eChapters

The Secchi disc is named after its Italian inventor Pietro Angelo Secchi. Transparency is a water-quality characteristic of lakes and reservoirs and can be measured quickly and easily using simple equipment. This characteristic varies with the combined effects of colour and turbidity. Some variation may also occur with light intensity and with the apparatus used.
Procedure
1. Morning (early) or afternoon (late) is suitable time to check transparency
2. Lower the Secchi disc and observed the depth at which it just disappears from view (L1)
3. Then further lift up slowly till it just reappears (L2).

pH is defined as the negative logarithm of hydrogen ion concentration. The amount of the acidic gas CO2 significantly affects the pH of natural water body. Fish have usually blood pH levels of 7.4, but little deviation has been observed, perhaps 7.0 to 8.5pH range is more suitable for the growth and reproduction of the fish. However, pH range 4.0 to 6.5 and 9.0 to 11.0 cause fish death in water pH less than 4.0known as acidic death point or even more than 11.0 known as alkaline death point. The pH of fresh water more fluctuating as compare to sea water due to release and consumption of CO2 and O2 respectively by bacterial oxidation and respiration. However, the pH of marine water often constant at 7.8-8.3 due to presence of buffer like HCO3-, CO2 -, CO3-2 etc.
Principle
The estimation of hydrogen (H+) ion activity through sensing electrode. Electrode composed of a narrow glass bulb with fixed concentration of HCI solution inside it. A wire made of an Ag-AgCI placed in to the bulb which work as electrode to fix voltage. Potential difference forms between the solution in the glass bulb and the sample solution when the electrode immersed into solution.

Water colour is consequences of the plankton, humus, metal ions (iron and manganese), weeds and peat materials, presence in water. Iron oxides cause reddish color whereas Manganese oxides causes brown or brackish colour in water. Water colour of an aquatic body also indicates the density of planktons. Brownish colouration without any foul smell is an indication of good growth of zooplankton. Phytoplankton or algae are usually green in colour and these green alage in large quantities turn the green color of water. Water color suggests plankton or other aquatic life growth, clear and transparent colour of water indicates low and poor growth of plankton. Brownish green to greenish brown colour of water indicates well for aquaculture.
Principle
Natural waters colour comprising yellow-brownish in appearance. It has been observed that potassium chloroplatinate (K2PtCl2) tinted with small amounts of CoCl2 yield colours that are very much like the natural colours of water. 1 mg/L of Pt (K2PtCl6) produces a standard 1 unit of colour. The intensity of colour increases as pH rises. For this reason recording pH together with colour is advisable.

Aquaculture is practiced in the majority of countries worldwide, however the significance of water quality standards remains largely unknown to farmers and new aqua entrepreneurs. They may achieve maximum fish production with minimal input costs if they are trained and stay up to date on water quality management in the aquatic ecosystem. The water quality categorised into three main of metrics as physical, chemical, and biological parameters. Dissolved oxygen (DO), biochemical oxygen demand (BOD), free carbon dioxide (CO2), pH, temperature, total dissolved solids (TDS), turbidity, ammonia, nitrite, nitrate, alkalinity, bacterial density primary productivity (chl a), plankton population, etc. play a significant role for fish production. However, even small variations in certain physical and chemical parameters—particularly pH, temperature, and dissolved oxygen (DO)—can cause stress in the animals, which may manifest as physiological changes, reduced reproductive capability, and altered behavior. Water parameters such as alkalinity and hardness are relatively stable, whereas others like pH, dissolved oxygen (DO), and temperature fluctuate regularly. Proper maintenance and monitoring of these water quality parameters in aquatic environments support fish health and enhance fish production. On the other hand, variability in dissolved ammonia, nitrites, and nutrients like nitrate significantly affects aquaculture production. It has also been observed that high feeding rates in aquafarms create eutrophic conditions in water bodies, leading to substantial algal blooms. These blooms are responsible for die-offs, and as a result, ammonia levels in the ponds rise rapidly. The environmental factors responsible for generating high ammoniacal concentrations may also lead to increased nitrite concentration in aquafarm. Both ammonia and nitrite are directly toxic or sublethal cultured aqua animals, leading to reduced resistance to diseases. In aquaculture system, ammonia is produced through the ammonification process, which occurs when organic matter is broken down by the microbial community. However, this decomposition also reduces dissolved oxygen levels in the system. Low dissolved oxygen surges the toxicity of ammonia to cultured animals. Ionized ammonia (NH4 +) and hydroxide ions occurs in equilibrium with unionized aqueous ammonia solution. The unionized form of ammonia (NH3) is toxic

Introduction
Recent scientific findings highlight the escalating threats to global agricultural production due to climate change. The surge in extreme weather events, amplified by erratic precipitation patterns, alongside diminishing soil fertility and declining plant productivity, has led to an upsurge in disease and pest pressures. This amalgamation of factors has propelled a distressing trend of crop failures on a global scale. Over the last century, the average global temperature has already risen by 0.74°C, and projections suggest this rise could accelerate dramatically, reaching an alarming 2.6–4.8°C by the close of this century. This impending temperature escalation from climate change endangers agricultural output, thereby posing a signifi cant risk to the world’s food security. Presently, a staggering 794.6 million individuals face undernourishment, with nutrition-related issues contributing to a staggering 45% of deaths in children under fi ve years of age. The situation is particularly dire in developing regions, where 779.9 million people grapple with undernourishment. The repercussions of reduced agricultural production extend beyond hunger; they encompass potential food shortages and infl ationary pressures, predominantly affecting populations in low-income regions. These adverse consequences underscore the imperative of addressing these challenges. While advancements in crop breeding have led to incremental genetic gains in major agricultural crops, the pace of progress remains inadequate to meet the mounting global food demands. It is evident that enhancing the rate of genetic gain through innovative breeding programs is vital. This endeavor holds the potential to expedite the development of crop varieties resilient to changing climates and endowed with higher nutrient densities. Such cultivars are essential for ensuring sustainable food production and bolstering food security for our burgeoning population.

Introduction
It has been universally acknowledged that breeding for hybrids is the most effective conventional plant breeding technique. When two genetically distinct parent lines typically inbred lines are crossed, the resultant progeny is referred as a hybrid. It has been demonstrated that hybrids are larger, more productive, and hardier than their parental lineages. When we talk about hybrids, it is also imperative to understand two other related jargons: heterosis and hybrid vigour. The word “heterosis” was first coined in 1914 by Gottingen to refer the hybridization process in which two homozygous individuals (inbreds) are crossed to produce a hybrid. Darwin first used the phrase “hybrid vigour” in 1876 to denote the superiority of the F1 offspring produced by heterosis (i.e., the hybrids show superior performance with increased characteristics when compared with the two parental lines).
In general, the goal of plant breeding is to create better crop varieties by utilizing genetic variation found in the germplasm of the given plant species. Traditionally, two genetically different accessions of the given crop were selected and crossed to produce a hybrid. The genotype of this hybrid is the outcome of the fusion of the male and female gametes, those produced a zygote, from which the progeny eventually emerged. It would be appropriate to recollect the point that a plant’s life cycle consists of a gametophytic generation that produces gametes. Therefore, the genotypes of the gametophytes reflect the genetic diversity of the gametes.
Gametophytes are derived from spores, which are created via sporophytic reproduction during the course of the plant’s life cycle. Meiosis is a specialized kind of cell division that produces spores from differentiated cells that are located in the reproductive organs of plants. Two important processes (viz., recombination and chromosomal segregation) occur during meiosis and this results into independent assortment and creation of novel combinations of the genetic components of a diploid genome into a haploid genome of the gametophytes. Consequently, the genotype of a progeny is made up of the genotypes of the male and the female gametes that merged to create a new sporophyte. Therefore, meiosis can be viewed as a crucial stage in the life cycle of a plant and is responsible for generating genetic diversity. To generate desired plants with novel traits, this diversity or variability is frequently employed. In many cases, a hybrid plant outperforms a homozygous (parental) plant because it combines the best traits of the two parents. However, the creation of such hybrids is quite difficult. In order to evaluate the combining ability of hybrids, multiple putative parental lines are first produced at homozygous conditions by employing several generations of inbreeding and selection. The best pairs are then kept, and the corresponding parental lines produce a vigorous hybrid. Although hybrids were originally generated in maize during the 1930s, they are now employed in a wide variety of economically important plant species because they significantly surpass their parental inbreds. The main reason quoted for the wide-spread application of hybridization in breeding programs is because of the reason that hybrid seeds are easier and faster to growing homogenous plants

Introduction
Plant breeding, according to Sansern et al. (2010), is the process of genetically altering plants to meet human demands. Prehistoric humans in various parts of the world domesticated only a small number of the hundreds of thousands of species that were then available. They did this by genetically altering these species’ components, which entailed both conscious and unconscious selection as well as differential reproduction of variants (Allard, 1999). A relatively small number of plant species have evolved over many years of trial and error to become the backbone of agriculture and, consequently, the world’s food supply (Mackay, 2001). This method of domestication includes the identification of specific valuable wild species along with a system of selection that resulted in alterations in the quality and quantity of cultivated crops.The modifications brought about by domestication involved altered organ size and shape, loss of many survival traits, such as bitter or toxic substances, the disintegration of seeds in grains protective structures, such as spines and thorns, seed dormancy, and change in life span increased for crops grown for roots or tubers and decreased for crops grown for seed or fruit. The domestication process followed mostly by mass selection (selection by bulking preferred kinds) is a potent method for facilitating quick changes while preserving genetic variability in the population (Okporie and Obi 2002).
Populations can exist in constantly changing surroundings due to genetic variation. More variation increases the likelihood that certain individuals in a group will have allele variants that are appropriate for the environment. Those individuals have a higher chance of survival to have offspring which carry that allele. Because of their success, the population will endure for additional generations. Selecting the best parents to utilize in artificial crosses is one of the key concerns for plant breeders since it encourages the expression of the largest genetic variability and the production of superior recombinant genotypes. The objective of plant breeding is to simultaneously improve all the desired traits. This task is complicated by correlations between various traits, which may result from pleiotropic genes, physical chromosomal links between genes, or population genetic structure. Choosing one feature will alter associated qualities, sometimes in a positive or in a negative way. As a result, selection may result in unexpected modifications, provided they fall within the typical range of variations seen in the crop and are therefore thought to be useful to consumers or the environment. Breeding practices in the 20th century improved a variety of genetic techniques, including methods for identifying and preserving more genetic diversity, creating variable populations for selection, and testing how to differentiate between the effects of genes and the environment. Naturally self-pollinating plants like soybeans or tomatoes, naturally cross-pollinated plants like maize, and plants whose vegetative propagation (typically cross-pollinated) allowed the direct fixing of improved types, all required different precise steps in the production process (Ubi, 2013).

Introduction
Crop breeding programmes are under increasing pressure for developing cultivars that possess the ability to adapt to diverse environments while maintaining higher quality and quantity, in response to the escalating worldwide demand for food. The primary goal of plant or crop breeding is to attain genetic enhancement, leading to the creation of new varieties that demonstrate higher yield and superior quality. Hence, the central aim of crop breeding initiatives is to develop novel cultivars that demonstrate improved resistance against fungal, bacterial, insect, or viral pathogens, alongside increased tolerance to abiotic stresses such as drought low temperature, salinity, dehydration, and heavy metal toxicity. Additionally these breeding efforts aim to improve quality attributes, including taste, size shape, colour, and cooking convenience (Lenaerts et al., 2019). The ability to anticipate emergent phenotypes resulting from genetic or environmental disruptions necessitates the utilization of methodologies capable of identifying metabolic pathways or canopy structures suitable for change. The insilico tools have the potential to guide breeding endeavours aimed at developing novel germplasm that exhibits robust adaptation to diverse environmental conditions. The precise simulation of organisms in a computational environment is a current and effective approach to enhance prediction abilities. Significant progress has been made in the field of predictive medicine through the implementation of community projects that utilize integrative, multi-scale modeling techniques. However, there are a lot of crop models that are just geographically and temporally restricted, which limits their ability to go beyond the data that is now available and, consequently, leads to insufficient forecasts regarding crop reactions in novel circumstances. The plant community has launched or continued a coordinated endeavour focused on the development of a virtual plant modelling through consolidative and multi-scale mapping, models and simulations (Marshall-Colon et al., 2017).

Introduction
The integration of bioinformatics into plant breeding has been shaped by several key milestones over the past few decades. Concepts like Breeding 4.0 (Wallace et al.,2018) and, 5G Breeding (Varshney et al., 2020) have gained global prominence, strengthened by the availability of extensive omics data. The advent of DNA sequencing technologies marked a key milestone in this field, catalyzing numerous genome sequencing projects worldwide such as Arabidopsis, rice, tomato, maize, wheat, etc. Next-generation sequencing (NGS) platforms, such as Illumina, PacBio, and Oxford Nanopore, have enabled rapid sequencing of entire plant genomes, facilitating the identification of genetic variations, including single nucleotide polymorphisms (SNPs), insertions, deletions, and structural variants (Deschamps & Campbell, 2010; Fuentes-Pardo et al.,2017). These advancements have significantly improved comparative genomics, enabling researchers to compare the genetic makeup of different plant species or varieties and identify genes associated with agronomic traits, such as yield, disease resistance, and environmental stress tolerance (Khan et al., 2024). As a result, these developments have revolutionized plant genetic research and crop improvement strategies, providing unprecedented opportunities to enhance agricultural productivity (Bellare et al., 2018; Shendure and Ji, 2008).
Bioinformatics has revolutionized plant biology by combining computational and statistical tools to analyze genomes, transcriptomes, proteomes, and metabolomes facilitating insights into genome structure, function, and evolution (Yadav et al., 2015; Saha et al., 2023; Roychowdhury et al., 2023). Genomics, emerged in the 1980s primarily focussing on mapping and sequencing genomes and there after laid the groundwork for functional genomics, which systematically explored gene functions (Hieter and Boguski, 1997; (Jackson et al., 2011). Further, advances in sequencing technologies, such as long-read platforms, have enabled detailed analyses of structural variants in crop genomes, crucial for identifying agronomic traits.
The large volumes of genomic sequence data have allowed researchers to identify genetic markers for crop improvement and candidate genes for trait development. However, the full potential of these genomic sequencing efforts depends on assigning functions to the thousands of genes with unknown roles. Model organisms such as humans, mice, Arabidopsis, rice, tomato, Medicago, and wheat have been instrumental in advancing genomic investigations (Bult, 2006). A notable example is the model organism Arabidopsis thaliana, which has provided a foundation for exploring fundamental biological phenomena using resources such as the TAIR database (Lamesch et al., 2012). Leveraging advanced bioinformatics techniques, researchers have enhanced crop productivity, mitigated diseases, and optimized resource management in agriculture. Advanced approaches like genome-wide association studies (GWAS) and transcriptome analysis continue to refine the understanding of genetic underpinnings, revolutionizing modern agricultural strategies (Mai et al., 2023).

Introduction
Loss of arable land due to population expansion, urbanization and climate change have substantially impacted agricultural production, driving the need to exploit advanced techniques for enhancing sustainable crop production (Bren d’Amour et al. 2017). The yield and productivity of plants are influenced by both their genotype and the growing environment, which govern the performance indices or phenotype (Reynolds et al. 2020). Conventional plant breeding plays a crucial role in ensuring food and nutritional security for the ever-growing global population by harnessing genetic diversity and selecting plants with superior agronomic traits (Singh et al. 2019). However, identifying plants with superior agronomic traits and novel genes (quantitative trait loci or QTLs) through conventional breeding is akin to finding a needle in a haystack (Bohra et al. 2022). Furthermore, the conventional breeding approach is time-consuming and often associated with linkage drag due to extensive inter-crossing/hybridization among elite, wild, and common landraces (Beaver and Osorno 2009). Despite these challenges, classical breeding does develop new plant varieties with improved traits that can withstand climate extremes. Nevertheless, the duration of breeding cycles required to successfully complete the breeding program remains a major bottleneck, taking around 7-9 years to develop an improved variety (Pratap et al 2021).
Efforts have been made to revamp conventional breeding techniques by exploiting molecular markers (Ribaut et al. 2010). These markers effectively capture genetic variations across large populations at an early plant developmental stage. Additionally, the use of molecular markers in plant breeding significantly reduces the time required to screen plant genotypes with desired traits. Otherwise, achieving this task would take 2-3 years (Amiteye et al. 2021). Molecular marker-based techniques, such as marker-assisted selection (MAS), markertrait association (MTA), and genome- wide association studies (GWAS), have become routine tools. They help predict and develop genetic models for plants containing desired traits (Bohra et al. 2020). Furthermore, plant breeders have successfully integrated these molecular markers with genomics, phenomics, transcriptomics, proteomics, metabolomics, and epigenomics approaches (Malik

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
Based on the mode of reproduction, plants are broadly classified into sexually propagated and asexually propagated crops and some of the agricultural crops and a large number of horticultural crops are asexually propagated. The most important asexually propagated crops cultivated on a global basis are potato (Solanum tuberosum), cassava (Manihot esculenta), sweet potato (Ipomoea batatas), sugarcane (Saccharum spp), yam (Dioscorea spp.), taro (Colocasia esculenta), banana (Musa paradisiaca), etc. In sexually propagated crops, seeds are the primary propagules and it is produced by the fertilization of male and female gametes. Whereas, asexual reproduction or clonal reproduction covers all those modes of multiplication of plants where normal gamete formation and fertilization do not take place and vegetative propagules are the means of reproduction. Since sexual reproduction involves meiosis, segregation and recombination, the creation of variation is a continuous process which is inevitable in these crops. On the other hand, in asexual propagation, progenies are identical to the parent clones and they are genetically similar without any variation and they reproduce via mitosis.
Characteristics of asexually propagated crops
• Majority of the asexually propagated crops are perennials, e.g., sugarcane, fruit trees, etc. The annual crops are mostly tuber crops, e.g., potato, cassava, sweet potato, etc.
• Many of these crops show reduced flowering and seed set, and some varieties of these crops do not flower at all. But many of these crops flower regularly and show satisfactory seed set.
• They are invariably cross-pollinated and highly heterozygous and show severe inbreeding depression.
• A vast majority of asexually propagated crops are either polyploids. eg., sugarcane, potato, sweet potato, etc., or have polyploid species or varieties.
• Many cultivated crops are interspecific hybrids, ex., banana, sugarcane, etc.
• These crops consist of a large number of clones, that is, progeny derived from a single plant through asexual reproduction. Thus, each variety of an asexually propagated crop is a clone.

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
Currently, about 350,000 species of flowering plants have been described under global flora, but only a few of them have been rigorously screened for plant breeding parameters and systematic research accomplished in terms of varietal development. According to the Great Medical Encyclopaedia, medicinal plants are those used as a source of raw material for preparation of medicinal products of natural origin. Medicinal and aromatic plants occupy a pivotal position in the socio cultural, health care and spiritual arena of rural people of India. Medicinal plants contribute significantly to the rural livelihoods for their sustenance and income generation. Medicinal and aromatic plants are being used since ancient time for the treatment of many diseases in traditional and recognized systems of healthcare and for therapeutic, fragrance and flavoring products in pharmaceutical and cosmetic industries besides as sources of natural dye, fat, essential oil, biopesticide, resin, protein, vitamin, condiment, spice, timber, fiber and other useful substances. Medicinal and aromatic plants-based livelihood systems are often mediated by the market forces and/ related directly to employment and income of the poor people.
Based on the research work carried out by International Development Research Centre (IDRC) in South Asia, MAP and other biodiversity-based livelihoods can not only become poverty alleviating but also been made socially equitable and gender balanced. According to the World Health Organization, 80% of people from developing countries depend mainly on traditional medicine for primary health care. India is one of the worlds’ richest sources of medicinal plants comprising of nearly 45,000 species, of which nearly 100 species find major commercial use as per the statistics of National Medicinal Plant Board, New Delhi. In 2017, the estimated global market value of herbal medicine and herbal supplements was in the region of $107 billion (Yao et al, 2019), and not surprisingly, the substantial demand and consumption of these products have resulted in shortages, and in some cases even the exhaustion, of several medicinal plant resources, leading to habitat destruction and the loss of genetic diversity.
Plant secondary metabolites specific to each medicinal herb are derived from the precursors obtained from the primary metabolic processes related to one plant species or related group of species. These metabolites protect plants against plants being eaten by herbivores or being infected by microbial pathogens. They serve as attractants for pollinators and as agents of plant-plant competition and plant microbe symbioses. The rise of chemical taxa of medicinal and aromatic plants can be considered as consequence of biochemical and metabolic processes mostly under genetic control. It is assumed that differentiation of cell is mostly manifested in chemo-differentiation at a molecular level and the fundamental differences of protein present in an organism, between different enzyme systems. Moreover, the identity of a medicinal plant is attributed to the dissimilarities in their metabolic profiling intra specific chemical adaptations influenced by the ecological and geographical conditions. This discrete chemical difference is known as poly chemism that occur in autogamous species like medicinal and aromatic plants

Introduction
Detailed understanding of the gene structure and functions are achieved in respect of the genes present in the nuclear genome. The knowledge of the gene functions is being applied in plant genetics and plant breeding. The different kinds of genetic variants are well captured and explained in crop improvement programmes. The organelle genomes, namely, chloroplast and mitochondria that are present outside the nucleus have not received much attention to understand this organization, structure, functions and in utilizing their genetic endowments in many of the plant development and functions. The organelle genomes present in the cytoplasm are providing cytoplasmic effect, cytonuclear and inter genome interactions that impact plant development, plant fertility and agronomic traits expression. It is estimated that 80% of the metabolites are affected by the variations in organelle genomes. The organelle genome also influences and regulates the activity of nuclear genes. The The chloroplast genome encodes proteins that are central to plant photosynthetic activity for plant photosynthesis producing sugar and mitochondria genomes as the energy powerhouse for the cells and they are very essential to provide support to the plant functions and biomass production that is converted to the crop yield. Together, the organelle genomes have disproportionate effects on the nuclear gene functions.
These two organelle genomes that exist outside the nuclear genomes, active in synthesizing food and energy for cell functions, are not as much considered and relied upon by the plant breeders although they are basic biological machineries. This chapter on the organelle genomes is designed to present the structure and genetic endowments and functioning of the chloroplast and mitochondrial

Introduction
The science of epigenomics has emerged as a key area of research across numerous biological disciplines. Epigenomics is the analysis of epigenetic changes occuring across many genes in a cell or entire organism, whereas the concept of epigenetics focuses on processes that regulate how and when certain genes are turned on and turned off. Understanding on the science of epigenetics can be traced back to the early hypothesis proposed by Aristotle to disprove the theory of preformation. Waddington’s initial conceptualization of epigenetics as a “conceptual tool” to integrate genetics and embryology established a foundational framework for subsequent research. Over time, advancements in molecular biology, developmental biology and evolutionary biology have since profoundly expanded and refined our understanding of epigenetics. Waddington further progressed in the 20th century with his introduction of the “Epigenetic Landscape” model (Baedke, 2013), marking a crucial milestone in the evolution of epigenetic theory.
In modern times, epigenetics refers to the study of heritable changes in gene expression or cellular phenotype that do not involve alterations to the underlying DNA sequence. Recent genetic and biochemical research has improved the understanding of various epigenetic regulation by three mechanisms including DNA methylation, histone modifications and non-coding RNA regulations. These mechanisms induce changes in chromatin conformation (active-open or repressiveclosed), which influences the gene expression that results in gene activation or gene silencing (Fig.1).
The transition between open and closed chromatin states, along with interactions among various epigenetic mechanisms, is essential to maintain optimal cellular function in diverse cell types, tissues and in response to varying developmental or environmental stimuli (Allis and Jenuwein, 2016).
Extensive studies in Arabidopsis led to a profound understanding of epigenetic mechanisms in plant growth and development. Later, intensive investigations was

Introduction
Eversince green revolution was introduced in 1960’s, the Indian agriculture has taken a series of transformations that resulted in paradigm shift from tradition farming to precision agriculture with an intend to address a wide array of challenges including burgeoning population, shrinking farm land, restricted water availability, imbalanced crop nutrition, multi-nutrient deficiencies, crop yield barriers and decline in soil organic matter. Agricultural scientists were looking for alternative strategy to tideover the bundle constraints with a single stop solution. Nanotechnology deals with atom-by-atom manipulations to evolve processes and products precised to overcome the farming challenges altogether that hardly possible to achieve by the traditional systems. Nanotechnology applications in agriculture include diagnostic devices for early detection of plant diseases (Chen and Hu, 2013), nano-agricultural inputs such as nano-fertilizer (Subramanian et al., 2015; yuvaraj and Subramanian., 2018; Nongbet et al., 2022; Verma et al., 2022; Mohanraj et al., 2024), nano-herbicides (Abigail and Chidhambaram, 2017; Forini et al., 2022) and nano-insecticides (Wang et al., 2022), nano-seed science, plant health management (Subramanian et al., 2016), nano-food systems (Anusuya et al., 2016; Jincy et al., 2017; Jan et al., 2023) besides environmental remediation (Rajkishore et al., 2023).
Even though the nanotechnology is being exploited in wide array of disciplines such as energy, environment, electronics, health sciences and few areas in agricultural sciences, the literature on the application of nanotechnology in plant breeding and genetics is scanty. Nanotechnology is a key component in the creation of genetically enhanced crops (Servin et al., 2015) with an increase crop yield or disease resistance (Kerry et al., 2017). Using genetic engineering or plant breeding, nano-enabled approach aids in the development of resilient and better plant genotypes (Patel et al., 2014). Plant breeding and genetic modification to create better crops frequently utilise nanotech-derived devices (nano sensors and nanoparticles) (Kumar and arora, 2020). Nanobiotechnology is to better understand the biology of various crops and the breeders may be able to increase agricultural yields or nutritional value (Sah et al., 2014). Atomically altered seeds, plant cells with silica beaks, hormone and antibiotic delivery in plants, particle farming, and iron seeding are a few examples. (Prasanna et al., 2018; Jha et al., 2013). Particle farming is the process of cultivating plants in predetermined soils to produce nanoparticles for industrial purposes. Plant production and growth are negatively impacted by abiotic stress. Salinity and drought are the two abiotic stressors that affect plants the most widely (Lavania et al., 2015; Zhao et al., 2017). Nano-enabled crop improvement can be achieved through four important aspects such as (1) genome editing, (2) genetic engineering, (3) abiotic and biotic stress management and (4) plant performance.

Introduction
In the ever-evolving landscape of agriculture, the intersection of science and technology continually reshapes the way we approach crop improvement. Among the most revolutionary advancements in recent years is the advent of genome editing technologies. These powerful tools offer unprecedented precision and efficiency in modifying the genetic makeup of plants, holding immense promise for revolutionizing the field of plant breeding. Genome editing plays a crucial role in plant breeding by enabling plant breeders to make precise and targeted changes to the DNA of crops, offering significant advantages over conventional breeding methods. Besides, crop improvement, these new breeding tools shorten the time needed to introduce desirable traits into crops, from decades to just a few years. They have revolutionized plant breeding by providing breeders with the ability to efficiently create crops that are more resilient, better adapted, and can produce higher yields with fewer resources, ultimately contributing to sustainable food production and addressing the challenges posed by climate change and population growth.
This comprehensive review aims to explore the transformative potential of genome editing technologies in genetic improvement of crop plants. The review will commence by elucidating the underlying mechanisms of genome editing technologies, offering insights into the molecular machinery that drives precise DNA modifications mediated by ZFNs, TALENs, CRISPR/Cas, base editing, prime editing and other new variants of CRISPR/Cas systems, highlighting their respective strengths and limitations. From enhancing crop productivity and quality to conferring resistance against biotic and abiotic stresses, these technologies offer a versatile toolkit for addressing pressing agricultural challenges. Case studies and examples from recent research will illuminate the successes and potential pitfalls of employing genome editing in crop improvement efforts. Besides, the regulatory and ethical considerations surrounding the deployment of genome editing in agriculture will be addressed. In conclusion, this comprehensive review seeks to provide a holistic perspective on harnessing genome editing technologies in plant breeding. By elucidating the scientific principles, applications, regulatory challenges, and ethical considerations, we hope to facilitate informed discourse and decision-making surrounding the integration of these transformative tools into agricultural practices. As we stand at the precipice of a new era in crop improvement, embracing the potential of genome editing holds the promise of unlocking sustainable solutions to global food security challenges.

Introduction
Chromosome engineering has emerged as a revolutionary approach, offering immense potential for genetic improvement by manipulating the structure and composition of chromosomes. Using genome engineering technologies, it is possible to introduce desirable traits into plants, such as disease resistance, increased yield, and enhanced nutritional content. To sustain the current standard of living, agriculture must yield significant increase in production (Gerland et al. 2014). Novel cutting-edge techniques developed for chromosome engineering hold great promise for addressing the challenges faced by modern agriculture, including climate change and food security. Engineering ability to precisely modify the genetic makeup of plants, chromosome engineering opens new avenues for creating novel cultivars with improved characteristics. While classical breeding has been successful in developing improved cultivars, it has its limitations. The process is time-consuming and often relies on probability to bring desired genetic changes. Since genes are organized into chromosomes, one important step to solve this issue is the development of novel genetic tools for chromosome reorganization and manipulation. When (Sears 1956) used X-ray irradiation to introduce foreign chromosome segments into the wheat chromosomes to transfer new traits, it was the beginning of plant chromosome engineering. Since then, plant chromosome engineering has evolved.
Applying methods such as chemicals and X-rays, induced mutagenesis was essential to the Green Revolution. Induction of polyploidy yielded more vigor and benefits like larger and higher-quality fruits (Osborn et al. 2003). Insect resistant and herbicide resistant transgenic crops successfully contributed to enhanced food production with less input into the farms. Genome editing enables precise modifications to increase disease resistance and stress tolerance (Ma et al. 2015). Considering practical features of chromosome engineering, this article discusses the use of induced mutagenesis, polyploidy induction, transgenesis, and genome editing, as the practical tools. The purpose of this chapter is to provide an in-depth analysis of chromosome engineering, exploring its scope, historical milestones, techniques, and its contributions to genetic diversity improvement and crop improvement. It also highlights the importance of efficient delivery techniques to overcome constraints such as off-target effects and concerns about genetically modified organisms (GMOs).

Introduction
The early human beings undertook extensive exploration of wild species in different plant species before selection followed by domestication for food and other purposes. The identification and selection of innumerable wild plant species and their domestication formed an integral part of early agriculture. Thus the organized cultivation of plant species is the result of selection in and among numerous wild species followed by domestication. It started around 9000-11000 years ago and has given birth to agriculture. The evolution of numerous human civilisations/settlements across the globe is largely shaped by agriculture. Selection continued during domestication which has led to the improvement in the wild plant species and transformed wild plant species into cultivated crop plants. Subsequently, the crop plants were differentiated into distinct landraces depending on morphological features, adaptation, economic use, etc. across different continents on Earth. Selection by humans and/or by nature is a continuous and dynamic process and will continue in future as well. However, a deep understanding of genetic diversity in crop species is essential for successful selection by human beings (Naqvi et al., 2022). The objective of the selection and domestication were dynamic and varied depending on cultural, social, economic and climatic factors. In general, the major objective of selection was to increase yield and bring desirable changes in valuable traits of economic importance. The significance of selection has increased over the years and will continue to increase in future as well. The procedure and methods followed while selecting traits or genotypes of economic importance have led to the birth of a new discipline, plant breeding. In the early years, plant breeding was more of an art than a science. As science progressed, the increased understanding of the genetics of traits complemented plant breeding with scientific back-up. Subsequently, genetics has become the basis of selection, the essence of plant breeding.
Globally, the demand for food, fodder, fuel, energy etc. is increasing continuously and increased crop production is considered as the most viable and sustainable answer or solution. The major driving force for increased demand is the growing population. However, the challenges to increasing crop production are also many namely, the decreasing arable land for agriculture, changing climate (increased extreme temperatures and altered rainfall patterns etc.), decreasing natural resources like water and energy etc. (Razzaq et al., 2021). Further, global warming also impacts the overall agricultural production across crops adversely. In this scenario, the role of plant breeding is vital to sustain higher crop production on a sustainable basis. The responsibility of plant breeders also increases in terms of the development of new, high-yielding, stress (biotic and abiotic) tolerant, high-quality and higher resource use efficient genotypes continually. Historically, conventional/traditional plant breeding has made significant progress in several crops in terms of increasing production, productivity, stress tolerance, nutritional value, etc. Conventional plant breeding relied fundamentally on extensive evaluation of available germplasm for a range of traits of economic importance and utilization of genetic diversity found in the landraces and closely related species (primary and secondary gene pools) (Prohens, 2011; Mangal et al., 2024). The success in conventional plant breeding largely depends on the expertise of breeders while undertaking phenotypic selection. It mainly involved selection within broad genetic base germplasm like landraces, open-pollinated varieties, exploration of wild and related species, and their evaluation for traits of interest, followed by hybridization and cyclical selection (Hallauer and Carena, 2009). The