eChapters

Preternatural development of recombinant DNA technology has established genetic engineering in animals the most important field in application of biology for human benefit, from production of genetically modified animals to providing crucial technologies to medical science sector. On the basis of the nature of the target tissues, genetic engineering may target single cell line, particular tissue sectors or the organism as a whole. The purpose of transformation may be basic research involving elucidation of gene function, study effect of directed mutations, examination of physiological and developmental processes in animals or may be target oriented, such as production of proteins or metabolites in large quantities in a cell line, incorporating rDNA in the germline cells, gene therapy, use of rDNA in disease diagnostics, or production of transgenic animals for specific purposes.

Advances in molecular biology have sharpened the tools of the breeders, and brighten the prospects of confidence to serve the humanity. The application of biotechnology to field crop has already led to the field testing of genetically modified crop plants. Genetically engineered Rice, Maize, Soybean, Cotton, Oilseeds like Rape seed, Sugar Beet and Alfalfa cultivars are expected to be commercialized in the late of 20^th century. Genes from varied organisms may be expected to boost the performance of crops especially with regard to their resistance to biotic and abiotic stresses

Genetic engineering involves isolation of DNA fragments within a cell recombining them outside. The basic technique is quite simple. Two DNA molecules are isolated and cut into fragments by one or more specialized enzymes, the fragments joined together in a desired combination, then restored to a cell from replication and reproduction. This method also referred to as recombinant DNA technology. Genetic engineering developed in the mid 1970 when it becomes possible to cut DNA and to transfer particular pieces of DNA containing specific bits of information, from one type of organism into other.

Introduction

It refers to all activities designed to identify materials that cannot be used directly in breeding programmes, and further to transfer these traits to an intermediate set of materials that breeders can use further in producing new varieties for farmers. It is a bridge between Genetic Resources and Crop Improvement. That is collaboration between germplasm curator and plant breeder.

Crosses between adapted and exotic materials, where different proportions of introgression are obtained and evaluated, have been denominated as semi exotic materials. That should be readily used in regular breeding programme for cultivar development.

Objectives of pre-breeding 8-10 Years • Improved germplasm and associated genetic knowledge that enhance resistance expression and diversity.

• Reduce genetic uniformity in crops through the use of a wider pool of genetic material to increase yield, resistance to pests and diseases, and other quality traits.

• Identification of desirable traits/genes and their subsequent transfer into a suitable set of parents for further selection.

• Improved parental stocks which can be readily utilized within breeding programs and improved selection methodologies.

• Identify potentially useful genes in a well-organized and documented gene bank Designing strategies that lead to development of an improved germplasm that are ready to use in varietal development.

Phenotype is a result of gene products brought to expression in a given environment. Genes specify the structure of proteins. All known enzymes are proteins. Enzymes perform catalytic function, causing the splitting or union of various molecules. All of the chemical reactions which occur in the cell constitute the subject of intermediary metabolism. These reactions occur as stepwise conversions of one substance into another, each group being mediated by a specific enzyme. All of the steps which transform a precursor substance to its end product constitute a biosynthetic pathway. Several genes are usually required to specify the enzymes involved in even the simplest pathways. Before gene-enzyme relationship could be postulated, soon after rediscovery of Mendelian principles of inheritance, it was discovered that genes were not merely separate elements producing distinct individual effects, but they could interact with each other to produce completely novel phenotypes. The simplest example of gene interaction could be the fact that allele A could be characterized by phenotype A, and the allele B by the phenotype B and an organism having both alleles A and B at the same time might show phenotype C. The occurrence of such interactions means that the phenotype we observe is not present in the genes themselves but arises from a complicated developmental process resulting from a biosynthetic pathway as illustrated below (Stansfield, 1969)

Any crop improvement programme primarily depends on the amount of genetic variability available and the extent to which the economic traits are heritable. A wide survey of genetic variability and a thorough understanding of the genetic makeup of the crop with the biometrial tools is very much indispensable for initiating an effective breeding programme.

Effectiveness in breeding programme depends upon three main factors viz., (i) the extent of genetic variation available, (ii) heritabiity of the variation and (iii) intensity of the selection pressure that can be applied. As most of the characters of economic importance and related characters which influence the performance of the economic character in a given set of environment are highly influenced by the environmental conditions, the heritable (genotypic) variation usually masked by non-heritable (environmental) variation and thereby creates difficulty in exercising the selection. Hence, it becomes necessary to partition the overall variability into heritable and non-heritable components to enable the breeders to plan for proper breeding programme.

The estimates of mean, variance and standard error are worked out by adopting the standard methods of Panse and Sukhatme (1961). Usually, randomized block design is the choice of the statistical design. Various genetic parameters are worked out from the mean squares. Assessment of genetic variation is usually made through the computation of genotypic variance and genotypic coefficient of variation. The proportion of the total genetic variance expressed as percentage of total phenotypic variance has been used as a measure of genetic variability of heritability in broad sense.

A. Define / Explain the following

1. Mitosis: The multiplication of a body cell into two daughter cells of equal size and containing the same number of chromosomes as in the parent cell is called mitosis or somatic division.

2. Meiosis: Meiosis occurs only in gonads (in germ mother cells) during the formation of gametes like sperm and ovum. Meiosis is a process by means of which double number or 2N or diploid chromosomes is reduced to its half number or n or haploid. It is also called reduction process.

Genetics and Gene

Genetics is defined as the branch of biology dealing with heredity and variation. The hereditary units which are transmitted from one generation to the next are called genes. Genes have been defined in various ways. These are units of inheritance located in linear order on chromosomes. The genes are considered as hereditary determinants of a specific biological function located in a fixed place on the chromosome. Chemically, gene is a segment of DNA (deoxyribonucleic acid) encoding one polypeptide and defined operationally by the cis-trans or complementation test. Gene is the functional unit of inheritance (a sequence of DNA) which is located on a certain position (locus, plural loci) on a chromosome. The locus is sometimes used interchangeably for gene. DNA, in conjunction with a protein matrix, forms nucleoprotein and becomes organized into structures with distinctive staining properties which are known as chromosomes. The chromosomes are located in the nucleus of the cell. Since genes are located on the chromosomes, in many ways behavior of genes is parallel to the behavior of the chromosomes. Two or more alternative forms of a gene are called as alleles. All genes on a chromosome are said to be linked and they all belong to the same linkage group.

In most of higher organisms including animals, the aspect of sexes has been normally confined to males and females which exist separately or even in the same individual. An individual possessing both male and female reproductive organs is usually referred to as hermaphrodite. In plants, where staminate (male) and pistillate (female) flowers occur on the same plant, the term used is monoecious. The most common plants under monoecious form are cucurbits. However, majority of the flowering plants have male and female parts within the same flower and this situation is referred to as hermaphrodite. There are relatively less numbers of plants having male and female flowers located on different plants and this is termed as dioecious condition. Among the common cultivated crops known to be dioecious are asparagus, date palm, hemp, hops and spinach.

Genome editing has revolutionized plant breeding, offering precise and efficient methods to enhance crop traits. This chapter provides an overview of genome editing’s principles, applications, challenges, and future prospects in plant breeding. The chapter explores genome editing technologies, with a focus on CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-associated protein 9), TALENs (transcription activator-like effector nucleases), and ZFNs (zinc finger nucleases). CRISPR-Cas9, in particular, has become the go-to tool for precision breeding, allowing scientists to target and modify specific genes with unprecedented accuracy. Applications of genome editing in plant breeding are diverse. It enables the development of crops with enhanced disease resistance, drought tolerance, and improved nutritional content. Additionally, genome-edited crops reduce environmental impact by requiring fewer chemical inputs and promoting sustainable farming practices. Accelerated breeding shortens the time needed to create new crop varieties, addressing urgent agricultural challenges. Looking ahead, the future of genome editing holds exciting possibilities. Continuous advancements in technology promise even more precise editing tools and high-throughput capabilities. Precision breeding will become the norm, allowing for tailored crop varieties and customized agricultural practices.

Abstract

Manipulation of a large number of genes is often required for the improvement of even the simplest character. Molecular marker trace valuable alleles in a segregating population and mapping them. Genome mapping has emerged as a powerful new approach for research in botany, agriculture and other related fields. Genome mapping methods help to locate specific DNA markers to delineate when one has reached particular gene of interest and forming a molecular map. DNA mapping encompasses a wide range of techniques useful for studying DNA at different levels of magnification. Genetic Linkage Mapping Using Molecular Markers, Development of Genetic Maps, Mapping populations and comparative genomics are elucidated.

Introduction

Understanding biology and genetics at molecular level has become very important for better understanding and manipulation of genome architecture. Molecular markers have contributed significantly in this respect and have been widely used in plant science in a number of ways including genetic fingerprinting, identification of duplicates and selecting core collections, determination of genetic distances, genome analysis, identification of markers associated with desirable breeding traits which are useful in marker assisted breeding, genomics and development of transgenics. Use of these markers also significantly reduce breeding time and cycles required for crop improvement. Molecular level understanding of the inheritance of agriculturally important traits creates new opportunities to streamline plant breeding.

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

Modern plant genomics generates highly complex and high-dimensional datasets that require advanced computational approaches for effective analysis. This chapter explores the application of artificial intelligence to plant genomic data analysis. Machine learning and deep learning techniques are discussed for identifying complex patterns, classifying genomic information, predicting phenotypes and supporting genomic selection. Convolutional neural networks, long short-term memory networks and transformer models are considered for analyzing genomic sequences and relationships. The chapter presents an AI-based framework integrating data processing, model development and prediction while highlighting the challenges associated with genomic data heterogeneity and dimensionality. It emphasizes the potential of AI for improving genomic research and plant improvement strategies

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.

The biological diversity of each country is a valuable and vulnerable natural resource. Sampling, identifying, and studying biological specimens are among the first steps toward protecting and benefiting from biodiversity. Knowledge about biodiversity and the ability to identify organisms that comes with it are global public goods. That is, this knowledge can create benefits for all countries - benefits that no one country can create by itself.

DNA Barcoding: Documenting Biodiversity with a Gene Sequence

“DNA barcoding” is an exciting new tool for taxonomic research. The DNA barcode is a very short, standardized DNA sequence in a well-known gene. It provides a way to identify the species to which a plant, animal or fungus belongs. The Consortium for the Barcode of Life (CBOL) is promoting international partnerships that will enable people in all countries to better understand and protect their biodiversity.

DNA barcoding is a taxonomic method that uses a short genetic marker in an organism’s mitochondrial DNA to identify it as belonging to a particular species. It is based on a relatively simple concept: most eukaryote cells contain mitochondria and mitochondrial DNA (mtDNA) has a relatively fast mutation rate, which results in significant variance in mtDNA sequences between species and, in principle, a comparatively small variance within species.

Introduction

Earth’s magnetic field (MF) is a natural component of environment and is an inescapable factor for all living organisms including plants. Earth has an inner core made of molten iron which rotates at a fairly high speed creating a magnetic field just like a dynamo. This Geo Magnetic Field (GMF) extends from the earth’s interior into outer space. It interacts with the solar wind, which is actually a stream of charged particles emanating from the sun. As earth is engulfed in a GMF, all living organisms, both plants, animals and all biological processes are under its influence. However, local differences in strength and direction of the geomagnetic field have been detected. The vertical component of GMF is maximum at the magnetic poles, which is around 67 μT, and the horizontal component is zero there. Conversely, at the magnetic equator the vertical component is zero and the horizontal component is maximum, about 33 μT (Kobayashi et al., 2004).

Turbulent flows of the fluid metallic inner core of earth mainly contribute to GMF and the effect of external MFs located in the ionosphere and the magnetosphere is very meagre (Qamili et al., 2013). As GMF extends beyond the earth’s surface it is this force along with magnetosphere that protects the earth and its biosphere, from the solar wind by deflecting most of its charged particles (Occhipinti et al., 2014).

Introduction

According to Frankel (1957), plant introduction is the transposition of a genetic entity from an environment to which it is attuned to one in which it is untried. According to Bennett (1965), the introduction of wild plants into cultivation and the successful transfer of cultivars, with their genotypes unaltered, to new environments is called as ‘primary’ plant introduction and the rest as ‘secondary’ introduction. However, both are equally meaningful for effective use of plant germplasm.

Types of Plant Introduction

1. Primary Introduction

2. Secondary Introduction

1. Primary Introduction

When the introduced crop or variety is well suited to the new environment, it is directly grown or cultivated without any alteration in the original genotype. This is known as primary introduction. E.g. IR. 8, IR 20, IR 34, IR 50 rice varieties; oil palm varieties introduced from Malaysia and Mashuri rice from Malaysia.

Gladiolus is a major commercial cut flower appreciated for its long spikes, attractive florets and wide range of colours. This chapter describes its origin, species, genetics, botanical characteristics and improved varieties. It explains corm and cormel propagation, climate, soil, planting time, spacing, nutrient management, irrigation, staking and other crop-management practices. The chapter also discusses major pests and diseases, physiological problems, harvesting stages, grading, postharvest handling, storage and yield. Emphasis is placed on producing long, straight and high-quality spikes suitable for domestic and export markets. The chapter provides practical production guidance for commercial gladiolus cultivation under Indian conditions. effectively.

9.1 Geospatial Technology

It is an organized collection of computer hardware, software, geographic data, and personnel. It is designed to efficiently capture, store, update, manipulate, analyze, and display geographically referenced information. It includes typical Geographic Information System (GIS) software packages (ArcGIS, ArcExplorer, MapPoint, Google Earth), Remote Sensing (Collecting and interpreting information about the environment from a distance using satellite imagery, radar, or aerial photography), Global Positioning Systems (GPS) (A system of radio-emitting and receiving satellites used for determining positions on the earth) and many others (Lisa Kennaway, 2009). Geospatial technology can be used in pest monitoring and detection, data visualization/query, survey data collection, management and analysis, risk and pathway analysis, change detection and many others.

6.1 World Trade Organization (WTO) and Trade-Related Aspects of Intellectual Property Rights (TRIPS)
6.1.1 Introduction
The globalization of trade and the rapid advancement in innovation—particularly in biotechnology—have necessitated the harmonization of intellectual property rights (IPR) across nations. The World Trade Organization (WTO), established in 1995, is the apex multilateral body that regulates international trade among member states. Within its legal framework, the Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS) plays a foundational role in setting minimum standards for IPR protection and aligning national laws with global trade norms.
In the realm of biotechnology, TRIPS has profound implications on patentability of life forms, technology transfer, public health, biodiversity, and traditional knowledge.
6.1.2 World Trade Organization (WTO): An Overview
• Established: January 1, 1995
• Headquarters: Geneva, Switzerland
• Membership: 164 members (as of 2024), including India
• Primary Objectives:
• Facilitate free and fair global trade
• Administer trade agreements
• Resolve trade disputes
• Monitor national trade policies
• Promote cooperation with other international organizations (e.g., WIPO, WHO)