eChapters

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.

Important Points to be Remember

• Lysosome was discovered by – Duve (1955)
• The term chromosome was first named by – Waldayer
• Power house of the cell – Mitochondria
• Two lines different for a single locus is called – Isogenic line
• Ploidy level in seeds – Embryo – 2n, Endosperm – 3n

BACTERIA HAVE SMALL, COMPACT GENOMES

We now know the complete DNA sequences for about a dozen bacteria

Bacteria seem to need about 500 to 5000 genes to conduct their lives

Because they are small, bacterial genomes are highly organized

Most of the time there are only a few bases between the end of one gene and the beginning of the next

Few introns are found in bacteria

Bacteria contain accessory “chromosomes” called plasmids; each has only a few genes

Genetic Analysis of Diseases

A genetic basis for a human diseases may be suggested from a variety of observations

Inheritance patterns of human diseases may be determined via pedigree analysis

Many genetic disorders are heterogeneous

Genetic testing can identify many inherited human diseases

Prions are infectious particles that alter protein function posttranslationally

A current focus of the research community is to advance our understanding of phytonematode biology in sufficient detail to develop novel management methods. Progress in this aim is held back by a lack of functional genetic tools: forward genetics in the sedentary endoparasites is restricted to the root-knot nematode Meloidogyne hapla, and relies on natural variants as the source of mappable polymorphisms (Olaf Kranse et al, 2021) and reverse genetics is entirely reliant on RNA interference and is limited by the variable penetrance and stability of the effect. Despite these restrictions, meaningful progress recently has been made. There is nevertheless an expectation that the development of functional genetic tools would accelerate progress in understanding the biology of plant-parasitic nematodes, and thereby also indirectly the development of novel control solutions.

1. Genes and Disease

When various plants such as rice, wheat, tomato and apple are infected with pathogens and cause disease, pathogens are generally different for each host plant type.

Venturia inaequalis, the fungus that causes apple scab, only affects apples. Fusarium oxysporum f. sp. lycopersici which causes tomato wilting, only affects tomatoes and so on.

It is the presence in the pathogen of one or more genes of pathogenicty, specificity, and virulence to the respective host that enables disease development in the host.

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.

Viruses are much simpler than cells

Protein capsid

Genetic information stored on DNA or RNA:

Types of genome:

Double strand DNA: sometimes circular

Single strand DNA: sometimes circular

Double strand RNA

Single strand RNA

Some can be crystallized

Reproduction is the physiological process by which organisms produce offspring. Sexual reproduction involves production of gametes. The gametes are produced by the gonads. The rest of the process of converting the gametes into the offspring involves other reproductive organs. The male and female animals have different genital organs that contribute to reproduction. The organs of reproduction (genital organs) in male include a pair of male gonads the testes (sing.-testis), the epididymis, ductus deferens, the seminal vesicles, a prostate gland, a pair of bulbourethral glands (Cowper’s glands), the male urethra, and the penis. In female the genital organs include a pair of gonads the ovaries, the fallopian tubes, the uterus, the vagina, the vulva and the mammary glands.

Male genital system

The overall function of the male genital organs is to continuously produce and store the male gametes the sperms, to maintain the continuous supply of semen, to detect estrus in female, and to inseminate and fertilize the female gametes. While the testes are the site for production of sperms, the epididymis, vas deferens and the accessory glands like prostate, seminal vesicles, and bulbourethral glands are responsible for the production of different secretions which mix together and are known as seminal plasma or seminal fluid. The seminal fluid provides a source of energy, buffers, antioxidants and other compounds needed for sperm survivability, maturation and motility. Once spermatozoa are mixed with the seminal fluid, the combined product is called the semen.

Uses of Microorganisms in Biotechnology

Somatostatin was the first human peptide hormone produced by recombinant bacteria

Many important medicines are produced by recombinant microorganisms

Bacterial species can be used as biological control agents

The release of recombinant microorganisms into the environment is sometimes controversial

Microorganisms can reduce environmental pollutants

With the advent of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein9 (CRISPR/Cas9) genome editing, a fast and efficient new breeding technology, precision breeding in vegetable crops has become possible now. Several genes have been edited and functionally characterized using CRISPR/Cas9 in tomato for multiple traits such as plant type, floral morphology, fruit traits, disease resistance, and abiotic stress tolerance. The CRISPR/Cas9 has been proven in successful introgression of de novo domestication of elite traits from wild relatives to cultivated tomato. The progress in CRISPR/Cas9 based improvement in vegetable improvement, has been discussed.
Vegetables are an important source of healthy diet, as they provide essential nutrients including vitamins, minerals, dietary fibre, antioxidants and other phytochemicals. Dietary fiber-rich vegetables improve digestion, while also lowering the risk of obesity, diabetes, high cholesterol and heart disease (Behera et al., 2021). A world vegetable survey showed that around 392 vegetable crops are cultivated worldwide, representing 70 families and 225 genera. Over 97 species of higher plants are being cultivated and consumed as vegetables in India. These crops belong to 20 different families such as Cucurbitaceae (25 crops), Fabaceae (16 crops), Brassicaceae (12 crop) and Solanaceae (6 crops). The world’s total vegetables production was 1,155 million tonnes in 2021 where China ranks first with a total production of 600 million tonnes, accounting for 52.18% of the total world production. The top 5 countries (China, India, the United States of America, Turkey and Vietnam) account for 70.36% of total world’s production. As far as India is concerned,  it is the largest producer of ginger (2.23 million tonnes) and okra (6.47 million tonnes) in the world, while ranking 2nd in potato (54.23 million tonnes), dry onion (26.64 million tonnes), cauliflower and broccoli (9.25 million tonnes), brinjal (12.87 million tonnes) and cabbage (9.56 million tonnes) (FAO 2023).

Millets are the staple food cropsacross the globe. The ability to thrive in harsh conditions established them as most suitable for current climate adversaries. The nutritional richness of millet reminded the need for adding them to our food basket.Despite possessing several desirable traits their cultivation is limited to a few pockets across the globe.Though significant progress has been achieved by conventional and transgenic breeding programs inmillets, there is a need for rapid improvement to meet the current needs.In order to accelerate the pace of breeding efforts, several molecular biology and biotechnology tools are being deployed by plant breeders. In the meantime, genome editing techniques like CRISPR, TALENS, ZFNs, Base and Prime editing have revolutionized the methods of genome engineering among which CRISPR has emerged as the most rapid, convenient and effective mechanism. The availability ofwhole genome sequence information, identified candidate genesfor various traits and successful transformation methods of millets promoted the application of CRISPR and resulted in the improvement of several traits. Initially, its application has been limited due to the restricted policies across the globe but the gradual change in the policies promoted genome editing across several parts of the globe. Thus, the application of genome editing for millet crop improvement can bring back those ancient grains to our food basket.

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.

1. Introduction

Fenugreek (Trigonella sp.) is one among the world’s oldest seed spice crops and has gained a supreme importance due to its extensive pharmacological properties (Basu and Prasad, 2011; Maloo et al., 2020). In ancient time’s fenugreek plant was well known and used as a medicinal drug by Egyptians (Rouk and Mangesha 1963). The Ebers Papyrus (one of the oldest preserved pharmaceutical documents) detailed therapeutic advantages and descriptions in Egypt circa 1500 BC (Betty, 2008). It has gained great importance due to its multifaceted uses which are being exploited by farmer’s and industrialist for different purposes.

In this era of molecular markers in genetic studies, genome analysis encompasses several stages of increasing resolution and sophistication, leading to the generation of high resolution chromosome maps. Since the entire plant kingdom cannot be covered under sequencing projects, molecular markers and their correlation to phenotypes provide us with requisite landmarks for elucidation of genetic variation.

A molecular marker is a site of heterozygosity for some type of DNA variation. Such a DNA marker in mapping analysis is analogous to a conventional heterozygous allelic pair. When they are used for mapping the genome, the identity of this DNA fragment is not important, but is simply used as a reference point to arrange and order the genetic information along the length of a chromosome. The molecular markers provide landmarks along the length of chromosome that facilitate the manipulation of chromosome segments in breeding and chromosome engineering programs.

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.

Diversity of gut microbial community

The human microbiota (the collection of microbes that live on and inside us) consists of about 100 trillion microbial cells that outnumber our ‘‘human’’ cells 10 to 1, and that provide a wide range of metabolic functions that we lack. It has been estimated that they encode 100-fold more unique genes than our own genome. Furthermore, the gut microbes contribute to energy harvest from food, and changes of gut microbiome may be associated with bowel diseases or obesity. To understand and exploit the impact of the gut microbes on human health and well-being it is necessary to decipher the content, diversity and functioning of the microbial gut community. If we consider ourselves as superior organisms encompassing these microbial symbionts, by far the majority of genes in the system are microbial. In this sense, completing the human genome also requires the characterization of the microbiome (the collection of genes in the microbiota).

Methods of counting viable and non-viable bacteria in gut

Before the advent of genome sequencing and genome-wide analysis method, our knowledge of molecular characteristics of diverse gut microbial population was extremely limited. To obtain an estimate of cultivability, microbial ecologists generally compare microscopic counts with total viable counts. The total viable count made on a nonselective agar based medium estimates the number of colony forming units (cfu) per gram of sample. The finding that total viable counts are typically lower than total microscopic counts was thought to be due to the number of dead cells. Indeed, dead bacteria in feces may constitute up to one third of the total bacterial community. However, recent nucleic acid based studies indicated that a majority of bacteria in a variety of ecosystems are different from those described in culture.

Introduction
Teleost fish, the largest group of vertebrates, comprise about 30,000 species on Earth, while shellfish include over a million species (Nelson, 2006). About 400 of them have been cultivated, according to Gjedrem and Robinson (2014). One of the most environmentally friendly ways that people may get protein is through fish farming. Over the past few decades, aquaculture has grown rapidly among all agricultural sectors. Fish aquaculture, however, is confronted with several significant obstacles. Most cultivated species have not undergone genetic modification through breeding and are still in their natural state. Although there are a few species-specific feeds, most farmed species do not have tailored diets. Pathogens such as bacteria, parasites, and viruses lead to various fish diseases, resulting in significant financial losses in aquaculture (Meyer and Schnick 1989). Diseases caused aquaculture to lose billions of dollars annually in revenue worldwide. Aquaculture has had
significant issues due to aquatic toxicants (Dunier and Siwicki 1993), which has led to environmental problems in the aquaculture sector (Cao et al., 2007). Innovative solutions and technology are needed to address these issues to make aquaculture advantageous and sustainable.