al., 2019a). It has great significance, especially in crops where natural sources for the genetic variations are limited. Mutation breeding and plant mutagenesis assume a huge part in expanding the genetic variability for desired traits in various food crops (Chaudhary et al., 2019). In plant breeding programs, physical and chemical mutagens are effectively applied for the advancement of new varieties with improved characteristics (Kodym and Afza, 2003). Now, it’s a mainstay of modern plant breeding, alongside recombinant breeding and transgenic breeding (Shu et al., 2012). In plant science research, different mutagenesis approaches have been utilized to distinguish novel genes and their functional regulations.

In mutation breeding study, three known kinds of mutagenesis are used. The first is radiation-​induced mutagenesis, in which mutations occur as a result of exposure to radiation (gamma rays, X-​rays, or ion beams); the second is chemically induced mutagenesis; and the third is insertional mutagenesis (site-​directed mutagenesis, a result of DNA insertions either through the genetic transformation and through the addition of T-​DNA or the activation of transposable elements) (Forster et al., 2012). Induced mutagenesis is considered as one of the most effective tools for the detection and elucidation of key regulatory genes and molecular mechanisms. It is a promising methodology for delivering new varieties with improved agronomic traits, such as biofortification and higher stress tolerance (biotic and abiotic stresses) (Chaudhary et al., 2019).

Mutation breeding is a three-​step process for direct release of improved crops, which is comprised of (i) inducing mutations which may take up to a year, (ii) screening for putative mutant candidates, and (iii) mutant varietal release. The foremost complicated and time-​devouring step is mutant selection. Generally, several years are required to identify useful traits that are stable throughout the propagation cycles, and the third step, mutant varietal release, follows the standardized procedures of the country where the material is developed. This regularly requires multi-​locational trials with farmer contribution (Jankowicz-​Cieslak et al., 2017). Several years are ordinarily required to recognize valuable characteristics that are uniform through propagation cycles. Whereas the timing of this may shift, it more frequently requires a shorter duration than the selection and testing stage. The procedure gets to be longer and more complicated in case the selected mutants are utilized as pre-​breeding material in hybridizations.

In molecular biology, scientific advancements have re-​enhanced mutation breeding by making it more effective and productive than ever before. With new innovative technological developments, mutation screening by genotype became feasible. The common strategies, Targeting Induced Local Lesions IN Genomes (TILLING) and EcoTILLING, where mutagens are used to induce mutation randomly in the genome to cause a high density of triggered mutations, can specifically distinguish allelic changes in the genome (Wang et al., 2012; Kurowska et al., 2011). TILLING utilizes large offspring populations through chemical or irradiation mutagenesis, but only the gene of interest is studied instead of phenotypic screening (Jung et al., 2018). This involves substantial knowledge of the underlying genetic processes, which, for many agronomic characteristics, are notable today. Genotype-​dependent mutation screens have been applied in all major crop species, and multiple mutants have been identified and recognized. Physical mutagens, such as fast neutron, UV, X-​ray, and gamma radiations, and chemical mutagens, including N-​methyl-​N-​nitrosourea (MNU), sodium azide, hydrogen fluoride (HF), methyl methanesulfonate (MMS), and ethyl methanesulfonate (EMS), have broadly been investigated over the last century. In addition, biological mutagens comprise Agrobacterium and transposon-​based chromosomal integration. The mutation induced by EMS is a profoundly powerful technique and is therefore commonly used to develop improved crop varieties in crop breeding. Recently, in plant science, the use of fast neutron (FN) bombardment to create a mutagenized population has been gaining prominence. FN results in significant deletions from a few bases to a million bases (sometimes > 1 Mb) and a greater proportion of double lesions that are not repairable, as well as chromosome alterations in the genome. FN has been shown to be a very powerful mutagen in plants and the FN-​treated lines are easily generated and deletion library is quickly assembled, which helps us to locate deletion mutant (Li et al., 2001). A random deletion library generated by FN mutagenesis lines may provide valuable and significant information for the reverse genetic approaches. Recently, Kumawat and colleagues (2019a) have highlighted the use of FN mutagenesis to build a resource of gene deletion lines. For functional genomics and even t...

Table of contents

• Cover
• Half Title
• Series Page
• Title Page
• Copyright Page
• Table of Contents
• Preface
• Editors
• Contributors
• 1. Novel Approaches and Advanced Molecular Techniques for Crop Improvement
• 2. The Chemical Dialogue during Plant–​Microbe Interaction: Implications in Sustainable Agriculture
• 3. Implication of Microbial Signals: Plant Communication
• 4. Molecular Aspects of Host–​​​​​​​Pathogen Interaction
• 5. Omics: A Potential Tool to Delineate the Mechanism of Biocontrol Agents against Plant Pathogens
• 6. Bioinformatics Approaches to Improve and Enhance the Understanding of Plant–​Microbe Interaction: A Review
• 7. Plant–​Microbe Interactions in the Age of Sequencing
• 8. Metaomics Technologies in Understanding Ethnomedicinal Plants and Endophyte Microbiome
• 9. Plant–​Rhizomicrobiome Interactive Ecology through the Lenses of Multi-​Omics and Relevant Bioinformatics Approaches
• 10. Future Prospects of Next-​Generation Sequencing
• 11. Revisiting Molecular Techniques for Enhancing Sustainable Agriculture
• 12. Nanotechnology in Plant Pathology: An Overview
• 13. An Overview of CRISPR and Gene Chip Technology to Study Plant–​Microbe Interaction
• 14. Functional Genomic Approaches to Improve Rice Productivity through Leaf Architecture
• 15. Tapping the Role of Plant Volatiles Inducing Multi-​Trophic Interactions for Sustainable Agricultural Production
• 16. Desiccation Tolerance in Orthodox and Recalcitrant Seeds
• 17. Chemical Ecology in Belowground Plant Communication
• 18. Possible Bioremediation Strategies for Arsenic Detoxification by Consortium of Beneficial Bacteria
• Index