eChapters

(I)  Breeds

Basically swine is a clean animal and in our country, mainly, poor people  are rearing them with the least available infrastructure and poor quality feed, usually garbage, and that is why swine  are forced to take garbage as a feed (Fig. 23). With good food and shelter, they can give birth twice a year with better productivity. Even 8000- 9000 years back swine stood at 3^rd position for being reared by humans after cattle and sheep. Swine comes under phylum Chordata as they have vertebral column and their class is mammalia. They come under Artiodactyla for being ungulate animals. Swine comes in Swede order and their species is swiss. They have 3 subspecies. The domesticated subspecies comes under Swede domesticus and wild pigs comes under Swede vitatus and Swede scrofa. In India there are 4 breeds of pigs. Wild, desi, exotic and crossbred.

One of the attractions of ornamental fish keeping is to multiply the fishes in captivity. Although techniques used for ornamental fish breeding are not much difficult, the breeding methods for specific ornamental fish species are closely guarded secrets. Farmers have operated almost entirely on their own, developing their own methods and rely on many years of experimentation. In India, the most important breeding centres for ornamental species are located in Kolkata, Mumbai, Chennai and Kochi. Ornamental fishes are broadly classified into two groups based on their breeding methods- Egg layer or oviparous and live bearer or viviparous species. Oviparous fishes lay floating, adhesive or non-adhesive eggs that may be scattered, laid in bubble nests or deposited on substrates or in shallow pits. The breeding and rearing of live bearers are easier than egg layers, which begin with handling the live bearers.

The indigenous ornamental fish which are very popular overseas, are being harvested from the wild and exported. This in the long run, may lead to depletion of stock due to over harvesting of our valued native fish species. Hence, breeding of native fish species is also equally important for a sustainable trade of ornamental fishery and to conserve the natural stock. Some fishes breed naturally with ease, whereas others are bred by artificial techniques like hand stripping and hypophysation. In nature, the fishes are stimulated by changes in environmental factors. These conditions can be simulated to some extent in the aquaria by providing specific biological requirements for spawning.

I. Breeding of Zebra danio (Brachydanio rerio)

Brachydanio rerio is commonly known as zebra danio. The zebra danio, as the name implies, is characterized by a number of bright blue or purple horizontal lines, which run from the head to the caudal fin. This pattern is repeated in the anal and caudal fins too. The flanks have prussian blue colouration and operculum has golden blotches. The dorsal fin of this species has an olive yellow base and there are blue gold markings on the anal fin.

Introduction

Man’s intervention in the evolution of plants, to adapt them to suit his needs, constitutes the practice of plant breeding. Historically regarded as an art and still too empirical to be accepted universally as a science, it has recently been described as a technology (Riley 1978). Whether art, science or technology, it certainly draws on a wide range of disciplines and embodies all those principles of organisation and management that determine success in any production-oriented programme.

Perhaps the biggest contribution that the plant breeder has made to increased production during the past 50 years has been in helping to alleviate the effects of natural hazards such as lodging, pests and diseases on crop production. While most of this progress has been through the manipulation of biotic stresses, much is still to be achieved under non-biotic stresses such as drought, salinity, temperature, etc. This argument is strengthened by the fact that in spite of the spectacular achievements made possible by the ‘Green Revolution’, the productivity level of most crop plants, including wheat and rice, has remained both low and static under stress conditions. Concerted efforts are needed through an approach of interdisciplinary research, since not much has been done to define criteria for stress assessment and evolving breeding approaches for incorporating stress tolerance in crop plants.

Introduction

Global food productivity will have to rise significantly to satisfy an expanding world population. Increased vegetable production is one option towards the efficient conversion of natural resources into food stuffs. As a group, vegetables are a diverse range of herbaceous plants that do not belong to any particular botanical species, genus or family. Individual members may be at various stages of domestication. Vegetables are typically annual herbaceous species, whose plant parts (leaves, stems, flowers, fruits, roots or tubers) are consumed as fresh or as cooked product, and as an additional source of vitamins, minerals, fibre, phytochemicals, protein and/or calories. Health benefits are also claimed for some vegetable species, mainly due to antioxidant activity and capacity to scavenge free radicals.

Domesticated plants have been fundamentally altered from their wild relatives; these species have been moved into and adapted to new environments. They have become dependent on the farmer’s hand and they have been reshaped to meet human needs and wants. Modern crops are the results of thousands of years of these evolutionary processes. Like all biological evolution, crop evolution involves two fundamental process; the creation of diversity and selection (Harris and Hillman, 1989). Crop evolution is distinguished by two types of selection; one natural and another artificial or conscious. These evolutionary processes must continue in order for agriculture, a living and evolving system to remain viable.

In the hands of plant breeder’s sexual hybridization is a powerful tool for producing superior plants by combining characters distributed in different members of a species or different species of a genus. Genetic variability within the species has been efficiently utilized by breeders in their efforts to improve crops. However, the existing variability in a breeding population may not be sufficient for modern plant breeding purposes, and thus great efforts have been made to broaden the existing gene pool of crops through utilization of wild germplasm.

The current status of advances in fruit breeding is through the development of different scientific approaches augmented by ever-increasing knowledge and application of genetics, statistics and biotechnology. These innovative approaches very specific for a species in most of the cases, are the major tools of the fruit breeders to tackle the different objectives of fruit improvement programme at present Fruit improvement is a very slow process due to the long generation cycle varying from species to species, thereby reducing the chances of exploiting genetic recombination. Besides this factor, most of the fruit species are either highly heterozygous or polyploidy in nature. Due to this reason the asexual propagation of fruit plants is a conventional means while wide segregation occurs upon sexual reproduction. Such expectation is not unlikely because the types selected as commercial varieties are definitely to be vigorous ones, and a positive correlation exists between vigour and heterozygosity.

This discussion on breeding of fruit plants involves different aspect of the species concerned is so essential as well as fundamental that discussion of them must procede any consideration of breeding methods themselves. The plant species are grouped into two-self-pollinated and cross-pollinated. These two groups have emerged on the basis of pollination mechanism which plays significant role in the method of breeding application. To emphasize the difference in the reproductive systems of these two groups one should know the details about floral biology, mechanism of pollination control, reproduction by asexual and sexual means and self and cross-pollinated plants.

Transgenic crops, developed through genetic engineering techniques, have revolutionized modern agriculture by conferring novel traits that enhance yield, quality, and resilience. This chapter delves into the intricate interplay between the scientific advancements in breeding approaches for transgenic crops and the critical ethical concerns and regulatory frameworks that accompany them. The chapter begins by introducing the concept of transgenic crops and provides an overview of the diverse breeding techniques employed to manipulate plant genomes. These techniques include Agrobacterium mediated transformation, biolistic transformation, CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats–associated protein 9) genome editing, RNA interference (RNAi), and site-specific integration methods. Each method is presented within the context of its potential benefits and limitations. The subsequent sections address the ethical considerations that arise from the creation and deployment of transgenic crops. The potential ecological and biodiversity impacts, cross-contamination risks with conventional crops, and issues related to patenting genetically modified organisms (GMOs) are explored. Furthermore, the chapter examines the ethical implications of genetically modified crops on human and animal health and questions surrounding the monopolization of seed resources. Looking to the future, the chapter outlines emerging breeding technologies and anticipates potential challenges in ethical consideration and regulation.

All hybrids and varieties perform better under conventional farming in response to excess use of chemical fertilizers and pesticides, which are harmful to humans, animals and environment. Hence, there is a need to develop varieties/hybrids exclusively for organic farming. Breeding aspects of organic farming include breeding tools/methods which are used to breed varieties/hybrids including testing and multiplication under organic conditions duly following the principles of organic farming as defined by IFOAM. These cultivars should have high nutrient use efficiency, resistance to diseases and pests, competitive ability against weeds, higher yield and stability across environments along with enhanced nutritional quality. This book chapter briefly discusses the aspects of breeding that are involved in generating cultivars suitable for organic farming.

1. Introduction

Currently, organic farmers rely heavily on conventionally developed and produced varieties. Nevertheless, in order to optimize their production under organic agriculture, it is necessary to develop cultivars that are more suitable for organic cultivation. According to some studies, the naturalness of organic agriculture should go beyond simply by avoiding chemical inputs and substituting natural and organic components during the transition from conventional to organic farming.

INTRODUCTION

The ultimate objective of forest tree breeding is to develop fast growing high yielding genetically improved superior strains in order to replace the wild natural forest stands so as to obtain higher forest productivity per unit area and time. A breeding programme, in fact, involves purposeful management of genetic variability present in a taxon. The variation is regulated through controlled mating. This obviously, needs detailed information on the nature and extent of genetic variation on one hand and equally on the reproductive biology of the species. A clear understanding of phenological behaviour, time of anthesis, time and duration of stigma receptivity, fertilization, mode of pollination, seed development etc. is necessary for attempting crosses between genetically different forms which is invariably involved in the breeding programmes. Although, tree breeding work has been done to a great extent on the temperate species (Devey et al. 2002; Murat et al. 2006; Gotzenberger et al. 2007), no serious efforts were made in the past on tropical forest species including Jatropha (Jatropha curcas), presumably due to the consideration that similar breeding methods may perhaps, be applied to the tropical trees as well. This, however, is not applicable, as the phenological and reproductive features are typical different to each species. It was in this background that the present research article was planned to collect information on floral biology, breeding behaviour and hybridization programme in Jatropha for subsequent application in its genetic improvement.

Crops plants are broadly classified into two groups based on their mode of reproduction viz. sexually propagated and asexually propagated. In sexually propagated crops seeds are the primary propagules and it is produced by the fertilization of male and female gametes. Whereas, asexual reproduction or clonal reproduction covers all those modes of multiplication of plants where normal gamete formation and fertilization does not take place and vegetative propagules are the means of reproduction. Since sexual reproduction involves meiosis, segregation and recombination, the creation of variation is a continuous process which is inevitable in these crops. On the other hand, in asexual propagation progenies are identical to the parent clones and they are genetically similar without any variation and they reproduce via mitosis. The most important vegetatively propagated food crops are potato, sugar cane, cassava, sweet potato, yam, plantain/banana, and fruit trees. Other crops with asexual propagations are some ornamentals, grasses, and forages.

Introduction
Based on the mode of reproduction, plants are broadly classified into sexually propagated and asexually propagated crops and some of the agricultural crops and a large number of horticultural crops are asexually propagated. The most important asexually propagated crops cultivated on a global basis are potato (Solanum tuberosum), cassava (Manihot esculenta), sweet potato (Ipomoea batatas), sugarcane (Saccharum spp), yam (Dioscorea spp.), taro (Colocasia esculenta), banana (Musa paradisiaca), etc. In sexually propagated crops, seeds are the primary propagules and it is produced by the fertilization of male and female gametes. Whereas, asexual reproduction or clonal reproduction covers all those modes of multiplication of plants where normal gamete formation and fertilization do not take place and vegetative propagules are the means of reproduction. Since sexual reproduction involves meiosis, segregation and recombination, the creation of variation is a continuous process which is inevitable in these crops. On the other hand, in asexual propagation, progenies are identical to the parent clones and they are genetically similar without any variation and they reproduce via mitosis.
Characteristics of asexually propagated crops
• Majority of the asexually propagated crops are perennials, e.g., sugarcane, fruit trees, etc. The annual crops are mostly tuber crops, e.g., potato, cassava, sweet potato, etc.
• Many of these crops show reduced flowering and seed set, and some varieties of these crops do not flower at all. But many of these crops flower regularly and show satisfactory seed set.
• They are invariably cross-pollinated and highly heterozygous and show severe inbreeding depression.
• A vast majority of asexually propagated crops are either polyploids. eg., sugarcane, potato, sweet potato, etc., or have polyploid species or varieties.
• Many cultivated crops are interspecific hybrids, ex., banana, sugarcane, etc.
• These crops consist of a large number of clones, that is, progeny derived from a single plant through asexual reproduction. Thus, each variety of an asexually propagated crop is a clone.

Expression of genetic potential for growth and yield of a crop variety is directly dependent upon the environment comprising both climate (weather) and soil components. As discussed in the preceding chapter, the term ‘salt-affected soils’ encompasses a broad group of adverse but distinct soil conditions, namely, saline, alkali (sodic) and acid soils with further variations such as coastal and inland locations as well as arid and water-logged situations (Swaminathan 1977; Bresler et al. 1982). Factors limiting growth and yield of crop plants in various categories of problem soils are different and specific. Likewise, adaptive strategies evolved by plants to cope with the prevailing edaphic stresses, such as salt stress, also vary a great deal as indicated in Table 1. It is not unexpected therefore, that even varieties within a crop often show notable differences regarding tolerance to adverse soil conditions (Epstein et al. 1980; Devine 1982; Shannon 1984; Sayed 1985). Hence, it is essential that the breeder must understand the inherent charaderistics of the problem soil with which he is concerned and should also simultaneously appreciate that basically it is the sensitivity of crop variety, rather than the soil parameters per se, that essentially determines the occurrence as well as the magnitude of actual soil problem (Rana 1977). Since the degree of tolerance (adaptation) of crop varieties to different kinds of salt affected soils is genetically controlled, it is axiomatic that it can be improved through genetic manipulations by adopting suitable breeding procedures.

Introduction

Stress is any unfavorable condition for a plant’s normal growth and development. In the case of crop plants, such adverse conditions are caused by biological (biotic) and non-biological (abiotic) environmental factors. Abiotic stress is the negative impact of non-living factors on living plants in a specific environment. Usually, abiotic stress is unavoidable, and we can only go for its management.

The most basic stresses include:

• Extreme (high/low) temperatures

• Soil-chemical properties

• Water deficiency

• Excessive moisture

• Element toxicity or deficiency

A. Salinity

Salinity is a predominant problem affecting crop productivity. Over 800 million hectares of land on earth are saline. This accounts for more than 6% of the total land mass on earth. Salinity is a global problem and is prevalent especially in the arid and semiarid regions, where leaching of salts is poor due to low rainfall or irrigation. Brine-affected soil occurs due to natural causes such as weathering and deposition of oceanic salts (eg. recently tsunami in India). In addition, human interference with the environment such as deforestation and/or desertification has resulted in the rising of water table, thus increasing the salt concentration in the root zone. This excess salinity poses a threat to sustainable crop production.

A plant is said to be healthy or normal when it carries out its physiological functions to the best of its genetic potential. These normal functions include division, differentiation, development, absorption of water and mineral from soil and translocation of these throughout the plants, photosynthesis and translocation of photosynthetic product to areas of utilization or storage, the metabolism of synthesized compounds, reproduction and storage of food supplies.

A plant becomes diseased when it is disturbed by pathogen under certain environmental conditions which interfere with one or more of its essential functions. Diseased plant refers to any disturbance brought about by living organism under environmental factors, which interfere with normal function of plant or in other words when any organ and part of plant is not doing their work properly and when either the growth or reproduction is not going forward in natural or regular manner.

Crop production is challenged by abiotic and biotic stresses results in low yield and high production costs.

Magnitude and intensity of stresses are increasing dramatically due to climate change causing recurrent droughts, increased temperature (heat) and emergence of new diseases and pests.

Diseases of plants are produced by a variety of organisms from plant and animal kingdoms viz., fungi, bacteria, viruses, nematodes and insects. The diseases reduce total biomass (dry matter) production and consequently yield of the crop by general stunting, damage to the leaf tissues, fruits and seeds or by killing the plants. The degree of damage would depend upon the intensity of infection but both need not be proportional. One serious effect of disease is the disappearance from cultivation of otherwise excellent but susceptible varieties.

Vegetable crops have been found to be highly susceptible to biotic stresses from the disease causing microorganisms and insects-pests. The ability of pathogen and insect-pests to attack and proliferate in the host plant is highly specific. There are wide differences in the host plants in response to the attack by pathogens and insects. Although control of the diseases and insects by the use of chemicals is possible to certain extent but indiscriminate use of fungicides or insecticides over the crop has several disadvantages. Besides increasing cost involved in chemical control, residual toxicity of the chemicals such as fungicides, antibiotics and insecticides in food chain and development of resistance against pathogens and insect-pests to different chemicals are serious problems.

Genetic improvement of host plants conferring resistance to diseases and insect-pests is considered to be the best approach in the management of diseases and insect-pests, and this is more particularly true in case of vegetable crops. Indiscriminate use of chemicals in the vegetable sector has led to health hazard. This has resulted in switching towards organic vegetables. However, cost of production of organic vegetables naturally will not permit the common people to consume these products. Therefore, the best option is to induce resistance in the host varieties. The resistant varieties could in turn be an important component in the organic vegetable farming, thereby reducing cost of production to certain extent.

In general, disease means an impairment of health or a condition of abnormal functioning. Plant disease is an abnormal deviation from the normal physiological functioning of the plants their by it causes quantitative and/or qualitative losses. Disease may caused by biotic agents (infectious) like fungi, bacteria, viruses, viroids, phytoplasma, spiroplasma, fastidious bacteria, protozoa, nematodes and parasitic higher plants or abiotic agents (non-infectious) like extreme environmental factors includes temperature, light, soil moisture, atmospheric humidity, environmental pollutants, carbon-dioxide concentration, soil nutrient deficiency, acid rain, soil pH and herbicides. 

Understanding Immunogenetics
The study of genetic basis of the immune response is known as immunogenetics. The term was introduced with the discovery of ABO blood groups and were first demonstrated through the existence of “natural” antibodies i.e., isoantibodies. The broad field of immunogenetics include study of normal immunological pathways as well as identification of genetic variations that result in immune defects, which may facilitate detection of new therapeutic targets for immune diseases. Hence, understanding and subsequent manipulation of host immune response (immunomodulation) is the most precise and effective tool to reduce disease incidences and nullify the limitations associated with antibiotic treatment or vaccination. Therefore, breeding for disease resistance has gained considerable attention from researchers in the recent past.
Immune Response Genes
Often it was observed that individuals respond differently to same infectious agent. A possible explanation may be the genetic variability between them. Indeed, many studies have looked for associations between genes involved in immunity and disease outcome and it has been found that certain immune response (Ir) genes play the crucial role. This concept was discovered in the mid-1960s and this discovery introduced an apparently new level of antigen recognition whose diversity and specificity had to be explained in addition to those of familiar immunoglobulins. Hence immune response (Ir) genes were defined as antigenspecific genes that control the ability of an animal to raise an immune response, either humoral or cellular to a particular antigen .

This chapter starts quoting first para of the book entitled Disease Resistance in Plants by Van Der Plank (1968). “In 1958 the American Phytopathological Society met to celebrate its Golden Jubilee and review the problems and progress in plant pathology during the 50 years, 1908 to 1958. J. C. Walker was elected to review the problems and progress in controlling plant diseases by host resistance, a fitting tribute to one who perhaps more than any other had contributed during those 50 years both to understanding of nature of resistance and to the practical application of resistance to problems in horticulture and agriculture. In his summary Walker wrote “By and large the development of resistant varieties must be looked upon as a continuing program. The potential variability of most pathogens (including viruses) will not permit any currently successful variety to remain so for an indefinite period”. This opening para tells the importance of breeding for resistance to diseases in crop plants on a continuous basis as the fight between host and the pathogen will go on and on.