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Plant breeding has long been one of humanity’s core scientific pursuits, driven by the need of securing nutritional food sources and adapt crops to diverse climates and environments. From early efforts to domesticate wild plants to the modern integration of genetic engineering, bioinformatics, and artificial intelligence, plant breeding has evolved into sophisticated science with far-reaching impacts on society, ecosystems, and economics. Now, food production in India has reached 325 million tons and vegetable 204.96 million tons and fruit production 112.62 million tons in 2022-23 for meeting food demand with annual increase of 2.3% and nutritional security. Though self-sufficiency of food is achieved with the ever-increasing global population, it is a need of the hour to break the yield plateau achieved through breeding to produce fifty percent more food in 2050. In the dawn of 24th century the need to have biofortified food emerged to alleviate undernutrition, micronutrient deficiency and to meet the gender specific nutrient demand. The increase in food production with added qualities is gradual/ incremental and need to increase per capita to meet the demand of increasing human populations. Conventional breeding has significantly increased agricultural production over the past decades by leveraging advancements in plant genetics, biometrical methods and various population improvement techniques, primarily based on phenomics. With the innovations and applications of molecular genetics and genomics, breeding selection and advancement have become more precise and faster. However, the gap between phenomics and genomics remains perceptible. The cutting-edge technologies like molecular markers, genomics tools and genome-wide association studies (GWAS) are widely used methods for identifying genetic variation associated with traits across diverse populations. Next generation breeding methods provide a strong foundation for developing high yielding, biofortified, and climate resilient crops. Furthermore, it is now possible to unravel the genes at species, crop wild relatives (CWR) levels and harness them for breeding improvement. The application of both molecular breeding and genomics in the plant breeding is both precise and rapid. GWAS/Genomics is widely used method for identifying genetic variations associated with traits across diverse population. Genome editing represents the latest and most widely applied cutting-edge technology for gene transfer in a hassle-free manner. Organelle genomes, including plastid and mitochondria, are other extracellular genomic resource contributing to genetic performance through intergenome interaction.

Introduction Domestication is the process of adapting wild plant species for human cultivation and consumption and it has played a pivotal role in shaping modern agriculture. Since the dawn of civilization, humans have selectively bred plants to enhance desirable traits, such as increased yield, improved taste, and resistance to pests and environmental stresses. Through domestication, early agriculturalists inadvertently altered the genetic makeup of wild progenitors, favouring traits that aligned with their needs and preferences. This process involved selecting and propagating plants with desired characteristics over successive generations gradually transforming once-unruly wild species into more docile, productive and palatable varieties. The domestication of crop plants was a gradual and ongoing process, often spanning thousands of years. It required keen observation experimentation, and an inherent understanding of plant biology and genetics even before these concepts were formally understood. This patient and persistent effort by our ancestors paved the way for the development of diverse and nutritious food sources, enabling the establishment of sedentary communities and the rise of complex civilizations. While modern breeding techniques have advanced significantly, the fundamental principles of domestication remain a cornerstone of crop improvement efforts. By understanding the historical significance and underlying mechanisms of domestication, we can better appreciate the invaluable contributions of our ancestors and continue to build upon their legacy, ensuring a sustainable and diverse food supply for generations to come. The current state of food systems is being challenged due to the heavy reliance on a limited number of resource-intensive staple crops. The emphasis on maximizing yield and the consequent reduction in diversity over the course of domestication history has led to the development of contemporary crops and agricultural practices that are environmentally unsustainable, susceptible to the impacts of climate change, lacking in essential nutrients, and contributing to social inequalities. For many years, researchers have advocated for diversification as a viable solution to tackle the issues surrounding global food security. In this context, we present a vision for a new phase of crop domestication, which aims to expand the range of crop diversity. This approach involves active engagement and benefits for three key components of domestication: a) the cultivated crops themselves, b) the surrounding ecosystems, and c) the human populations depending on these crops. We delve into the potential of current tools and technologies to initiate a revival of diversity within existing crops, enhance the value of underutilized crop varieties, and introduce new crops into cultivation. This multipronged strategy aims to reinforce genetic diversity, promote resilient agroecosystems, and establish a more varied and robust food system. The successful execution of this renewed phase of domestication hinges on a bold commitment from researchers, funders, and policymakers to invest in both fundamental and practical research efforts. As we navigate the challenges of the anthropocene epoch, characterized by significant human impact on the environment, the process of domestication offers a pathway to construct more diverse and adaptable food systems that can better serve humanity’s needs.

Introduction Angiosperms produce attractive and intricately structured flowers, within which their reproductive process occurs. In flowering plants, as in other plant groups, a diploid spore-producing generation (sporophyte) alternates with a haploid gamete-producing generation (gametophyte). The flower contains specialized structures, such as the stamen (or androecium) and the pistil (or gynoecium), where the respective male and female gametophytes are formed. The pollen grain serves as the male gametophyte, while the embryo sac serves as the female gametophyte. These gametophytes are responsible for producing sperm and egg cells, respectively facilitating their union during fertilization. The pollen grain contains the male gametophyte in angiosperms or gymnosperms. Conversely, spores function as a resting and dispersal phase for cryptogams (Moore et al., 1991). The study of pollen grains (produced by seed plants, angiosperms and gymnosperms) and spores (produced by pteridophytes, bryophytes, algae and fungi) is known as palynology. This discipline examines the structure and formation of pollen grains and spores, their dispersal and their preservation under various environmental conditions. Palynology serves as a valuable research tool for understanding many aspects of plant and animal metabolism. Moreover, a deeper understanding of pollen can aid plant breeders in enhancing efforts to improve global food and fiber supplies. In the anthers of higher plants, neither the developing pollen nor the surrounding tissues exhibit autonomous growth and development. Instead, the developing anther functions as a system where the gametophytic and sporophytic generations of the plant communicate, coordinate and co-participate in development. This chapter aims to understand the various aspects of gene activity that occur during pollen development.

Introduction Definition of heterosis The word “heterosis” was coined by G.H. Shull in 1914 as a convenient abbreviation for awkward phrases like ‘stimulation of heterozygosis’. When two genetically diverse parents are crossed, the resulting F1 or hybrid progeny has superior performance over both of its parents which is known as heterosis. The F1 or hybrid has superiority in vigour, adaptability, stress tolerance, growth rate, population fitness, biological and economic yield. Luxuriance on the other hand is a more general term often confused with heterosis, used to describe plant’s overall healthy and abundant growth, regardless of its genetic background (Allard, 1960). Charles Darwin introduced the concept of hybrid vigour in 1876, a term closely related to heterosis. The exceptional hybrid vigour in the F1 generation stems from the theory of dominance and codominance, offering numerous advantageous characteristics, particularly economically significant ones. Heterosis is confined to F1 or hybrid generation only. The F2 and subsequent generations do not show heterosis due to factors like recombination and segregation, which lead to shuffling of the genes and produce variety of new combinations, hence they are neither homogenous like F1 nor have hybrid vigour. One of the main characteristics of heterosis is that it is highly variable from crop to crop as well as from cross to cross. So, some of the crosses will exhibit higher heterosis than the other crosses. This is because heterosis is controlled by many factors which include the genetic diversity of parents, combining ability of parental lines, genetic background, additive, dominance, epistasis nature of gene imparting heterosis which will be dealt in detail in next sections of the book. Heterosis, manifested in positive (yield, quality, disease resistance) or negative (plant height, maturity duration) aspects, is more prevalent in crosspollinated species than in self-pollinated ones. It can be fully exploited in hybrids or partially exploited in synthetic and composite varieties. The performance of hybrids relative to parents exhibits distinct features, as illustrated in Figure 1, including better-parent heterosis with optimal trait values surpassing either parent. Mid-parent heterosis exceeds the parental average but holds limited agronomic relevance. Phenotypes are broadly categorized as additive (similar to parental average) or non-additive, further subdivided into partially dominant, dominant, and over/under dominant. Factors influencing heterosis include genetic diversity, combining ability, genetic background, and the interplay of additive, dominance, and epistatic genetic factors, explored in detail in subsequent sections.

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 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 The genetic diversity of crops has been subjected to considerable humandriven selection throughout time, in particular, is often limited by conventional plant breeding techniques. Under these conditions, crops with low yields and a high risk of disease and pest infestation may be produced. Thus, there’s a need to introduce a technique where solutions to all the problems can be addressed. CIS breeding opens us a wider range of opportunities for improving crops by enabling the deliberate incorporation of natural genetic differences from closely related plants. The word “CIS” in CIS breeding means “on the same side/same kingdom”. CIS breeding is an advanced method for genetic improvement in which genes from closely related plants are inserted into the desired crop. This method creates crop varieties that are greatly improved in terms of growth capacity, yield potential and pest and disease resistance. CIS breeding is a pioneering technology designed to integrate novel traits into established crop varieties without the introduction of foreign genetic material. Utilizing the similar gene combinations and the plant’s intrinsic genetic systems, it is a natural form of genetic improvement that improves traits including yield, drought resistance, disease resistance and nutritional qualities (Anjanppa and Gruissem, 2021). Comparing to conventional breeding where gene transfer can occur through random cross- breeding or mutagenesis and risk of unintended effects are high, in CIS breeding, one or few genes are transferred from related species as well as risk of unintended effects are also low. Some countries, regulate it as conventional breeding and other regulate it as GMO breeding.

Introduction Current state of global warming and climate change affecting crops through altered pest and disease incidence patterns, changes in temperature and CO2 levels which adversely affected the crop production (Habib-ur-Rahman et al. 2022). This threat is particularly pronounced in food-insecure regions, especially in Asian countries. Climate change not only jeopardizes crop and livestock health but also impacts soil and water resources and livelihood of rural communities. Furthermore, it contributes to food insecurity by increasing prices and reducing overall food production. The complexity of these effects highlights the need for modern agricultural techniques to mitigate risks and ensure global food security (Habib-ur-Rahman et al. 2018). Crop improvement, an integral facet of agricultural development, remains a cornerstone in addressing the burgeoning global food demands. Conventional plant breeding methods have played a pivotal role in developing improved crop varieties that exhibit enhanced quality, higher yields and resilience to biotic and abiotic stresses. However, plant breeding methods involving continuous selection and intermating among closely related individuals can result in a reduction of genetic diversity within a cultivated crop species. The narrow genetic base makes crops more vulnerable to emerging threats, such as new pests or diseases and limits their ability to cope with changing climatic conditions. In India, the Green Revolution along with substantial plant breeding activities, led to a significant increase in crop yields, particularly in staple crops like wheat, rice and maize. However, one of the major consequences of green revolution is the development of narrow genetic base in cultivated crop species (Begna 2021). Moreover, the reliance on a narrow genetic base, a consequence of crossing only two parents, curtails the exploration of broader genetic diversity. This limitation restricts the potential for effectively combining and expressing desired traits in the resulting crop varieties. Most of conventional plant breeding techniques were primarily focused on monogenic traits, while many agronomically important traits are quantitative in nature, controlled by polygenes, and influenced by the environment. This poses challenges for breeders relying only on phenotypic selection. Notably, traits influenced by multiple genes, such as resistance to diseases or tolerance to environmental stresses, are particularly challenging to manipulate using traditional breeding methods. Quantitative trait loci (QTLs) are genomic regions that influence polygenic traits, first described by Geldermann (1975). Identifying QTLs associated with improving yield and quality traits is pivotal for catalysing a new Green Revolution (Arrones et al. 2020; Pradhan et al. 2015). Marker-assisted selection (MAS), introgression breeding and QTL pyramiding offer efficient avenues for developing improved cultivars. However, identifying QTLs associated with quantitative traits remains a challenge for plant breeders (Arrones et al. 2020). The basic requirement for the detection of QTLs involves appropriate mapping population, marker systems, phenotyping methods and suitable experimental designs (Arrones et al. 2020; Collard et al. 2005)

Introduction The increase in the world population coupled with climatic fluctuations such as drought, floods, and high temperatures poses a serious threat to food security (Ray et al., 2013). Many researchers have quoted the importance of enhancing the genetic gain of primary crops at a faster rate to meet global food demands (Lin et al., 2016). It remains a challenging task for plant breeders to evolve resilient varieties in a shorter period by employing conventional approaches. The slow progress in crop improvement is mainly attributed to long breeding cycles/generations (Samantara et al., 2022). To overcome the drawbacks involved in traditional methods and to safeguard food security, speed-breeding methods are now being adopted at large or small units to achieve rapid genetic gains in many crop species. The speed breeding techniques include the use of controlled environments with manipulation provisions for light duration, intensity and temperature. This approach is more advantageous for helping plant breeders hasten crop development in several major photosensitive crops (Singh and Janeja, 2021). Breeding a new crop variety via a conventional approach requires the selection of complementary parental genotypes with desired traits, followed by crosses and a series of selections and advancements of superior progenies to release candidate cultivars that meet market demands (Shimelis and Laing, 2012). Notable breeding goals in crop cultivar development programs include increased yield potential and nutritional quality and enhanced tolerance to biotic and abiotic stresses (Breseghello and Coelho, 2013). In any crop improvement program, the following breeding procedures can be distinguished in the order presented: (a) selection of desirable parents with complementary traits to be combined; (b) crosses involving the selected parents and the development of progenies; (c) selection and genetic advancement of the best progenies based on target traits; (d) selection of the best progenies for screening in multiple target production environments to identify the best performing and stable candidate cultivars; and (e) cultivar registration and seed multiplication and distribution to growers (Shimelis and Laing, 2012). These conventional breeding procedures are used in most crop cultivar improvement

Organic Agriculture Organic and biodynamic farming use natural methods to grow crops, avoiding inorganic fertilizers, pesticides, and other chemicals throughout the growth stages. This approach relies on natural biological systems, preserving their relationships and self-regulation, unlike conventional farming, which heavily depends on synthetic inputs. As a result, plant and animal varieties bred for intensive agriculture often do not align with organic principles. To unlock the full potential of organic farming, genetics of seeds should also be organic, ideally bred and grown exclusively in organic conditions to best suit these systems. Organic plant breeding Improving the genetic diversity of the crops and their adaptation to the future organic growing conditions and climate change need to be done through organic plant breeding. The choice of varieties for organic farming that are mostly derived from conventional bred varieties, sustainable use of natural input resources and at the dynamic equilibrium of the entire agro ecosystem are the main features. The organic breeding programs should match with the reproduction system of the respective crop. Seeds and vegetatively propagated crops are important resources for organic breeding. The Organic agriculture system relies on natural inputs and pesticide free and non GMO crops, vegetable and fruits aiming providing healthy food. In an overall manner, organic agriculture is the expression of underlying ecology, fairness and health. Organic agriculture is presently practiced in organically converted and managed land area equal to 2% of the cultivated area in India. International Federations of Organic Agriculture Movement (IFOAM) (2015 and 2017): Organic agriculture is defined as a production system that sustains the soil health, ecosystem and people. It relies on ecological processes, bio diversity, and local conditions. Organic farming is part of organic agriculture and it is basically based on the underlying principles of health, fairness, ecology and care. The well-known characteristic of organic farming is, it produces food without the use of any synthetic fertilizer or pesticides and also without the use of GMO. Trends and perspectives in organic plant breeding are recognized as a highly collaborative and possess strong interrelationships.

Introduction In recent years, there has been a growing interest in alternative nutritious food sources (McClements, 2020) and such group of foods that has gained significant attention is millets. Millets are a diverse group of small-seeded grasses that have been cultivated and consumed for thousands of years. They are rich in essential nutrients such as proteins, fibers, vitamins, and minerals, making them an important addition to a balanced diet. Millets are not only rich in essential nutrients but also have several health benefits. They are known to have nutraceutical properties, low glycemic index, making them suitable for individuals with diabetes. Additionally, millets are a good source of antioxidants, which can help in reducing the risk of chronic diseases such as heart disease and cancer. The diverse range of millet varieties also provides flexibility in incorporating them into various dishes, making them suitable for different culinary preferences and dietary requirements. Therefore, the usage of millets can play a crucial role in promoting sustainable and healthy eating habits. Malnutrition continues to be a pressing issue worldwide, particularly in developing countries (Ashok et al., 2020). The lack of access to nutritious food is one of the main causes of malnutrition, leading to various health problems such as obesity, diabetes, cardiovascular diseases, cancer, and celiac disease (Birania et al., 2020). To address this issue, millets have emerged as a promising solution. Despite being nutritionally superior to other cereals, millets have traditionally been limited to consumption by the poor and those with conventional dietary practices. However, there is a growing recognition of the potential of millets in combating malnutrition and improving public health. Millets, such as finger millet, pearl millet, and sorghum, are often referred to as “superfoods” due to their high nutritional content (Singh et al., 2020). These grains are rich in protein, carbohydrates, fats, vitamins, minerals, and dietary fiber, making them an ideal source of essential nutrients (Ashok et al., 2020). Additionally, millets are easily available and costeffective, making them a viable option for addressing malnutrition on a larger scale (Birania et al., 2020). Furthermore, millets are resilient crops that can withstand environmental changes and water shortages, making them an ideal choice for sustainable agriculture. In this chapter, we delve deeper into specific aspects of millet nutrition, examining their micronutrient profiles, health benefits, culinary versatility, and potential applications in combating malnutrition and promoting sustainable agriculture. By understanding the nutritional richness of millets, we can uncover innovative solutions for improving human health and fostering agricultural resilience.

Introduction World food security has become largely dependent only on a handful of crops like; wheat, rice, and corn which are the major cereals that support more than 50% of the global calorie demand. While these grains are an essential part of various diets, however they are devoid of essential micronutrients. As a result, it is estimated that micronutrient deficiency affects an estimated 2 billion people worldwide raising health concerns over our high dependence on cereal crops. As agriculture sector is considered as backbone of nation and therefore utilizing a handful of crops have placed the global food security at risk. In this context, Food and Agriculture Organization (FAO) has identified many plants as under-utilized, which can significantly contribute for improving nutrition and health, enhance food basket and livelihoods, future food security and sustainable development (FAOSTAT, 2023). These underutilized crops offer an immense potential in the functional food sector to combat hidden hunger crisis and offer the options of income generation. Cereals such as rice, maize and wheat are monocots and belong to family Poaceae, however buckwheat, chia, quinoa and amaranthus although resembles with cereals are dicots and are categorized as Pseudocereals. These crops have been placed under the category of important crops by UNESCO due to dwindling cultivation and exploitation in the wild besides, these pseudocereals has gained a worldwide importance in the nutraceutical industry due to the rich nutritional profile compared to cereals and are considered as crops of the 21st century (Pirzadah et al., 2020). These are enriched with various active principals such as; polyphenols, flavonoids, amino acids, dietary fibre, lignans, vitamins, minerals, antioxidants, unsaturated fatty acids and other essential components like fagopyritols. The protein quality and quantity in pseudocereals is far better compared to cereals and this property qualifies their entry into the functional food industry (Rodriguez et al., 2020). Pseudocereals are rich in amino acids such as; arginine, tryptophan, lysine and histidine that proved essential for infant and child health thus, projected pseudocereals as an appropriate food supplement for child nutrition. The food production agro-systems must be adapted to climate change to ensure food security and stability. However, pseudocereals are climate resilient crops and can be grown even on marginal lands that are not fit for cereals thus, are considered as future crops to tackle mal-nutrition and future food crises. To explore these neglected or lost crops, there is an increasing interest in research and development that needs heightened direction and focus (Mabhaudhi et al., 2019). In this context, there is a need to adopt recent biotechnological interventions for the crop improvement and domestication of pseudocereal crops. This chapter focuses on nutritional profile of emerging pseudocereals viz., Buckwheat, Chia, Quinoa and Grain amaranth, phylogeny, genetic resources, breeding behavior and advanced breeding methods and their integration into the global food system

Nutritional significance of millets Millets, nutrient-dense grains rich in proteins, vitamins, minerals, and dietary fibre, are emerging as vital components of a balanced diet, particularly in regions where they serve as staple foods. Their high content of essential amino acids, iron, calcium, zinc, and B vitamins makes them crucial for addressing micronutrient deficiencies (Hassan, 2021). As gluten-free grains, millets are suitable for individuals with celiac disease or gluten intolerance, broadening their dietary appeal. Additionally, millets are rich in health-beneficial phenolic compounds, making them suitable for food and feed. Finger millet, with its diverse phenolic profile, has higher antioxidant activity than pearl millet. These phytochemicals positively impact human health by lowering cholesterol and phytates. Incorporating millets into human and livestock diets can improve health, reduce disease risks, and ease the pressure on maize (Hassan, 2021). Essential nutrients in millets Millets are particularly rich in carbohydrates, providing a sustained energy source essential for daily activities. Unlike refined grains, millets have a low glycaemic index, releasing glucose slowly into the bloodstream. This characteristic helps manage blood sugar levels and prevents spikes, making millets an excellent food choice for individuals with diabetes. Numerous studies have demonstrated that regular millet consumption can offer a variety of health benefits. The high fiber content in millets supports digestion, prevents constipation, and promotes a healthy gut microbiome (Jacob, 2024) Consuming millets can lower the risk of chronic diseases such as cardiovascular disease, type 2 diabetes, and certain cancers. The antioxidants present in millets protect against oxidative stress and inflammation, which are key contributors to many health conditions. Furthermore, millets high fibre content and low glycaemic index promote feelings of fullness, regulate blood sugar levels, and help maintain a healthy body weight. Millets are ancient small grains grown in arid and semi-arid regions of the world, serving as staple foods for many people in Asia and Africa. Abundant sources of minerals and vitamins, they are often referred to as Nutri cereals. Millets contain valuable phytochemicals that provide therapeutic properties for various disorders and diseases, giving them nutraceutical value. (Mishra, 2022) A wide array of biochemical compounds is present in the plant parts and grains. In the oldest texts of medicine in India and China, millets are noted for their medicinal value. Expanding interest and emerging facts highlight their therapeutic uses, with ample evidence showing that millet consumption aids in correcting lifestyle and metabolic disorders. The therapeutic properties of millets can be viewed in two ways: supplementary nutrition through minerals and vitamins, and therapeutic value through phytochemicals and specialty compounds like flavonoids, phenolics, and anthocyanidins that have antioxidant potential (Chellappan 2024). Millets are gluten-free, have a low glycaemic index, and their phytochemicals help correct lifestyle disorders and prevent ailments such as carcinogenesis. Supplementary benefits include the treatment of anaemia and

Introduction A plant seed consists of an embryo and reserve food material (endosperm/ cotyledon) which is surrounded by a protective seed coat. The seed ensures that the next generation of plants exists. The embryo is made up of one or two cotyledons attached to a central axis. The upper part of the axis contains a plumule at its tip. The plumule grows into the shoot system. The lower part of the axis consists of the hypocotyl and a radicle. The radicle grows into the root system. The endosperm is the food reserve that the embryo uses during the early stages of germination. Before the embryo is able to produce its own food through photosynthesis, the endosperm provides vital nutrients to the embryo. Seed stands as an essential and fundamental agricultural input. It can be characterized as a propagative entity that facilitates the continuation of species from one generation to the next. Alternatively, it can be described as a mature fertilized ovule. Seeds play multifaceted roles for their parent plants, encompassing embryo nourishment, dispersion to novel locations, and entering a state of dormancy during adverse environmental circumstances. Seeds originate from various sources like self-pollination, cross-pollination, vegetative propagation, and mechanisms such as apomixis, resulting in diverse varieties or hybrids. Maintaining the genetic consistency of cross-pollinated seeds presents notable challenges. Certain fruit crops encounter obstacles in natural seed propagation due to factors like seed heterozygosity, diminished endosperm size, or minuscule seed dimensions. Additionally, some seedless fruits cannot be propagated conventionally through seeds. Seeds frequently become susceptible to seed-transmitted diseases, facilitating the transmission of diseases across different geographical areas. These constraints in seed-based propagation have spurred the exploration of alternative techniques for species proliferation. This exploration led to the emergence of the concept of synthetic seeds within the realm of plant tissue culture. Synthetic seeds are also known as synseeds or artificial seeds or somatic seeds, seed analog, or manufactured seed. The concept of synthetic seeds has been described in various manners by different researchers. Capuano et al., (1998) defined synthetic seeds as somatic embryos that are enclosed artificially, originating from shoot buds, cell aggregates, or any suitable plant tissue for sowing purposes. These synthetic seeds are capable of developing into plants under controlled in vitro or ex vitro conditions and can maintain this potential even after prolonged storage. Another definition of synthetic or artificial seeds comes from Gray and Purohit (1991) and Redenbaugh (1993), who refer to them as somatic embryos designed for use in the commercial propagation of plants.

Introduction Vegetables are an essential diet component for human beings and nutritional security because of their short season, high yielding potential, nutritional capacity financial viability and potential to create on-farm and off-farm agricultural employment. India ranks as the world’s second-largest producer of fruits and vegetables. In India, vegetables and fruits accounts for about 92% of the total horticultural production. Daily diet consisting of vegetables is primary sources of proteins, vitamins, minerals, dietary fibers, micronutrients, antioxidants and phytochemicals. Additionally, vegetables have wide range of phyto-chemicals such as anti-carcinogenic factors and anti-oxidants constituents (e.g. flavonoids, glucosinolates and isothyocynates) (Silva Dias, 2019). In India an area of 11.35 million hectares is employed for the production of vegetables which is around 204.84 million metric tonnes (APEDA, 2023). Novel genotypes adaptable to various horticultural systems must be developed due to rapid climate change, customers demand and the resurgence and emergence of plant’s pest and diseases (Cardi et al., 2017). Plant tissue culture is emerging as a technology which has significant impact on agriculture sector by producing plants to meet out the growing global demand. It provides the huge potential areas currently offering a glimpse into the future. Apart from this, it has advanced significantly in the area of vegetable sector. Vegetable crops can be improved through efficient in vitro plant regeneration system of biotechnological approach consisting of meristem culture, haploid production and somatic hybridization (Kumari et al., 2020). Genetic engineering is a novel approach to produce improved crops varieties with greater yield potential and pest resistant. Genetic transformation plays an important role in genetic engineering process in order to improve genetics of crop plants. The world’s demand for nutritious and cheap food market have prompted the scientists to step up their efforts to genetically modify the economically significant plants. Traditional breeding methods have several limitations such as more time consuming to develop a plant with desired traits and sexual incompatibility barrier and these limitations can be overcome by adopting effective strategies for regeneration and transformation of valuable plants. Genetic engineering has shown to be an excellent method for improving vegetable crops under different adverse conditions (Gerszberg, 2018). Plant tissue culture and molecular biology are the technical foundations of genetic transformation technology, which is used to produce enhanced crop varieties, disease-free plants (virus-free), genetic transformation, secondary metabolite production, and varieties resistant to various biotic stresses such as diseases-pests, and abiotic stresses like high temperature, drought, and salinity (Hussain et al., 2012).

Introduction The process of culturing plant cells, tissues, organs and protoplast on artificial media under controlled and aseptic circumstances is known as ‘Plant Tissue Culture’. It is predicated on the idea of “Cellular totipotency”, which describes a cell’s capacity to develop into a whole plant in the right cultural environment. This characteristic of cells has broad applications in the manipulation of plant cells to enable fast plant multiplication and the in-vitro regeneration of whole plants following the genetic transformation. Around a century ago, the idea of tissue culture was first put forth, to grow entire plants in vitro from somatic cells (Haberlandt, 1902). The tissue culture system has advanced with the identification of different concentration, ratios of auxin and cytokinin, which are critical for the regeneration of adventitious roots and shoots (Skoog and Miller, 1957). Appropriate explant, or plant organ removed, including cotyledons, leaves, roots, shoot apices, nodal segments, hypocotyls, anthers, embryos, and seeds. The explants are thoroughly cleaned with sterile double-distilled water, surface sterilized with a disinfectant such as sodium hypochlorite or mercuric chloride and aseptically cultured in an artificial medium in test tubes/ flasks, jars, and Petri dishes. Several factors influence a plant’s capacity to regenerate, such as the presence of a plant growth regulator (Gerdakaneh et al., 2020), the explant type (Dhar and Joshi, 2005) and the basic medium’s composition (Sundararajan et al., 2017). The most widely used media include major elements, carbohydrates, growth regulators (auxins, cytokinins etc.), microelements, vitamins, amino acids and several media compositions have been created specifically for plant tissue culture (Atkinson et al. 2012). While 2,4-dichloro phenoxy acetic acid (2,4-D) at concentrations of 0.5-4.0 mg/L typically induces callus, or a homogeneous mass of undifferentiated cells, auxins at concentrations ranging from 0.1 to 5.0 mg/L, favour rooting by cell elongation. Similarly, cytokinin’s induce fast cell division and the growth of shoot buds/shoots. Agaragar, agarose, and GelriteTM are examples of chemically inert, powdered gelling agents added to the culture medium to solidify it before it is autoclaved. After the medium has been added to the culture containers, they are autoclaved. Explants in the culture vessels are injected under aseptic circumstances in a laminar air-flow cabinet equipped with high-efficiency particulate air (HEPA) filters (pore size 0.2–0.3 mm). Explants that are placed in the right growth medium under the right circumstances dedifferentiate, or mature cells that have increased DNA/ RNA and protein production return to their meristematic state. Regrowth in the agar-gelled medium results in an amorphous mass of cells known as ‘callus’. Suspension culture, a method of cultivating cells in a liquid medium, produces a suspension of individual cells. Every three to four weeks, the developing tissue must be sub-cultured onto a new medium because an increase in cells or calli causes the medium to run out. In the end, the organogenesis pathway is utilized to create ordered structures like roots, branches, flower buds, etc. from these cells and tissues. The synthesis, preservation, and application of

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.,

Introduction Plant being sessile are subjected to a myriad of biotic and abiotic stresses that impede growth and resulting significant losses in crop productivity globally (Bhat et al., 2019; Ganie & Reddy, 2021). In this context, there is an immediate need to develop high yielding climate-resilient crop varieties for ensuring food security in the face of increasing population growth. Although conventional breeding has achieved notable success in the development of high-yielding crop varieties (Bhat et al., 2020), but this approach is slow to maintain pace with ever increasing population. In this regard, more recent approach of genomics-assisted breeding (GAB) has emerged as a pivotal approach to develop the high-yielding climate resilient crop varieties (Bhat et al. 2021). Although, low-throughput sequencebased markers like simple sequence repeats (SSRs) have been extensively utilized in molecular breeding programs, but they have the limitations of reduced genomic coverage and high cost (Varshney et al., 2014; Zargar et al., 2015). In this context, the emergence of second-generation DNA marker systems has provided higher genomic coverage and low cost in marker-assisted breeding. For example, recent advancements in next-generation sequencing (NGS) and genotyping platforms have substantially enhanced marker density and genomic coverage while reducing costs (Przewieslik-Allen et al., 2019); thus rendering them commercially available for both model and non-model crop species (Huang & Han, 2014; Rasheed et al., 2017). These high-throughput genotyping platforms provides millions of DNA polymorphisms (Bassi et al., 2016; Ganal et al., 2012), thereby enhancing gene mapping resolution and prediction accuracy in genomic selection (GS) (Robertsen et al., 2019; Yu et al., 2019). Most of the agriculturally important crop traits, such as yield, quality, and stress tolerance, possess complex inheritance i.e., governed by multiple genes with minor effect on trait of interest as well as are highly influenced by genotype-by-environment (G × E) interactions (Voss-Fels & Snowdon, 2016). The conventional linkage mapping approach has elucidated the genetic basis of agriculturally important complex traits but this approach involves the use of bi-parental mapping populations which are constrained by the limited genetic diversity, low resolution, and restricted recombination events (Brachi et al., 2011; Collard et al., 2005). Consequently, the genome-wide association study (GWAS) has emerged as a powerful approach for dissecting the genetic basis of complex quantitative traits in crop plants, resulting higher resolution and allelic diversity (Varshney et al., 2020; Zhu et al., 2008). Moreover, owing to the availability of cost-effective and high-density genotyping platforms, has allowed the routine use of GS in the crop breeding which is more recent approach of GAB (Crossa et al., 2017). In recent years, the advent of next-generation sequencing (NGS)-based genotyping techniques has significantly allowed the genotyping of extensive germplasm collections, enabling comprehensive GWAS and GS analyses (Annicchiarico et al., 2017; Zargar et al., 2015). Nonetheless, the predominant limitations impeding the utilization of SNPs in the GWAS and GS approaches encompass their inherently biallelic nature, the occurrence of rare alleles, and the prevalence of linkage drag (Voss-Fels & Snowdon, 2016; Wray et al., 2013). In

Introduction A breeding value is essentially the additive effect of a trait of interest that can be passed on stably to offspring. In artificial selection, the breeding values of the genotypes are determined. Hence, the key question is how to quantify the breeding value of a genotype for a phenotypic trait of interest that is part of a breeding program. As part of the process of breeding livestock, the estimated breeding value (EBV) is predicted based on a model that relates the phenotype over a population of genotypes with their pedigree information by using the best linear unbiased prediction (BLUP). Nevertheless, this method is not feasible for populations with no pedigree information or a complex population structure, which is typically the case in plant breeding when there are no pedigree records. With genomic selection (GS), this problem is addressed by determining the genomic estimated breeding value (GEBV), which addresses the problem by using genome-wide markers and combining them with various machine learning approaches in order to estimate the breeding value (Meuwissen et al. 2001). It is for this reason that the GS models are developed in a training population that is both genotyped and phenotype. GS model that has been created can be used for predicting phenotypic traits in unseen genotypes as well as for genotype selection in another population, called the breeding population (testing population) that has genotyped data only. The GS procedure described here can be applied to predict phenotypic traits for inbred as well as hybrid populations. As a result of this procedure, GS cuts in half the time it would take for a breeding cycle to be completed in order to develop new cultivars. All GS approaches rely on a method that is statistical in nature as they use a mathematical relationship between genotypic and phenotypic data in order to predict genotypes values. Genetic improvement of crops has been a cornerstone of agricultural development, making a significant contribution to the food security and economic growth of the global economy. Plant breeding poses a great deal of challenge when it comes to selecting the best individuals. The use of visual selection has not yielded the desired genetic gain compared to the results derived from the estimation of breeding values.

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

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 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 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 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 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 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 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 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 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 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 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 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 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).