eChapters

The understanding of VAM symbiont and VAM symbiosis is of prime importance in manipulating VAM associations for the welfare of plants. Many contributions have been made worldover in the areas of taxonomy, morphology, anatomy, histology, cytology and genetics of VAM fungi and/or their associations with the plants. However, the share of Indian mycorrhizasts in such contributions is negligible. The following description gives an account of work done by the mycorrhizasts of the country in these areas.

There aremany different points of view aboutthe nanotechnology. These differences start with the definition of nanotechnology. Some define it as any activity that involves manipulating materials between one nanometer and 100 nanometers. However the original definition of nanotechnology involved building machines at the molecular scale and involves the manipulation of materials on an atomic (about two-tenths of a nanometer) scale.

The debate continues with varying opinions about exactly what nanotechnology can achieve. Some researchers believe nanotechnology can be used to significantly extend the human lifespan or produce replicator-like devices that can create almost anything from simple raw materials. Others see nanotechnology only as a tool to help us do what we do now, but faster or better.

The third major area of debate concerns the timeframe of nanotechnology-related advances. Will nanotechnology have a significant impact on our day-to-day lives in a decade or two, or will many of these promised advances take considerably longer to become realities?

Finally, all the opinions about what nanotechnology can help us achieve echo with ethical challenges. If nanotechnology helps us to increase ourlifespans orproduce manufactured goodsfrom inexpensive raw materials, what is the moral imperative about making such technology available to all? Is there sufficient understanding or regulation of nanotech based materials to minimize possible harm to us or ourenvironment? Only timewill tell how nanotechnology will affect our lives.

The biosecurity risk assessment informs the biosecurity plan, which documents the mitigation measures put in place to address risks. Risks that fall outside of the risk tolerance threshold should be controlled through additional or enhanced mitigation measures. A cost-benefit analysis can assist in determining the mitigation measures in which to invest. Financial constraints and resource limitations may present challenges when looking to manage unacceptable risks. As a starting point, senior management may choose to initially focus mitigation measures on the most consequential risks and then control remaining risks as resources become available. In other instances, if the risks are determined to be too high or costly to mitigate, the organization’s project or program may need to be modified or cancelled. Recommendations for mitigation measures should be documented in the final report of the biosecurity risk assessment.

Abstract

Mitochondrial (mt) genomic study may reveal significant insight into the molecular evolution and several other aspects of genome evolution such as gene rearrangements evolution, gene regulation, and replication mechanisms. Other questions such as patterns of gene expression, mechanism of evolution, genomic variation and its correlation with physiology, and other molecular and biochemical mechanisms can be addressed by the mt genomics. Rare genomic changes have attracted evolutionary biology community for providing homoplasy free evidence of phylogenetic relationships. Gene rearrangements are considered to be rare evolutionary events and are being used to reconstruct the phylogeny of diverse group of organisms. Mitochondrial gene rearrangements have been established as a hotspot for the phylogenetic and evolutionary analysis of closely as well as distantly related organisms. This evolutionary episode has significant contribution among animals as well as plants and serves as an important genomic evolutionary event for the analysis of mitogenomes on large scale.

NEW CELLS ARE PRODUCED BY DIVISION OF PREVIOUSLY EXISTING CELLS

All cells come from previously existing cells

To make a new cell identical to itself a cell must perform 4 tasks:

It must grow and make additional copies of all its organelles, enzymes, etc..

It must duplicate its DNA

It must accurately separate the DNA into 2 units, so that each cell gets a full set

It must divide into 2 cells (cytokinesis)

Modern and transgenic breeding approaches consist of modern plant breeding triangle, high-throughput phenotyping (HTP), marker-assisted selection (MAS), marker-assisted backcrossing (MABC), genomic selection (GS), genome-wide association study (GWAS), and genome editing. MAS accelerates trait identification through DNA markers, improving efficiency in selecting plants with desired traits. MABC employs molecular markers to facilitate gene introgression from donor parents (DPs) to superior recurrent parents (RPs). GS employs genome-wide markers to predict performance, revolutionizing breeding by considering both major and minor-effect quantitative trait loci (QTLs). Genome editing techniques like CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats associated protein 9) enable targeted gene modifications for desired traits. Genome editing involves selecting target genes, designing guide RNAs for Cas9, and introducing the CRISPR-Cas9 system into plants. This technology has been utilized to enhance crop productivity, sustainability, and disease resistance. Transgenic crops are designed to carry specific traits, such as pest resistance, virus resistance, abiotic stress tolerance, and nutritional enrichment. Agrobacterium tumefaciens is highlighted as a tool for transgene introduction, offering advantages like low copy number integration and stable expression. Genetic engineering remains a promising avenue for creating disease-resistant crops and ensuring global food security.

Introduction
The 2022 edition of the United Nation’s global forest sector outlook for 2050 presented an update on the current patterns of wood consumption, its rising tendency, and projected future demand of primary processed wood to total 3.1 billion cubic meters of round wood equivalents (FAO, 2022). In addition, up to 199 million m³ would be required to substitute for non-renewable materials. Planted forests contributed around 46 percent to the global industrial round wood supply in 2020. However, globally the supply of wood from planted forests is always lower than the actual demand. Increasing population, urbanisation, economic development and consumption pattern are some of the major driving causes behind the demand in growth of wood and wood products. Wood security is defined as long-term availability of wood and wood products (sawn wood, veneer, plywood, particleboard, pulp, wood fuel and other primary wood products) for domestic and industrial requirements. The deficiency in the wood supply chain will continue to increase, and when the world population touches 9.4 to 10.2 billion, a 22 to 34% increase, the demand-supply imbalance will also increase. This supply gap would result in a shift in consumption patterns and lead to increase in environmentally harmful products such as petroleum-based plastics. Hence to meet the basic wood demand in 2050, at world level an additional 33 million ha of highly productive plantation forest would need to be established to meet the industrial round wood demand (FAO, 2022).
New demands for forest ecosystem continue to surge based on the Sustainable Development Goals, and mitigation of climate change related issues, water and other goods and services. Along with policy measures to directly act on existing forest resources conservation, increase in tree plantations with management interventions to increase productivity is necessary to fulfil the wood supply demands (McMaho and Jackson, 2019). Globally, the area under plantation forestry is on the rise (McEwan et al. 2020). Numerous studies (Silva et al. 2019; Carle et al. 2020; Pinnschmidt et al. 2023), highlight that plantation forests increasingly fulfil the ecological services provided by natural forests. Particularly, short rotation exotic trees with high productivity have found a niche in high-intensity industrial plantations, driving the expansion of the pulp and paper industry into a

Introduction
Maize (Zea mays L.) is the second most widely crop grown globally after wheat, with 205 million hectares under cultivation. The area cultivated under maize is steadily increasing and expected to overtake that of wheat by 2030 (Erenstein et al., 2022). With production exceeding 1.2 billion metric tons, maize surpasses the production of other highly cultivated cereals like wheat and rice mainly due to its higher yields (Erenstein et al., 2022). Maize is cultivated in the Americas, Africa, and Asia, for multiple end-uses (Nuss and Tanumihardjo, 2010). It is a staple food in several countries across Africa and Latin America, and in a few countries in Asia, with an overall contribution of 15-20% of daily calorific needs (Shiferaw et al., 2011).
The global maize yield tripled from the 1960s with the average yield rising from 2 tons/ha to the current 5.8 tons/ha, mainly due to the adoption of highyielding hybrid cultivars and complementary input use (Erenstein et al., 2022). Maize is naturally an outcrossing species and inbreeding is unnatural. When maize is subjected to inbreeding and the resulting inbred lines from genetically distant backgrounds are crossed, hybrid vigor or heterosis is realized (Springer and Stupar, 2007). Hence, the development of the homozygous inbred lines is a very important step in hybrid maize breeding.
In the well-evolved maize breeding programs, the germplasm is well characterized into different heterotic groups where the hybrids developed by crossing inbred lines from different heterotic groups exhibit high heterosis (Ertiro et al., 2017a; Sang et al., 2022). For the development of inbred lines, maize breeders develop F1 populations by crossing two inbred lines within the same heterotic group (Prigge et al., 2011; Sang et al., 2022). Inbred lines are developed from the F1 population by recurrent self-pollination for 6-8 generations; this can take up to 3-4 years or even more, depending on the availability of off-season nurseries for generation advancement. The resulting inbred lines are highly homozygous (~98-99%), but not 100% homozygous. The doubled haploid (DH) technology emerged as a viable alternative to the time-consuming and resourceintensive recurrent selfing method to produce 100% homozygous inbred lines in just two crop seasons (Prasanna et al., 2012; Chaikam et al., 2019a).
In addition to significantly reducing the time taken to develop homozygous lines, the use of DH lines in maize breeding offers several other benefits: a) As DH lines are completely homozygous at all loci, they are stable and do not show further inbreeding depression; b) DH lines are also best suited for evaluating distinctness, uniformity and stability (DUS) criteria, thereby better facilitating plant variety registration and intellectual property protection (Röber et al., 2005); c) The use of DH lines facilitates selections on completely homozygous lines which is more reliable and effective compared to selections on segregating families with different levels of heterozygosity (Chaikam et al., 2019a); d) Use of DH lines also simplifies breeding operations like planting, managing the nurseries, seed shipments, record keeping, etc. as selfing nurseries spread over several generations are replaced by just two generations for DH line development (Prasanna, 2012; Röber et al.,

Allele-Specific PCR

This diagnostic or cloning technique is used to identify or utilize single- nucleotide polymorphisms (SNPs) (single base differences in DNA). It requires prior knowledge of a DNA sequence, including differences between alleles, and uses primers whose 3' ends encompass the SNP. PCR amplification under stringent conditions is much less efficient in the presence of a mismatch between template and primer, so successful amplification with an SNP-specific primer signals presence of the specific SNP in a sequence.

Amplification Refractive Mutation System (ARMS) - PCR

In ARMS, the primer pair is designed so that one of the 3' ends coincides with a variant nucleotide in the target sequence. When the primer mismatches the template the frequency of extension is very low and consequently the effective number of sequence copies available for amplification is greatly reduced. ARMS PCR exploits a thermostable polymerase that lacks 3' exonuclease activity (usually Taq polymerase). Such enzymes extend primers bound to their target sequences very inefficiently when the 3' base is mismatched. Because the 3' exonuclease activity required for mismatch repair is not present, the extension of such primers in PCR is a rare event and amplification is retarded. However, once mismatch extension has occurred amplification proceeds normally from the newly synthesised target strand. Thus an important principle of ARMS is that non-matching (i.e. non-matching at only the 3' end of one primer) template may be amplified. The factors that contribute to this apparent ‘failure’ of ARMS are that when very high numbers of template molecules are added to the reaction, amplification is likely to proceed because the small proportion of mismatched primer extensions reach the sensitivity threshold of the reaction. Second, certain mismatches are extended more efficiently than others so that proportion extended in each PCR cycle varies.

Introduction
The most extensive diversity is found in the realms of plants and insects, encompassing over 1 million arthropod taxa, primarily comprising insects, which have been comprehensively described, along with more than 350,000 plant taxa. Notably, a substantial portion of the described insect species serve as either pollinators or herbivores. Over millions of years, insects and plants have coevolved, constantly adjusting and adapting to each other’s characteristics. Plants have developed numerous morphological and biochemical features to withstand damage from insects, while in response, insects have evolved a range of defensive and adaptive mechanisms. These mechanisms include behavioural, morphological, physiological, biochemical, and genetic traits, enabling them to either tolerate or adapt to the defensive traits of plants (Schmelz et al., 2006; Wu et al., 2007; Howe & Jander, 2008; War et al., 2018). Plant defenses against insect pests can be broadly categorized into two main types: antibiosis and antixenosis resistance. Antibiosis involves the direct impact of plant defensive traits on insect growth, development, and survival. In contrast, antixenosis defense relies on morphological or chemical factors that alter insect behaviour, deterring them from feeding and laying eggs on the plant. The trichomes, spines, cuticles, thorns, and lignified cell walls, are the morphological traits of defense that directly protect plants from insect pests. The biochemical defense mechanisms are typically activated in response to insect attacks and are characterized by their dynamic nature (War et al., 2018). Plant volatiles serve a significant function in the indirect defense of plants against insect herbivores. They accomplish this by either deterring the insect pests or by luring the pests’ natural adversaries. Among the various attributes associated with plant defense, chemical barriers, whether they are induced by stress or present constitutively, along with the nutritional composition of the plant, are regarded as particularly crucial for impeding insect growth and development (Peters & Constabel, 2002; War et al., 2019).
Chemical resistance entails the production of secondary metabolites, whether inherently present (constitutive) or induced as a response to a threat, to fortify the plant’s defense mechanisms (Figure 1). Constitutive defense metabolites, initially stored in an inactive state, referred to as phytoanticipins, become activated when herbivores attack. This activation is facilitated by the enzyme ß-glucosidase, which subsequently triggers the release of various aglycone metabolites possessing biocidal properties (Morant et al., 2008). Metabolites that are induced in response to herbivore activity are referred to as phytoalexins. These compounds encompass a variety of substances such as isoflavonoids, terpenoids, alkaloids, and more. They are recognized for their capacity to influence the growth and viability of herbivorous organisms (Walling, 2000). Furthermore, a notable role in imparting host-plant

Introduction to Molecular Biology Techniques Molecular biology is the domain of biology concerned with DNA replication, RNA synthesis (transcription), translation, and the role of proteins in cellular function, while molecular biology techniques are the keystones of modern biology, facilitating scientists to decode these molecular foundations of life. These molecular techniques aim to analyze and understand the structure, function, and interactions of biomolecules such as DNA, RNA, and proteins. These techniques facilitate an understanding of complex life processes such as gene expression, genetic variations, and cellular mechanisms. Researchers have used these molecular tools to unravel complex biological processes from genetic inheritance to cellular signaling pathways. The knowledge gained has been applied to solve challenges in various domains of biological science such as medicine, agriculture, and environmental science. During 1960’s methods to identify, isolate and manipulate molecular components were developed by molecular biologists. The field of molecular biology emerged in mid 20th century, driven by groundbreaking discoveries such as the deduction of the double-helix of DNA

Spectacular productivity gains have been achieved in wheat and rice in south and south-east Asia and also several other developing countries in Latin America and central Asia due to introduction of dwarfing genes in these two crops purely through conventional plant breeding approaches and these developments were christened as “Green Revolution” (Reynolds and Borlaug, 2006). The wheat breeding progrmme was being spearheaded by Norman Borlaug at CIMMYT (International Maize and Wheat Improvement Centre, Mexico) supported by Sanjay Rajaram and the rice breeding programme was under leadership of Gurdev Singh Khush at IRRI (International Rice Research Institute, Manila, Philippines) coinciding with these exciting developments during mid-sixties to mid-seventies. In recognition of these quantum jumps in yield of wheat and rice, Borlaug was awarded Nobel Peace Prize for Peace in 1970. Later on World Food Prize was instituted by joint efforts of Borlaug and his colleagues to honour Agricultural Scientists and others on pattern of Nobel Prize who had made significant contributions to sustainable food production and food and nutritional security globally. M. S. Swaminathan happened to be Director General, Indian Council of Agricultural Research when Green Revolution was taking roots in India and because of his enormous contributions to provide effective leadership to ensure that Green Revolution happened in India, M. S. Swaminathan is credited as “Father of Green Revolution in India” and he was the first recipient of World Food Prize in 1987 for spearheading the introduction of high-yielding wheat and rice varieties in India. G. S. Khush along with Henry Beachell received 1996 World Food Prize for achievements in enlarging and improving the global supply of rice during a time of exponential population growth and Sanjay Rajram was the 1914 World Food Prize recipient for his scientific research that led to huge increase in world wheat production.

Molecular characterization involves the use of techniques that are available to analyze variation in plants and animals at the DNA level. Differences in gene sequences can be directly observed and described with a precision previously impossible to achieve. Many of the techniques that have been developed have already been used in evolutionary and taxonomic studies. They have immense value in studies of accessions identity and for the detection of novel useful variation in the plant germplasm. Molecular markers provide genetic information of direct value in key areas of conservation both ex situ and in situ. For ex situ conservation the key issues are:

Summary

Molecular evolution is the process of evolution at the scale of DNA, RNA, and Protein. Molecular evolution emerged as a scientific field in the 1960s as researchers from molecular biology, evolutionary biology, and population genetics sought to understand recent discoveries on the structure and function of nucleic acids and protein. It covers two broad areas of study : the evolution of macromolecules, and reconstruction of the evolutionary history of genes and organisms. The evolution of macromolecules refer to the characterization of the changes in the genetic material (DNA or RNA sequences) and its products (Proteins of RNA molecules) during evolutionary process, and to the rates and patterns with which such changes occur, and also the mechanism responsible for such changes. The second area also known as “molecular phylogenetics”, deals with the evolutionary history of organisms and macromolecules as inferred from molecular data and the methodology of tree reconstruction.

Summary

Molecular farming is the large scale production of pharmaceutically important and commercially valuable proteins in plants and animals. Molecular farming in plants has the potential to provide an inexpensive and convenient system in the production of unlimited quantities of recombinant proteins for use as therapeutics, diagnostics, vaccines, antibodies, plasma proteins, cytokines and growth factors. Plants are also being used for the production of oils, starches, plastics, enzymes for food processing and other uses and spider silk etc. However, quality and safety of the final product and wider effects of molecular farming on health and environment need to be addressed. The benefits of molecular farming should not be outweighed by risks to human health and environment.

Rice (Oryza sativa L.) is the most popular crop and source of food for more than one-third of the world’s population. About 90 % of the world’s rice is grown in Asia and more than 3 billion Asians rely on rice for 30–75 % of their total calories (Braun and Bos 2004). It has been cultivated in four different ecosystems viz., irrigated, rainfed low land, upland and flood-prone (Halwart and Gupta, 2004). Since rice planting has been started around 8,000 to 9,000 years ago, the level of diversity would be more than it expected. The genetic diversity plays a major role in survival and adaptability of a species, as changes happen in environment. Organism needs to make changes in the phenotype that enables it to adapt and survive in unfavorable conditions. The inadequate knowledge on diversity of a species reduces the chance of widening the genetic base of that species. The venture of green revolution in Indian agriculture has narrowed down the genetic base of any popular crops. Therefore, collection, conservation and utilization of germplasm are very much needed in the present scenario for improving the varieties against biotic and abiotic stress.

Morphological and biochemical trait based diversity studies being largely influenced by environment as phenotype and/or enzymes are altered by the environmental and developmental changes. Therefore, adapting DNA based molecular markers for genetic diversity studies would be more reliable to overcome the environmental influence. Being molecular markers as a versatile tool, it establishes its strong holds in several fields of life science. Molecular marker based technique does not require DNA sequencing but it is generally based on nucleic acid hybridization or polymerase chain reaction (PCR). The PCR based tests has several advantages over hybridization technique as it is cheaper, speedy and sensitivity. Therefore, PCR based markers have been used extensively in genetic diversity study for assessing genetic variation within the species. The recent advent of molecular and computational tools now enables the estimation of genetic diversity and allele frequency between the genotypes easy.

Molecular markers or DNA markers are considered to be one of the most successfully applied component of molecular biology techniques that have relevance in almost every sphere of biology, from paleobotany to transgenic technology. In true sense, a marker is a characteristic of an individual that differentiates the individual from others. Morphological descriptions like cotyledon colour of Pea, eye colour of Drosophila, shape and size of fruits in summer squash etc. are examples of typical morphological markers. However, a single morphological marker is not sufficient for describing the uniqueness of an individual, for many pea plants will have green cotyledon or many Drosophila may have red eye. To define the uniqueness of an individual, we have to find a number of marker traits characteristic of that individual. Unfortunately, morphological variations are not sufficient to differentiate between a large number of individuals, or between groups or sub groups within a species, simply because the level of polymorphism is low. Besides, morphological characters or phenotypic expressions are affected by environmental changes, so stability of expression is low and sometimes uncertain.

Introduction
Molecular markers have revolutionized various fields of biological research by providing precise tools to elucidate genetic diversity, map genes, and facilitate marker-assisted selection (MAS) in breeding programs. These markers, ranging from simple sequence repeats (SSRs) to single nucleotide polymorphisms (SNPs), offer invaluable insights into the genetic architecture of organisms, enabling researchers to link specific DNA sequences to desired traits. By harnessing the power of molecular markers, scientists can expedite the development of stress-tolerant crops, enhance agricultural productivity, and address global challenges such as food security and climate change.
A. Definition of molecular markers: Molecular markers play a crucial role in identifying genetic variations or disparities among individuals, populations, or species. These markers are specific sequences of DNA (or RNA) that can be found in blood, other body fluids, or tissues, serving as indicators of normal or abnormal processes, conditions, or diseases. Additionally, they can be fragments of DNA associated with a genome, aiding in the identification of specific DNA sequences. Molecular markers are indispensable tools in the fields of genetics, molecular biology, and biotechnology, enabling the identification of specific DNA sequences and genetic variations within populations.