eBook Chapters

Male-sterility
Normal development of the male reproductive organ (stamen) and male gametophyte (pollen grain) is essential for successful completion of sexual reproduction in angiosperms. Abnormalities at any stage of stamen and pollen development can result in male sterility. Male sterility in plants implies the inability to produce or to release functional pollen. Male sterility is caused due to failure in the formation or development of functional stamens, microspores or gametes and /or release of pollens from the anther. Male-sterility can result from mutations in nuclear genes alone or mitochondrial genes or mitochondrial genes coupled with nuclear genes. The resulting conditions are known as genic male sterility (GMS), cytoplasmic male sterility (CMS) and cytoplasmic-genic male sterility (CGMS), respectively.
Classification of male-sterility
1. Genetic male-sterility
This male-sterility is caused due to mutations in nuclear genes alone or mitochondrial genes or mitochondrial genes coupled with nuclear genes which results abnormalities at any stage of stamen and pollen development.

The potential yield levels in major crops have reached almost to a plateau. The current world population of 7 billion is likely to reach 9 billion by 2050 putting huge pressure to produce more from the available arable lands as acreage of major crops is predicted not to increase any further. The deficit of food requirements will have to be met partly by bridging the gap between farm yield (the average yield of the crop in a particular region/country/world) and the potential yield (the yield obtained usually in the breeders’ plots grown across the region of interest with the best yielding new varieties and without biotic stresses as diseases and pests, and abiotic stresses such as drought, flooding, salinity, heat and cold and partly by increasing potential yield per se.

Even after public concern the scientists feel that the GMO foods are quite safe. According to them the genetically-engineered crops are very safe to eat as much as the non-GE of the same crop. According to them the environment has improved by reducing the use of pesticides. GMO stands for genetically modified organism. Soy, corn, or other crops are very common as GM crops which are made by genetically engineered DNA. Many have come to the conclusion that GM foods are safe, healthy and sustainable. However, some people are against them. There are many benefits of GM crops like less water or pesticides to be used. Genetically engineered crops fight diseases to save the foods. At the same time the industries/ farmers that grow them are also benefitted. These foods have higher nutritional profiles, both in the US and abroad like corn which is one of the most prominent GMO foods. Soy is found in tofu, vegetarian products, soybean oil, soy flour and many other products. The other major crops taken for genetic modification are Papayas, Canola and Cotton. For dairy products a lot of work is being done on the genetic engineering of animals in a big way. This is going to be the most intractable environmental challenge of the 21^st Century. Presently, around 92% of the U. S. corn (GE), 94% of soybeans and 94% of cotton are genetically engineered.

GENETIC ENGINEERING

Genetic engineering is a means of improving the food supply even before harvest or slaughter by improving yields, increasing disease resistance, and enhancing the nutritional qualities of various foods. Broadly speaking, genetic engineering refers to any deliberate alteration of an organism’s DNA. Genetic engineering has been practiced for thousands of years, ever since humans began selectively breeding plants and animals to create more nutritious, better tasting foods. In the past two decades, genetic engineering has become increasingly powerful as scientific advances have enabled the direct alteration of genetic material. Genetic engineering is alternately called as ‘ recombinant DNA technology’ or ‘gene cloning’. Genes have been cut and pasted from one species to another, yielding, for example, disease- resistant squash and rice, frost-resistant potatoes and strawberries, and tomatoes that ripen-and therefore spoil-more slowly.

Genetically modified organism (GMO) is a microbe or more complex plant or animal in which DNA has been altered for a particular purpose such as manufacturing proteins, making improvement to the organism, research into the nature of genes and biological process, correcting genetic defects.

Transgenic plants are those plants, in which a foreign gene(s) has/have been introduced and stably integrated into the genome. The inserted gene sequence is known as Transgene. Almost three decades ago, in early 1983, the first cloning of the recombinant genes in tobacco signified the beginning of plant molecular biology in its own right. Since then the number of genes transferred and studied in plants has increased exponentially and the first transgenic crop (‘FlavrSavr’ tomato) was commercialized on May 18, 1994. However, the impact of transgenic crops was perceptible only after 1995 when transgenic maize, soybean and cotton were released for cultivation in USA.

MENDEL’S RULES OF GENETICS DO NOT ALWAYS WORK

Mendel’s rules:

Segregation of alleles

Independent assortment of genes for different characters

Hold for characters:

Which have dominant & recessive traits

Determined by single genes

Genes are on separate chromosomes

Different types of chromosomes, or

Different homologues of same type of chromosome

These conditions are not always met, so there are many complications

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.

1. What is Genome Sequencing?

Genome sequencing is the process of determining the complete DNA sequence of an organism’s genome. The genome is the genetic material that contains all the instructions necessary for the growth, development, functioning and reproduction of an organism. It is composed of DNA (deoxyribonucleic acid., which is a long molecule made up of four building blocks called nucleotides adenine (A), thymine (T), cytosine (C), and guanine (G).

2. Why is genome sequencing important in plant pathology?

Genome sequencing is essential in plant pathology for several reasons

i. Genome sequencing in plant pathology identifies and characterizes plant pathogens at the molecular level.

ii. It helps trace the evolution of pathogens and their genetic adaptations.

iii. Genomic data enables the development of precise diagnostic tools for rapid pathogen detection.

iv. Understanding host-pathogen interactions informs disease management strategies.

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

4.1 Genetic Improvement of Aquaculture Species

1. Introduction

1.1 Importance of Genetic Improvement in Aquaculture

Aquaculture serves as a critical component of global food production, supplying a substantial portion of seafood consumed worldwide. However, the industry faces challenges such as disease outbreaks, environmental changes, and increasing demand for sustainable practices. Genetic improvement plays a crucial role in addressing these challenges by enhancing the traits that contribute to productivity, disease resistance, and environmental adaptability in aquaculture species.

1.2 Role of Genomics and Biotechnology

Advancements in genomics and biotechnology have revolutionized the way aquaculture species are bred and managed. Genomics enables the detailed study of an organism’s genetic makeup, allowing researchers to identify specific genes associated with desirable traits. Biotechnological tools, including genome editing and molecular markers, facilitate precise manipulation of these genetic traits, accelerating the breeding process and improving the efficiency of trait selection.

Introduction

Animals have delicate balance of heat production and heat loss, which is maintained by thermoregulatory mechanisms in response to environmental temperature and humidity combinations. When the heat loss is overrun by heat gain, heat stress occurs. During heat stress, increase in the core body temperature due to failure of homeostatic mechanism reduces productivity of the animals below their original genetic potential in growth, milk production, milk constituents and reproduction (Ravagnolo and Misztal, 2002). Impending climate change scenario is a unanimously accepted reality. Increase in the anthropogenic greenhouse gases (CO₂, CH₄and NO₂) cause radiation leading to excess warming of the earth’s environmental system. According to IPCC, the predicted temperature rises for the end of 21^st century may be in the range of 1.8^oC to 4^oC (IPCC, 2007). The climate change has complex impact on the livestock production. Temperature or heat stress will be one of the major environmental factor to in?uence the health and productivity of livestock population. The least tropically adapted livestock may be severely affected by heat stress. The manage mental and ameliorative practices can deal with the heat stress in short term, however the long term focus of developing genetic heat stress tolerance in livestock population will be a significant and impactful strategy.

Introduction

The study of infectious diseases, alongside other clinical and natural strengths, is going through fast change introduced on by the approach of reasonable next generation sequencing (NGS) advancements (Koser et al., 2012).These technologies become adopted as routine methods easily, and laboratory techniques are transformed throughout the process. The amount of genomic bacterial data generated is huge. As of this writing, for example, over 200,000 Salmonella genomes alone are in the public domain with hundreds being added weekly. A whole genomic DNA sequence characterizes the maximum practicable level of structural detail on the individuating traits of an microbial organism or population. It can therefore be used to provide more accurate microbial genome recognition, evolutionary relations and a detailed catalogue of epidemiologically important characteristics. This has a significant role to play for outbreak research, diagnosis and treatment of infectious diseases, microbiology and epidemiology (Allard et al., 2019). Besides, DNA sequences are also a universal dataset which can theoretically be used to determine any biological function. This means that antimicrobial resistant (AMR) can be detected and to track the development and spread of AMR bacteria in a hospital or the community.

Introduction
The method of selective breeding involves selecting particular breeding prospects to accumulate beneficial alleles and increase the prevalence of desired traits in a population. Characteristics, including growth, disease resistance, reproduction, development, and coloration, are frequently addressed in aquaculture (Maluwa, 2022). Selective breeding, whereby people are picked to have offspring with desired traits, is the foundation of genetic improvement initiatives in all organisms. This is a type of directed evolution in which the breeder determines fitness instead of the organism’s innate capacity for survival and procreation. Darwin’s theory of natural selection was affected by selective breeding, which existed before the mechanics of heredity were discovered. Darwin agreed that deliberate human selection used excellent outcomes (Hill, 2017). By choosing better parents, a species’ desirable features can be improved. Common carp (Cyprinus carpio) were first cultivated in ponds in China 4,000–5,000 years ago, marking the beginning of fish farming. Environmental effects, growing competition for water, and increased demand due to population development and declining wild fish sources are some of the issues aquaculture faces as it grows. Controlled mating and lineage monitoring were two early breeding techniques that resulted in severe inbreeding and decreased output. Mendel’s plant experiments established the groundwork for quantitative and contemporary genetics when they were made public in
1900 (Gjedrem and Baranski, 2010). Mendel’s experiments were confirmed in 1900, marking the beginning of selective breeding for plant production. Fifteen years later, Farm animals were treated using the same methods (Hagedoorn, 1950). Genetically modified stocks are used for most plant and farm animal production. Genetic advancement in aquaculture is still sluggish, though. Although the first aquaculture family-based breeding program began in 1975, by 2010, only 8.2% of aquaculture production was based on genetically modified stocks (Neira, 2010; Rye et al. 2010).

Introduction

The expanding number of people around the world necessitates an increase in the amount of food that is yielded. As stated by the Food and Agriculture Organization of the United Nations (FAO), global food production ought to be ramped up by a factor of two in the next few years in to meet the requirements of the growing global population in terms of consumption (FAO, 2006). This is because the global population is expected to continue growing at a rate of approximately one person every two seconds until the year 2050. It is possible that the predicted production disparity could be filled by making improvements in genetics, animal health, and the excellence of animal husbandry.

The production of animals has expanded significantly over the course of the last several decades as a direct result of the application of quantitative genetics in animal breeding. However, due to technological limitations, the use of genetic markers in breeding programmes has only been implemented to a relatively small extent (Deng et al., 2016). The concept of genomic prediction, which was first introduced approximately twenty years ago, has completely transformed the planning and execution of animal breeding operations.

The global human population is increasing exponentially with time, and it is expected to reach 9.6 billion by 2050 (UN 2013). With rapid population growth, food consumption is predicted to more than double in the next 40 years. Due to limited land resources for cultivation and a stabilising trend in agricultural productivity, the role of livestock sector is increasing significantly to meet the rising food demand. Meanwhile, global livestock production has increased significantly in both number and productivity. Unprecedented urbanisation has a significant impact on food consumption patterns in general, as well as demand for livestock products. Animal diseases are a significant factor in reducing livestock productivity, particularly in developed countries. The limitations of traditional animal breeding hinder further improvement of livestock productivity. The use of biotechnological tools has major applications in improving animal health and production, increasing disease resistance, using assisted reproductive techniques, improving rapid diagnostic techniques, and improving vaccines in livestock systems. These interventions cover advancements in feeding, nutrition, genetics, reproduction, animal health control, and overall improvement of animal husbandry. Since genomic tools and selection have been widely adopted in developed countries to improve both productivity and quality of animal products, the prospects for increasing productivity in developing countries using genomic tools and selection have not been adequately investigated.

Introduction

Estimated breeding values (EBVs), often estimated for sires, are used in traditional animal breeding (TAB) programmes to make selections based on an animal’s performance and that of its relatives. Using, typically, the best linear unbiased projections, EBVs are calculated using attributes measured in own performance, pedigree, sib, and/or progeny evaluation schemes in specialised testing stations and/or selected farm conditions (BLUP; Henderson, 1975). One of the main time-consuming challenges for phenotypic evaluation to enable a meaningful estimation of breeding values is generation intervals of 4 to 5 years in beef cattle, more than 5 years in dairy cattle, and 2 to 2.5 years in pig breeding schemes (Schefers and Weigel, 2012). Modern breeding techniques like marker-assisted selection (MAS) and, more recently, genomic selection (GS) are based on the use of genetic DNA markers to aid in selection and breeding (Williams, 2005). The fundamental reason why MAS, that only further uses a few markers as a selection tool, hasn’t made as much progress as was initially anticipated is that finding trustworthy markers is challenging, particularly when dealing with complex traits. Only relatively few consistent markers could be identified, despite successful identification of many quantitative trait loci (QTL; Hu and Reecy, 2007)

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

4.1 Introduction
4.1.1 Overview of Genomics in Biotechnology
The genome of an organism serves as the ‘blueprint of life’ (Baeza, 2024) and functions as an information repository (Goldman & Landweber, 2016), containing the necessary information for the synthesis of molecules, cells, and tissues (Abera et al., 2017). A study of the entire collection of genes within an organism’s genome is known as genomics (NIH, 2022; WHO, 2025). Genomics encompasses aspects of genetics, focusing on the comprehensive characterization of an organism’s entire set of genes rather than on individual genes (Baeza, 2024). The investigation of living organisms has undergone a transformation through the application of genomics and related fields, providing unique insights that enhance various applications aimed at improving human life, economic conditions (Kalaitzandonakes et al., 2023), and environmental sustainability (Mudaliar et al., 2023).
According to a genomic analysis, 80% of the 6,000 rare disorders have genetic causes (Brittain et al., 2017). Cancer, a genetic disease, has revealed through DNA sequencing the mutational events and oncogenic drivers (D. Wang et al., 2023). Genomic tests contribute significantly to the prediction and prevention of diseases, including familial hypercholesterolaemia (FH) (Brittain et al., 2017). Agricultural industries are currently confronting multiple challenges, including global changes in climate (Bai et al., 2024), growing populations (Putri et al., 2019), resource depletion (Feng et al., 2023), reduction of cultivable land (Mirzabaev et al., 2023), and the prevalence of pathogens (Hossain & Roslan, 2023). Advances in genomic technologies, such as DNA sequencing and gene editing, have transformed the field. DNA sequencing includes; Nextgeneration sequencing (NGS) (Marudamuthu et al., 2023), Ribonucleic acid sequencing (RNA-seq) (Upton et al., 2023), whereas, gene editing methods includes; Clustered Regularly Interspaced Short Palindromic Repeat- CRISPR associated protein 9 (CRISPR/ Cas9) (Q. Liu et al., 2021), Transcription activator-like effector nucleases (TALENS) Zinc-finger nucleases (ZNF) (Malzahn et al., 2017) and Oligonucleotide directed mutagenesis (ODM) (Ravikiran et al., 2025) as well as doubled haploids (Chen et al., 2024), molecular markers (Kumar et al., 2024) and mapping populations (Temesgen, 2021), offers potential solutions against such agricultural challenges (Hossain & Roslan, 2023). Genome sequencing techniques are applied to various fields of industrial biotechnology such as; strain development or improvement (Salazar-Cerezo et al., 2023), enzyme discovery (Zaparucha et al., 2018) and analysis of microbial community (Hosokawa et al., 2022). The potential to enhance microbial strains through the incorporation, deletion, or alteration of

Abstract

Synonymous and non-synonymous substitution result in isomerization and deformity in protein structure. Both play more or less important role in evolution. Interestingly, cyanobacterial phycobiliproteins (PBPs) are composed of proteins which are coded by codons by mRNA translation. These proteins are categorized into three groups e.g., C-PC, C-PE and C-APC having a and b subunits. The skeleton and arrangement of amino acids in subunits can provide structural and functional integrity of PBPs as well as GC₃ associated substitution of synonymous and non-synonymous codons.

Genome Sequencing: A Continuation of Genetics

• The human genome project involves the assembly of a DNA sequence map for the 3 billion base pairs present in all 23 human chromosomes.
• Two groups, the International Consortium and Celera Genomics, used two opposite strategies to obtain a draft sequence of the human genome.
• The use of bacterial artificial chromosomes (BACs), shotgun clones, and positional cloning has yielded a detailed look at the human genome and is facilitating the identification of disease causing genes.

The Sanger Method of DNA Sequencing

The Sanger method of DNA sequencing involves an enzymatic extension reaction to generate complementary copies of an unknown DNA sequence.

Incorporation of “dideoxy” base causes chain termination and separation of extension products on polyacrylamide gels reveals the sequence bases in the unknown DNA.

DNA sequencing occurs on a vast scale today through the use of automated DNA sequencing machines.

Introduction

Due to global population growth, rising wages, and urbanisation, the demand for animal products has been expanding quickly in many areas of the world (FAO, 2018). Meeting the rising demand for animal products, which is expected to reach 8.6 billion by 2030 (FAO, 2018) as the world’s population is projected to increase by 80 million per year (Preisinger, 2012), is one of the biggest difficulties facing modern farm animal industry (Eggen, 2012). Animal products and value-added foods are being consumed as a result of urbanisation and income growth (Hoffmann, 2005; FAO, 2011). By 2050, the world’s population will be close to 10 billion, even as the economic conditions continue to improve the demand for animal products will significantly rise. In order to boost animal production, it will be necessary to acquire a more in-depth understanding of animal biology through genomics and other related f ields of study. Understanding animal physiology remains a significant problem in the context of sustainable agriculture and animal husbandry, particularly for developing animal farming systems that cater to the new and diversified consumer demand. Livestock and poultry productivity has been greatly increased through traditional selection based on genetic merit estimated from phenotypic and pedigree data. Most breeding plans do not take population impacts on genetic diversity into consideration, and selection is geared more towards the best genetic response for the upcoming generation than the best long-term response (Meuwissen, 1997). Breeders have employed genetic analyses to find superior animals for more than 40 years.

Fruits contribute to nutritional security and thus are an important part of food system. To meet the future demand, development of varieties with improved yield and quality is the focus of researchers involved in fruit breeding. Though conventional breeding has resulted in the development of improved commercial varieties of different fruit crops, however conventional breeding is time consuming and faces several challenges due to long juvenile phase, highly heterozygous nature of most of the fruit crops. Challenges like changing climate, consumer preference, socio-economic conditions like reduced availability of land, labour and increasing cost of inputs, require fast and efficient methods to develop the varieties to meet the demands, which is not feasible with conventional breeding. Marker assisted breeding has given impetus to breeding efforts in several fruit crops, however it’s use is limited only for the traits controlled by a few major QTLs.
During last few years, enormous genomic resources have been developed for fruit crops using next generation sequencing technology. Such advances in genomic research in many fruit crops have paved the way for precision breeding using genomic assisted breeding (GAB) tools. GAB has helped in characterisation and utilisation of genome resources and using allele variation for cultivar development (Varshney et al. 2021). Advances in sequencing technology and affordability has allowed the genome wide analysis (GWAS) on diversity panels of different fruits resulting in identification of allelic variation associated with the traits of interest. Also, identification of superior alleles of candidate genes makes them amenable to genome editing based precision breeding. Genome wide genotyping and phenotyping offers tools for developing strategy for genomic selection (GS). Genomic selection relies on the prediction of breeding values of tested genotypes based on the large number of markers spread over entire genome. These tools promise to further improve breeding efficiency in fruit crops.

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.

Livestock breeding for genetic improvement faces many challenges including feed conversion efficiency, fertility and adaptation to changing climate. These improvements have to be realized while maintaining or improving the nutritional properties of meat, milk and other animal products while giving emphasis to animal health and wellbeing also. Environmental stresses induced by climate change affect livestock productivity, reproductive efficiency and health, resulting in severe economic losses. Under the current climate change scenario, the viability of producing animals for human consumption is in jeopardy. In order to lessen the negative effects of heat stress in today’s world, it is urgently necessary to develop methods that are centered on breeding animals with increased thermal tolerance and climate resilience. The breeding of animals having genetic potential to sustain under changing environment conditions can be achieved through the various molecular genetics tools.

INTRODUCTION

Throughout the history of agriculture, humans have struggled to reduce the adverse effects of plant disease on their crops. Early agriculturalists realized the benefits of cultural practices such as crop rotation and the use of organic soil amendments in promoting plant productivity. It is now well established that many of these effects are achieved by promoting the natural microbiological processes that keep plant disease in check. Cultural practices were mainstays of traditional agricultural systems and still provide the primary approaches for management of many soilborne diseases today. For example, disease suppressive soils, into which pathogen(s) can be introduced without causing the expected levels of disease severity, can result from alterations in cropping patterns or other cultural practices. Recently,

Genetic improvement of farm animal species is accelerating in developed countries with adoption of Genomic selection (GS) due to availability of complete reference genome sequence i.e. gene sequences that can be used to compare and study animal genetic traits. GS has been considered most promising for genetic improvement of the complex traits controlled by many genes (Quantitative traits) each with minor effects as using the conventional methods of selection and breeding the rate of genetic gain per generation is very slow with respect to human demand for livestock products. With this method, animals or plants can be selected for selective breeding on the basis of their genetic merit predicted by whole genome molecular markers spanning over the entire genome. Genomic selection may allow the identification of superior individuals for traits such as increased disease resistance which are not currently considered in animal breeding plans because of technical difficulties. The method can predict the genetic merit of young bulls with greater accuracy as compared to convention methods of genetic merit estimation. Genetic gain (ΔG) in animal breeding programs depends upon the intensity of selection (i), accuracy of predictions (r), genetic variance (σ2g) and generation interval (IG): ΔG = i * r * σ2g / IG (Ibañez Escriche & Gonzalez-Recio, 2011).

Safety is a prime concern for humans and animals. Without evaluating the safety of a chemical, no regulatory authority in the world allows the chemical to be used by humans. There are stipulated guidelines for toxicity evaluations. Among the toxicity assays genotoxicity assays are important and have occupied centre stage due to increase in understanding of the genome.

Genotoxicity describes the property of chemical agents to damage the genetic information within a cell to cause mutations, which may even lead to cancer. While genotoxicity is often confused with mutagenicity, all mutagens are genotoxic; however, not all genotoxic substances are mutagenic. Generally and depending on the agent, a cytotoxic agent may be genotoxic (causing DNA damage), mutagenic (causing gene mutation) or it may be harmful for cell organelles (e.g. cell membrane) or it may even be teratogenic. Therefore, every cytotoxic agent is not genotoxic.

Why we Need to Evaluate Genotoxicity?

Toxicity can be at any level according to the nature of chemicals and type of exposure. Duration of toxicity can also be short lived or long lived within a generation or continue to next generation. Genotoxicity effects are able to continue in next generation(s), in which the exposed population may not suffer seriously but the next generation may suffer without being exposed to the same chemicals. Therefore, genotoxicity evaluations need serious attention.

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.

Abstract

Fungal rot and wilt caused by Sclerotinia sclerotiorum is a devastating disease of vegetables causing huge loss. The fungus has a broad host of more than 400 species including diverse vegetable crops, viz., carrot, potato, tomato, green pepper, eggplant, lettuce, peas and beans, cole crops, bottle gourd, pointed gourd, etc. Being able to overwinter in the soil in form of sclerotia upto 5 years and having such a wide host range, management of the disease becomes very difficult. Thus development of resistant varieties can be the only long term strategy for control of the pathogen. The screening of the existing genotypes and identification of resistant genotypes forms the base of any resistant breeding programme. The widely available genotypes of different crops have been screened by several researchers and resistant genotypes have been identified in cauliflower, vegetable soybean, peas, tomato, etc. These genotypes are further used in breeding programmes for as donors for resistance to Sclerotinia sclerotiorum.

Keywords: Vegetables, Sclerotinia, Resistance breeding, Genotypic screening

Abstract

Genus Artemisia L. (Asteraceae) has a long history of use in herbal medicine, owing to the presence of rich bioactive phytochemical diversity of it constituent species. Himalaya is hub of several species and species under this genus have been traditionally used in different ways for curing ailments by inhabitants of the areas where their populations sprawl. Few species such as A. annua and A. maritima are cultivated for their use in medicine. In addition, the species of the genus have found wide usage in matters connected to digestive system especially for treatment of worms and for preparation of herbal teas. Artemisnin, a potent source of anti-malarial drug extracted from some species, is most valuable bioactive phytochemical of this genus. Other important chemical constituents include santonin and scoparine. Reported studies suggest that the bioactive constituents present in this genus shows several biological activities such as antimicrobial, anti-inflammatory, anticancerous and other allied ones activities. Expansion of range and acclimatization in new habitats is exemplary in this genus. Present work reports the ways of range expansion, economic importance, conservation strategies and future prospects of this genus.