Current Developments in Biotechnology and Bioengineering: Crop Modification, Nutrition, and Food Production

Current Developments in Biotechnology and Bioengineering

Crop Modification, Nutrition, and Food Production

Editors

Suresh Kumar Dubey

Ashok Pandey

Rajender Singh Sangwan

Table of Contents

Cover image

Title page

Copyright

List of Contributors

About the Editors

Preface

1. World Agriculture and Impact of Biotechnology

1.1. Introduction

1.2. Impact of Whole-Genome Sequencing and Genomic Approach on Agriculture

1.3. Impact of Exome Sequencing on Agriculture

1.4. Impact of Proteomics Approach on Agriculture

1.5. Impact of Genetically Modified Technology on Agriculture

1.6. Plant Molecular Farming

1.7. Conclusions and Future Perspectives

2. Effect of Climate Change on Agricultural Crops

2.1. Introduction

2.2. Climate Change

2.3. Soil Ecology and Plant–Microbe Interactions Under Changing Climate

2.4. Projected Impact of Climatic Changes on Crop Production

2.5. Adaptation Strategies

2.6. Conclusions

3. Insect-Resistant Plants

3.1. Introduction

3.2. Pests Commonly Found in Food Crops

3.3. Genes for Insect Resistance From Various Sources

3.4. Role of Secondary Metabolites

3.5. Chemical Compounds Mediating Defense

3.6. Plant Breeding Methods to Develop Insect-Resistant Plants and Their Selection

3.7. Genetic Engineering of Plants

3.8. Effects on Soil Microorganisms

3.9. Effects of Bacillus thuringiensis Endotoxins on Health

3.10. Conclusions and Perspectives

4. Engineering Resistance to Plant Viruses: Present Status and Future Prospects

4.1. Introduction

4.2. Virus Resistance

4.3. Host Plant Gene Resistance

4.4. Pathogen-Derived Resistance

4.5. Pathogen-Targeted Resistance

4.6. Concluding Remarks and Future Perspectives

5. Drought-Tolerant Plants

5.1. Introduction

5.2. Transcription Factors and Their Role in Drought Response

5.3. Biochemical Response in Drought-Tolerant Plants

5.4. Conclusion and Future Perspective

6. Genetically Engineered Crops Against Bacterial and Fungal Diseases: A War of Attrition

6.1. Introduction

6.2. Strategies for Engineered Resistant Crops Against Bacterial and Fungal Pathogens

6.3. Conclusion and Future Prospects

7. Chloroplast Metabolic Engineering for Sustainable Agriculture

7.1. Introduction

7.2. Manipulation and Engineering of Metabolic Pathways

7.3. Genetic Manipulation to Make Plants Resistant to Environmental Stresses

7.4. Secondary Metabolites Biosynthesis

7.5. Use of Microbes for Sustainable Agriculture and Metabolic Engineering

7.6. Conclusion and Perspectives

8. Transgenic Plants and Soil Microbes

8.1. Introduction

8.2. Plant–Microbe Interactions

8.3. Transgenic Technology in Plant Improvement

8.4. Direct and Indirect Effects of Transgenic Plants

8.5. Methods Used to Assess the Impact of Genetically Modified Plants on Rhizospheric Microbial Abundance and Diversity

8.6. Case Studies: Microbial Communities Affected by Genetically Modified Plants

8.7. Conclusions and Perspectives

9. Marker-Assisted Selection in Disease Resistance Breeding: A Boon to Enhance Agriculture Production

9.1. Introduction

9.2. What Is Marker-Assisted Selection?

9.3. Resistance Breeding Strategies Using Marker-Assisted Selection

9.4. Documented Releases and Registrations of Varieties Resulting Through Marker-Assisted Selection Breeding Programs

9.5. Case Studies

9.6. Conclusions and Perspectives

10. Abiotic Stress in the Production of Food Grains and Methods to Alleviate the Impact of Stress

10.1. Introduction

10.2. Water Stress

10.3. Salt Stress

10.4. Temperature Stress

10.5. Heavy Metal Stress

10.6. Metabolic Engineering for Stress Tolerance

10.7. Transgenesis for Stress Tolerance

10.8. Conclusion

11. Novel Technologies for Plant Functional Genomics

11.1. Introduction

11.2. Early Break Through Techniques for Functional Genomics

11.3. Next-Generation Sequencing Technology

11.4. Genome Engineering/Editing Technologies

11.5. Conclusions and Future Perspectives

12. Biotechnological Interventions for Production of Therapeutic Secondary Metabolites Using Hairy Root Cultures of Medicinal Plants

12.1. Introduction

12.2. Hairy Root Cultures and Strategies for Phytochemical Production

12.3. Media Optimization

12.4. Elicitation

12.5. Precursor Feeding (Precursor Feeding, Biotransformation, and Co-culture Systems)

12.6. Metabolic Engineering

12.7. Ploidy Alteration

12.8. Conclusion and Outlook

List of Abbreviations

Index

Copyright

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List of Contributors

K.V. Chaitanya,     GITAM University, Visakhapatnam, India

N. Chaurasia,     North-Eastern Hill University, Shillong, India

K. Divya,     GITAM University, Visakhapatnam, India

S.K. Dubey,     Banaras Hindu University, Varanasi, India

D. Easwar Rao,     GITAM University, Visakhapatnam, India

A. Gupta,     Department of Science and Technology, New Delhi, India

G.S. Jeena,     CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India

S.F. Kianian,     USDA-ARS Cereal Disease Laboratory, St. Paul, United States

D. Kumar,     H.N.B. Garhwal University, Srinagar, Uttarakhand, India

J. Kumar,     University of Minnesota, St. Paul, United States

R.K. Mall,     Banaras Hindu University, Varanasi, India

S. Mehrotra,     Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India

Y. Mishra

Panjab University, Chandigarh, India

Banaras Hindu University, Varanasi, India

A. Pandey,     Banaras Hindu University, Varanasi, India

S.S. Pandey,     CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India

J. Pathak,     Banaras Hindu University, Varanasi, India

A. Pathania

CSK HP Agricultural University, Palampur, Himachal Pradesh, India

DAV University, Jalandhar, Punjab, India

U.J. Phukan,     CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India

I.V.S.N. Prathyusha,     GITAM University, Visakhapatnam, India

Rajneesh,     Banaras Hindu University, Varanasi, India

Ch. Rama Krishna,     GITAM University, Visakhapatnam, India

N. Rialch,     CSK HP Agricultural University, Palampur, Himachal Pradesh, India

P.N. Sharma,     CSK HP Agricultural University, Palampur, Himachal Pradesh, India

R.K. Shukla,     CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India

A.K. Singh,     Banaras Hindu University, Varanasi, India

S.K. Singh,     National Institute of Plant Genome Research, New Delhi, India

Shailendra P. Singh,     Banaras Hindu University, Varanasi, India

Sudhir P. Singh,     Center of Innovative and Applied Bioprocessing, Mohali, India

R.P. Sinha,     Banaras Hindu University, Varanasi, India

G. Sonkar,     Banaras Hindu University, Varanasi, India

V. Srivastava,     National Institute of Plant Genome Research, New Delhi, India

T.S. Swapna,     Kerala State Biodiversity Board, Thiruvananthapuram, Kerala, India

B.S. Tiwari,     Institute of Advanced Research & University, Gandhinagar, Gujarat, India

P.K. Verma,     National Institute of Plant Genome Research, New Delhi, India

S. Verma,     National Institute of Plant Genome Research, New Delhi, India

About the Editors

Suresh Kumar Dubey

Suresh Kumar Dubey is an Associate Professor in the Molecular Ecology Laboratory at the Department of Botany, Banaras Hindu University, India. His interests include the structure and function of the microbial community involved in controlling methane emissions, the screening and use of microbes for their potential role in bioremediation, studies on the prevalence of some pathogenic microbes in clinical and food samples, and their response to drug resistance. He has been the editor of the Indian Journal of Microbiology since 2009 and has won multiple awards for his work, including the Biotech Research Society of India Young Scientist Medal 2004, DST-BOYSCAST Government of India fellowship 2006, INSA visiting fellowship 2012, and JSPS Invitation Fellowship 2012, among others.

Ashok Pandey

Professor Ashok Pandey is Eminent Scientist at the Center of Innovative and Applied Bioprocessing, Mohali (a national institute under the Department of Biotechnology, Ministry of Science and Technology, Government of India), and former chief scientist and head of the Biotechnology Division at the CSIR’s National Institute for Interdisciplinary Science and Technology at Trivandrum. He is an adjunct professor at Mar Athanasios College for Advanced Studies Thiruvalla, Kerala, and at Kalasalingam University, Krishnan Koil, Tamil Nadu. His major research interests are in the areas of microbial, enzyme, and bioprocess technology, which span various programs, including biomass to fuels and chemicals, probiotics and nutraceuticals, industrial enzymes, solid-state fermentation, etc. He has more than 1100 publications and communications, which include 16 patents, 50+ books, 125 book chapters, and 425 original and review papers, with an h index of 75 and more than 23,500 citations (Google Scholar). He has transferred several technologies to industries and has been an industrial consultant for about a dozen projects for Indian and international industries.

Professor Pandey is the recipient of many national and international awards and fellowships, which include Elected Member of the European Academy of Sciences and Arts, Germany; Fellow of the International Society for Energy, Environment and Sustainability; Fellow of the National Academy of Science (India); Fellow of the Biotech Research Society, India; Fellow of the International Organization of Biotechnology and Bioengineering; Fellow of the Association of Microbiologists of India; honorary doctorate degree from the Université Blaise Pascal, France; Thomson Scientific India Citation Laureate Award, United States; Lupin Visiting Fellowship; Visiting Professor at the Université Blaise Pascal, France, the Federal University of Parana, Brazil, and the École Polytechnique Fédérale de Lausanne, Switzerland; Best Scientific Work Achievement Award, Government of Cuba; UNESCO Professor; Raman Research Fellowship Award, CSIR; GBF, Germany, and CNRS, France fellowships; Young Scientist Award; and others. He was chairman of the International Society of Food, Agriculture and Environment, Finland (Food & Health) during 2003–04. He is the Founder President of the Biotech Research Society, India (www.brsi.in); International Coordinator of the International Forum on Industrial Bioprocesses, France (www.ifibiop.org); chairman of the International Society for Energy, Environment & Sustainability (www.isees.org); and vice president of the All India Biotech Association (www.aibaonline.com). Professor Pandey is editor-in-chief of Bioresource Technology, Honorary Executive Advisor of the Journal of Water Sustainability and Journal of Energy and Environmental Sustainability, subject editor of the Proceedings of the National Academy of Sciences (India), and editorial board member of several international and Indian journals, and also a member of several national and international committees.

Rajender Singh Sangwan

Dr Rajender Singh Sangwan is founder chief executive officer of the Center of Innovative and Applied Bioprocessing (CIAB), a national institute at Mohali (Punjab) under the Department of Biotechnology (Government of India). Also, he continues to be co-affiliated with CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow (India), as Chief Scientist.

Dr Sangwan (MSc, 1981; PhD, 1987, from Haryana Agricultural University, Hisar, India) has worked as faculty at the CSIR–Central Institute of Medicinal and Aromatic Plants (CIMAP) at Lucknow since 1986 at various levels up to chief scientist as well as founder head of the Department 23of Metabolic and Structural Biology. His profile of project/program/mission leadership include the New Millennium Indian Technology Leadership Initiative Program on Ashwagandha at CSIR–CIMAP, CSIR's Inter-Laboratory Network Program on Chemical and Biological Transformations for Value-Addition, CSIR's Inter-Institutional Network Research Program on Plants and Animals as Bioreactor.

As a founder head of CIAB, he leads translational research and innovation programs on bioprocessing of agrifood and other bioresources. CIAB represents the first institutionalized Secondary Agriculture Initiative in India for R&D on value-added products of an edible and nonedible nature through the integration of chemical and biological processes. His current research interests pertain to Translational Research and Innovations for Secondary Agriculture Biotechnology, covering primary and secondary phytochemicals/metabolites, edible and nonedible value-added products from bioresources, secondary agriculture technology applications, nutritional and nutraceutical products, and alternate bio/production approaches including synthetic biology. He has more than 125 publications in leading international journals and books attracting more than 3000 citations with an H index of 33 and an i10 index of 71. He has several patents and elite medicinal and aromatic plant varieties to his credit. He is a member of several academic and governing bodies of scientific organizations.

He has been awarded several scientific and academic honors and forms of recognition including IUBMB Young Scientist (travel) Award (1992); CSIR Young Scientist (1994); Professor Umakant Sinha Memorial Award of Indian Science Congress (1997); fellow, National Academy of Agricultural Sciences; fellow, National Academy of Sciences (India); and CSIR Technology Award in Life Sciences (2015).

Preface

This book is a part of the comprehensive series, Current Developments in Biotechnology and Bioengineering (Editor-in-Chief: Ashok Pandey), comprising nine volumes and principally aiming to provide a benchtop reference book for students, scholars, teachers, scientists, and policy makers concerned with different subdisciplines. We realize that it would be interesting but impossible to cover all topics in one book. Accordingly, this book is devoted to issues related to the role of biotechnology improving crop yield, food quality, disease resistance, resilience to abiotic stresses, etc.

Increasing urbanization, pollution, and climate change have greatly constrained the sustained availability of safe and nutritionally rich food. These have created unprecedented pressure on global food supply and the search for eco-friendly technological solutions to ensure food for all. Limited land resources coupled with risks associated with excessive use of agrochemicals largely constrain safe agricultural production. Under such conditions, and to meet the global food demand, biotechnological tools and techniques may prove to be more innovative and acceptable because they are more ecologically conducive and environmentally sound. Advances in this domain of science have shown vast opportunities to harvest crops with increased yield and nutritional value through crop modification at a genetic level. Innovations in science and technology have led to the evolution of reliable methods and approaches to increasing crop productivity and agricultural sustainability. Biotechnological and bioengineering tools and techniques in particular have added many new dimensions to such innovations, offering efficient and cost-effective means to ensuring quality food for all. Realizing this fact, the current edition, designed with 12 chapters, provides in-depth discussion on current and future innovations in biotechnological research to improve agronomic traits such as crop yield, stress tolerance, production of biomass, feedstock, and the quality of dietary supplements.

Chapter 1 focuses on exploiting genetic sequencing, genomic breeding, and proteomics to develop crop species with increased yield and quality of produce and resilience against climatic extremes. Enhancing crop production to meet rising demands resulting from increasing populations against the threats of climate change, Chapter 2 deals with the merits and possibilities of mitigation research, capacity building, policies, and national- and global-level cooperation to minimize the adversities of climatic extremes. A comprehensive review on insect-resistant plants is presented in Chapter 3. This review focuses mainly on progress in the development of insect-resistant crop varieties and mechanisms involved in resistance development in plants against insects. In recent years the use of resistant plants has emerged as the most effective and economic way to mitigate losses caused by viral pathogens. Chapter 4 highlights the limitations of virus-resistant cultivars and examines current strategies and future prospects of developing virus-resistant transgenic plants. Drought is another major factor that constrains the qualitative and economic success of agricultural sector. Transcriptional regulation by AP2/ERF, WRKY, and NAC transcription factors and regulation by kinases, phytohormones, and antioxidants have a central role in the cascade of drought response. Chapter 5 focuses on signaling networks and their downstream regulation under drought response in plants along with future prospects in this area of research. A detailed review on plant–microbe interactions is presented in Chapter 6. Chloroplasts represent a subcellular compartment that houses the process of primary production through photosynthesis. A detailed account of plastid metabolic engineering and photosynthetic machinery that are directly linked, enhancing crop yield, is presented in Chapter 7. Chapter 8 highlights the use of high-throughput molecular techniques such as next-generation sequencing to assess the in situ effects posed by transgenic plants on soil microbes. Chapter 9 deals with various aspects of marker-assisted selection, its components and prerequisites, and its application in disease-resistant breeding. The chapter also focuses on various breeding strategies such as marker-assisted backcross breeding, gene pyramiding, and combined selection using both marker-assisted and phenotypic selections exploiting molecular markers for disease-resistant varieties. Advances in genome editing and engineering such as zinc-finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats/Cas9 have made precise control possible over genome sequencing and its regulation across all disciplines including agricultural crops. Chapter 10 enunciates different approaches for the improvement of crop productivity under the influence of many abiotic stresses. Chapter 11 describes novel technologies and their applications in plant genomics. Plant secondary metabolites have been identified as effective in curing human diseases. Chapter 12 provides current perspectives on plant hairy root cultures as an important model for therapeutic secondary metabolite production in a sustainable manner. The imperative interventions of biotechnology to enhance the accumulation of such molecules are also discussed.

The contents of different topics are designed by authors who are experts in their specific areas of research. The basic and advanced technologies have been defined in their specific segments and explained in the simplest manner for students and educators of different subdisciplines. In addition, practical approaches, tool, and techniques including experimental design, wherever necessary, all are addressed in an easily understood manner. The book is particularly useful for those offering courses at graduate-, postgraduate-, and doctoral-level programs in biotechnology/bioengineering and agricultural sciences. We are grateful to the authors for their valued contributions.

We would like to acknowledge the reviewers for their valuable comments to improve the final quality of the different chapters included in this volume. We thank Dr. Kostas Marinakis, Book Acquisition Editor, Ms. Anneka Hess, and the entire production team at Elsevier for their help and support in bringing out this volume. Without their commitment, efficiency, and dedicated work, this volume could not have been accomplished.

Editors

Suresh Kumar Dubey

Ashok Pandey

Rajender Singh Sangwan

1

World Agriculture and Impact of Biotechnology

J. Pathak, Rajneesh, A. Pandey, Shailendra P. Singh,  and R.P. Sinha∗     Banaras Hindu University, Varanasi, India

Abstract

Global agriculture is facing a serious threat from climate change, which may result in reduced productivity. Increasing food prices and greater global food insecurity are the outcomes of decreased productivity, and the persistence of such conditions may lead to a further increase in food prices, which could lead to social unrest and famine in certain instances. To ensure continued food security for an increasing global population, we must focus on improving crop productivity by exploiting new genetic sequencing and advanced genomic breeding and proteomics technologies. These technologies hold promise for crop improvement by developing crop species for particular environmental conditions. These technologies also allow plant breeders to target new crop species and traits effectively and simultaneously, such as resilience, quality, and yield, which are crucial to food security. Molecular breeding has a crucial role in improving crops. Although genetically modified (GM) crops hold good promise in enhancing crop productivity, GM crops face several challenges in agricultural growth, development, and sustainability. In this chapter, we discuss advances in the field of agriculture using advanced tools of biotechnology.

Keywords

Agriculture; Crop productivity; Genetically modified organisms; Genomics; Proteomics; Sequencing

1.1. Introduction

Unprecedented increases in the world's population has led to competing demands for the production of food, fodder, and essential ecosystem services which are necessary for the sustenance of life [1]. By 2050 the world population is expected to pass 9  billion, with food security as a major global challenge [2]. The Food and Agriculture Organization [3] defines food security as having physical and economic access to sufficient, safe and nutritious food, for an active and healthy life. Improvement in crop productivity with the aid of new genetic sequencing and advanced omics technologies along with conventional breeding practices is required to ensure continued food security because conventional breeding techniques alone cannot fulfill the future food demand for an increasing population size [1,4,5]. Hence, plant breeding techniques should focus on traits that have maximum potential yield under continuously changing climatic conditions. Food security can be enhanced by diversifying agriculture, by domesticating and using a larger number of plants species [6]. Mining the gene pools of crop wild relatives (CWRs) could increase the diversity of alleles available to breeders.

Genome analysis in wild plant populations may lead to the discovery of novel genetic resources [7]. Adaptive genes are promising for improving crop productivity under specific environmental conditions, and such genes could be revealed by high-throughput genome-scale genotyping [8]. Advances in plant genomics have resulted in a better understanding of crop diversity at species and gene levels and offer DNA markers which are of great importance in genetic improvement [9,10]. Therefore, genomics could be a potential tool to address the challenge of increasing food quality and yield in a sustainable manner through advanced breeding techniques [11]. Genomics-assisted breeding is predicted to have a crucial role in the development of crops which are resilient to climate change [11]. Knowledge of genomics could be used further to identify and transfer agronomically valuable genes from allied gene pools and crop relatives to elite crops, and hence could potentially assist in meeting the global food demand. Exons assist in interpretation of allelic variation with respect to their phenotype, and phenotypic traits could be revealed by exome sequencing which could serve as a significant tool for better crop production [12]. Exposure to abiotic and biotic stressors induces various stress-related responses in plants accompanied by the development of stress-specific adaptations and/or acclimations. A proteomics approach offers an excellent tool for studying plant response under fluctuating environmental conditions and can be useful for identifying and functionally characterizing novel protein(s) involved in the amelioration of different stressors [13]. The abundance of proteins primarily associated with defense mechanisms determines the efficiency of stress-specific responses in plants, which involves alterations in resource allocations for various purposes, including biomass production.

The development of genetically modified (GM) crops is another example of the use of biotechnology to enhance productivity and/or resistance to various abiotic and/or biotic stressors. However, application of GM crops to increase global food production is still a matter of global debate, and therefore pros and cons of GM crops need to be analyzed before their commercialization [14]. GM technology is an opportunity to make high profits for the industry sector and it can also act as a sustainable tool to increase crop productivity. However, whether GM crops can contribute to agricultural growth, agricultural development, and agricultural sustainability still needs to be answered. Therefore, an integrated approach of conventional breeding, the application of biotechnology, genomics, proteomics, and genetic engineering could provide a sustainable solution to the problem of global food security. In this chapter we discuss the potential role of biotechnology in enhancing crop productivity and the development of sustainable agriculture with particular emphasis on genomics, proteomics, and GM crops.

1.2. Impact of Whole-Genome Sequencing and Genomic Approach on Agriculture

An effective crop breeding program is the most crucial requirement to meet the ever-increasing global food demand and counter the potential adverse impacts of climate change [15,16]. Information from various genome studies can be used to detect novel structural variations, decode novel/exotic alleles from wider gene pools, retrieve lost genetic diversity, and resolve complex quantitative traits [17]. Genetic improvements of crops should focus on higher productivity, adaptation to climate resilience, and nutritional value. A key strategy for enhancing crop improvement is the effective use of available genetic resources [6]. In this respect, genomic breeding could be an efficient tool to obtain more productive crops in a shorter time, which can be achieved by studying the correlation between the genomic sequence and crop performance under a given environmental condition [18–20]. Comprehensive information on genetic components that control heritable traits can be obtained through genome-wide association studies (GWAS) [18,19,21]. In GWAS, the phylogenetic relatedness of the individual lineages is first determined, followed by identification of causal trait loci. Tedious phenotypic screening could be bypassed by drawing quantitative trait loci (QTL) from a wild relative into an elite line; however, for this approach, genomic sequencing of baseline diversity populations is essential. These loci serve as genetic markers that help predict traits via in silico selection of breeding material and hence accelerate the breeding process [5]. Crop improvement has been benefitted significantly through GWAS and QTL mapping, however, Next-generation sequencing [22] and high-throughput phenomics [23] approaches have substantially improved the usefulness of genomic breeding.

Exploitation of the advanced technologies of genomics and phenomics has the potential to make plant breeding programs more quantitative and predictive. Synergies among genomics, proteomics, transcriptomic, metabolomics, and phenomics have the potential to enrich and accelerate plant breeding to a great extent (Fig. 1.1) [23]. Results obtained from synergistic studies conducted under various environmental conditions can be used to develop a model that can predict the impact of a particular stress on crops. Studies on genome variations in wild populations growing in contrasting environments may help in understanding how plants adapt to climate variability. This information can be used by plant breeders to develop climate-resilient crops [15]. Genetic mapping has accelerated the dissection of genetic control of agricultural traits in breeding programs by enabling QTL analysis, marker-assisted selection, association mapping, genomic selection, and the direct calculation of high-value genotypes [24].

Figure 1.1  Advance biotechnological approaches for crop improvement. ICAT , Quantitative proteomic approaches including isotope-coded affinity tags; iTRAQ , isobaric tags for relative and absolute quantitation; TMT , targeted mass tags; MudPIT , multidimensional protein identification technology; SRM/MRM , selective reaction monitoring/multiple reaction monitoring; SWATH , sequential window acquisition of all theoretical fragment ion spectra; NGS, next-generation sequencing.

Prediction of the impact of climate change on crop resistance is a difficult task and the impact is variable because it depends on the crop and environment. Genomics-assisted breeding, with the help of advances in DNA sequencing technologies and the sequencing of CWR, and with advanced genomics tools, could contribute significantly to reducing the adverse impact of climate change on crop fitness and productivity [6]. High-density genotyping assays which are cost-effective and permit genome-wide prediction are well-recognized as important selection criteria in crop breeding. High-density genotyping has been used in soybeans [Glycine max (L.) Merr.] in which soybean genotypes with improved water use efficiency were employed to develop cultivars with a higher yield under drought stress [17]. Thirty-nine single nucleotide polymorphism (SNP) markers tagged at 21 different loci were identified in soybeans using GWAS [25]. A similar approach can be used to improve other important crops; however, further research is required to evaluate the usefulness of identified markers for desirable traits.

1.2.1. Genomics of Crop Wild Relatives

The discovery of novel genetic resources and crop improvement can be achieved by analyzing the genome of wild plant populations [7]. Genomics has a potential role in the use and management of ex situ plant genetic resources. Genetic bottlenecks associated with domestication or crop improvement results in partial variation in certain parts of the genome which can be identified by sequencing CWRs [26,27]. Information obtained from sequencing results of CWRs can be applied to introduce desirable traits into crop plants. Advances in DNA sequencing technologies provide opportunities to understand plant and crop species at the whole genome level [28]. Table 1.1 provides a list of wild crops whose genomes have been sequenced or are in progress.

Data obtained from sequencing the genomes of different species provide information on genetic diversity and the relationship between crop plants which can be also used as a reference genome for closely related species. Information obtained from chloroplast genome sequencing can be used to determine genetic diversity in CWR populations and germ plasm collections [7,51]. The genome sequence of some CWRs such as Arabidopsis thaliana, Oryza sativa, Brachypodium distachyon, and Setaria viridis has provided an excellent platform to characterize and understand genetic variation in domesticated crop species [6]. Significant advancements in crop productivity have been achieved by using genes obtained from CWRs [52]. Widespread genome sequencing of CWRs would further accelerate the discovery of novel genes and their efficient introduction into crops. CWRs also serve as a source of QTL, which can be employed to improve the yield of crop plants [53].

Table 1.1

List of Wild Crops Whose Genome Sequencing is Either Completed or in Progress

NA, not available.

Adapted from M. Brozynska, A. Furtado, R.J. Henry, Genomics of crop wild relatives: expanding the gene pool for crop improvement, Plant Biotechnology Journal (2015) 1–16, http://dx.doi.org/10.1111/pbi.12454.

1.3. Impact of Exome Sequencing on Agriculture

Plant exomics has emerged as a potential approach in addition to whole-genome sequencing, transcriptomics, proteomics, and metabolomics to transform the future of crops [12]. All of the sequences in a genome coding for proteins and which are responsible for phenotypic regulation are called the exome [54]. Exome sequencing involves the following steps [12]:

1. identification of genes

2. designing of primers or capturing chip

3. creation of small sequence fragments during a sequencing reaction.

These small fragments can be stored as a library or can be used to determine the phenotypic traits.

4. identification of thousands of exome SNPs

5. computational and statistical analysis to identify beneficial traits.

1.3.1. Technologies Employed for Exome Sequencing

Next- or second-generation sequencers such as the 15 Roche/454, a genome sequencer; a genome analyzer from Illumina/Solexa; SOLiD of Applied Biosystems; and Polonator from Dover Systems can be used for exome sequencing. These next-generation sequencing technologies work on the principle of immobilization of DNA templates on a solid surface which is usually made of beads [54].

1.3.1.1. Pyrosequencing

Pyrosequencing uses the Roche/454 FLX platform and is used to sequence larger exon fragments in faster run times [54].

1.3.1.2. Reversible Terminator-Based Sequencing

The Illumina/Solexa Genome analyzer uses reversible terminator-based sequencing, which was initially developed to sequence DNA fragments affixed with microspheres; however, it can also be used to sequence clonally amplified DNA.

1.3.1.3. Ion-Semiconductor-Based Nonoptical Sequencing

Ion Torrent Personal Genome Machine sequences DNA by using ion-sensitive transistors and employs advanced semiconductor technologies [55].

1.3.1.4. DNA Nanoball Sequencing

In this methodology complete genomics carries out DNA sequencing by means of combinatorial probeanchor technology through unchained ligation. Amplification of DNA is done in the form of nanoballs instead