eChapters

The relationship between gene and chromosome was suspected at the time of rediscovery of Mendelian^, Laws. During that period Montgomery (1901) and Walter Sutton (1902) working on grasshoppers showed that chromosomes occur in distinct pairs, often of recognizable shape and size, and that synapsis involves the union of maternal and paternal chromosomes, while Winiwarter (1901) concluded from his studies in rabbit ovaries that bivalents in the first meiotic division resulted from the chromosome pairing side by side and not end to end as believed by some other workers of that time . Theodor Bovery (1902) showed from his work on polyspermy in the fertilization of sea urchin eggs that the chromosomes of an individual were not equivalent (genetic information) to one another and hence a full chromosomal complement is essential for normal development of cell. Correns (1902) and Cannon (1902) pointed out close parallelism between Mendelian segregation and chromosome reduction during meiosis and concluded that genes are located on chromosomes but they, like de Vries, supposed that maternal and paternal chromosomes move to opposite poles during meiosis. In the same year Guyer established an understanding that random assortment between different pairs of chromosomes would give the independent assortment of genes required by Mendel. Ultimately Sutton (1903) brought together the ideas from cytology and genetics to clearly show the role of chromosomes in heredity and hence to establish the field of cytogenetics. Boveri also through his work, advanced many of the same ideas and thus the hypothesis correlating genes and chromosome transmission was established, which is known as the “Sutton-Boveri Hypothesis or chromosome theory of inheritance”.

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).

Chromosomes are giant molecules of DNA

Found in nucleus: never leave except in cell division

Carry hereditary units, genes

Two homologous copies in diplod cells

Unwind when replicating or making RNA

Wind up (condense) in cell division

Attach to spindle and separate in meiosis & mitosis

Crossing over in prophase of 1st meiotic division

Chromosomes are equally distributed in mitosis, meiosis

Gametes have half the number of chromosomes as body cells

Sister chromatids are observed to split apart longitudinally in anaphase

Portrait of a Chromosome

• Cytogenetics is the study of chromosome abnormalities and associated effects on health or other traits.
• Excess or deficient genetic material can cause syndromes or end prenatal development.
• Chromosomes consist of highly coiled DNA, RNA, histones, and nonhistone proteins.

Telomeres and Centromeres are Essential

Telomeres consist of repeat sequences and protect chromosome tips.

A centromere is a constricted site where spindle fibers attach during cell division.

Centromeres are regions of repeated DNA bound to centromere-associated proteins.

Chrysanthemum is an economically important flower crop cultivated extensively for cut flowers, loose flowers and ornamental purposes. This chapter presents its origin, taxonomy, genetics, botanical features and commercially important varieties. Production technologies include propagation, nursery management, planting, spacing, nutrient management, irrigation, pinching, disbudding, photoperiodic manipulation and protected cultivation. Major pests and diseases and their management are described along with harvesting, grading, postharvest treatment and yield. The chapter emphasizes the importance of crop regulation and environmental management for producing uniform, marketable stems. It provides practical guidance for growers and students studying commercial chrysanthemum production and floriculture. under diverse Indian production conditions.

Chrysanthemum is one of the important commercial loose flower crops in India, valued for its wide range of flower forms, colours, sizes and long-lasting florets. It is extensively used for religious offerings, garlands, Veni, bouquets and ornamental purposes. The chapter describes its origin, distribution, genetics, botanical characteristics and important annual and perennial types. It provides information on suitable varieties, climate, soil, propagation and field establishment. Production practices including nutrient management, irrigation, pinching and other cultural operations are explained systematically. The chapter also discusses important pests and diseases, harvesting, postharvest management and yield, providing a practical foundation for commercial chrysanthemum cultivation and floriculture teaching.

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.

The prime objective of any plant breeder is to develop high yielding varieties and make the quantity of quality seed of those varieties to farmers for commercial cultivation to realize the benefits of superior varieties. This necessitates, the production of seed of improved varieties in large scale in order to make them available to farmers without losing their genetic purity. Seed production is a continuous process. The seed of improved varieties are produced in several stages, each class producing a special class of seed. The various classes of improved seeds are recognized in order to facilitate seed production and to ensure continuous supply of quality seed. A seed production programme for the production of quality seed has different classes of seeds viz; nucleus seed, breeder seed, foundation seed, registered seed and certified seed. The Association of Official Seed Certifying Agencies (AOSCA) has defined these seed classes as follows:

1. Nucleus Seed

Basic or nucleus seed is the original seed of a released and notified variety. Nucleus seed is multiplied by single plant progeny system, using the concept of maintenance breeding, where purity of the original parental stock is maintained. It is available in very limited quantities and taken from the individual plant of a variety for purification. It is directly under the controlled of concerned crop breeder. This seed has hundred percent genetic and physical purity. Breeder seed is multiplied out of this material and about 500-1000 plants are kept for continued multiplication of nucleus seed.There is no need of any type of tag on nucleus seed but concerned breeder issue a certificate for purity.

1.    Kernel type: Dent, Flint, Floury, Waxy, Sweet and Pop corn 
        •    Dent corn (Zea mays indentata Staurt.)
        •    Flint corn (Zea mays indurate Staurt.)
        •    Pop corn (Zea mays everta Staurt.)
        •    Sweet corn (Zea mays saccharata Staurt.)
        •    Flour/soft corn (Zea mays amylacea Staurt.)
        •    Waxy corn (Zea mays ceatina Kulesh)

A mutagen is a physical or chemical agent that changes the genetic material (DNA) of an organism and thus increases the frequency of mutations above the natural incidence. Errors during DNA replication, repair and recombination also causes spontaneous mutations naturally. Mutagens may be of chemical, physical or biological origin. The properties of each mutagen vary by causing damage to the DNA, and most often result in replication error.

Nanotechnology has emerged as a transformative interdisciplinary field, enabling the design and manipulation of materials at the nanoscale with exceptional physical, chemical, and biological properties. Nanoparticles (NPs), the most fundamental components of nanotechnology, exhibit unique size-dependent characteristics such as high surface area-to-volume ratio, enhanced reactivity, and tunable functionalities that make them valuable in diverse applications including agriculture, medicine, and environmental management. This chapter provides a comprehensive overview of the classification, synthesis, and characterization of NPs. NPs are categorized based on origin, composition, dimensionality, and morphology, encompassing organic, inorganic, and composite forms. The synthesis of NPs follows two major approaches—top-down and bottom-up—employing physical, chemical, and biological methods. Conventional techniques such as ball milling, laser ablation, and chemical reduction are discussed alongside emerging green synthesis strategies that emphasize sustainability and biocompatibility. Characterization techniques including UV–Visible spectroscopy, DLS, SEM, TEM, FTIR, XRD, and AFM are highlighted for determining nanoparticle

15.1 Introduction

It is important that we understand some terms like clay, mineral, clay mineral, activated clay, and nanocomposite clearly. In fact, “clay” is a soil separate consisting of particles of <2 µm (equivalent to <0.002 mm) in equivalent diameter (Brady & Weil, 2002; pages 18-19) in both USDA and International systems. While in nanotechnology, uniqueness of micro- and nana- aggregates is of crucial consideration. (In Chapter 8: The Colloidal Fraction (Brady & Weil, 2002) size dimensions of minerals are given eliminating any chance of confusion.) Now let us look at some definitions provided in the Glossary of the Clay Minerals Society (CMS) Nomenclature Committee – Clay Science Project (www.clay.org; August 2011).

One ofthe biggest issues the world is facing today is the lack of clean and pure water. Due to rising water demands, rigid health regulations, and xenobiotic pollutants, traditional wastewater treatment technologies cannot provide safe water. The present era necessitates innovative approaches to wastewater treatment technologies and improved water resource conservation and management materials. By utilizing innovative nanomaterial, nanotechnology guarantees a continuous provision of potable water and contributes to the preservation of water sources. Nanomaterials expedite rapid processes for the purification, conservation, and reuse of wastewater, complementing other enduring industrial methods. 

Synonym : PCR-RFLP (PCR- Restriction Fragment Length Polymorphism)

The Cleaved Amplified Polymorphic Sequence or CAPS method is a technique in molecular biology for the analysis of genetic markers. It is an extension to the Restriction Fragment Length Polymorphism (RFLP) method, using polymerase chain reaction (PCR) to more quickly analyse the results.

Like RFLP, CAPS works on the principle that genetic differences between individuals can create or abolish restriction endonuclease restriction sites, and that these differences can be detected in the resulting DNA fragment length after digestion.

In the CAPS method, PCR amplification is directed across the altered restriction site, and the products digested with the restriction enzyme. When fractionated by agarose or acrylamide gel electrophoresis, the digested PCR products will give readily distinguishable patterns of bands. Alternatively, the amplified segment can by analyzed by Allele specific oligonucleotide (ASO) probes, a process that can often be done by a simple Dot blot.

4.1 Climate Change

Climate change refers to long-term shifts in temperatures and weather patterns. These shifts may be natural, such as through variations in the solar cycle. But since the 1800s, human activities have been the main driver of climate change, primarily due to burning fossil fuels like coal, oil and gas. Burning fossil fuels generates greenhouse gas emissions that act like a blanket wrapped around the Earth, trapping the sun’s heat and raising temperatures. Burning of crop residues also adds to climate changes

Examples of greenhouse gas emissions that are causing climate change include carbon dioxide and methane. These come from using gasoline for driving a car or coal for heating a building. Clearing land and forests can also release carbon dioxide. Landfills for garbage are a major source of methane emissions. Energy, industry, transport, buildings, agriculture and land use are among the main emitters.

Climate change presents horticulture with increasing challenges including heat stress, water scarcity, erratic rainfall, extreme weather, new pest pressures, and changing crop suitability. This chapter examines strategies for developing climate-resilient horticultural systems through improved cultivars, efficient irrigation, protected cultivation, mulching, canopy management, soil-health practices, and diversification. Climate-smart production also requires better forecasting, monitoring, risk management, and resource efficiency. Future horticulture is expected to integrate biotechnology, artificial intelligence, precision agriculture, automation, renewable energy, and resilient production systems. The chapter emphasizes adaptation rather than dependence on a single technology, promoting integrated approaches that maintain productivity, quality, profitability, and ecological sustainability under changing climatic conditions.

Steps for Cloning

Prepare DNA.

Select restriction enzymes for your insert and vector, and determine the appropriate reaction buffers.

Combine the following in a microfuge tube (30 µL total volume):
2 µg DNA
1 µL Each Restriction Enzyme
3 µL 10x Buffer
3 µL 10x BSA
x µL H₂O (to bring total volume to 30 µL)