eChapters

Abstract

The advent of modern chemical industry has resulted in the release of huge amounts of novel organic compounds, as industrial by-products, pesticides, other agrochemicals etc into the environment. These new compounds tend to resist biodegradation, with potential consequences such as persistence in the environment or bioaccumulation in food chains. Early detection of toxic chemical compounds in the environment, particularly in water, and their biological effects on organisms has therefore become increasingly important. The traditional approach to environmental pollution assessment is based on chemical analytical methods which only provide information about the absolute concentrations of known chemicals in the environmental sample without an adequate interpretation of its toxicity to biota. In order to get more relevant information about environmental pollution risk, it is therefore inevitable to supplement the chemical analytical data with the results of methods providing information on biological impacts. The negative biological effects of pollutants present in all kinds of environmental samples can be assessed using different living organisms or cells as ‘analytical devices’. The biological response following the exposure of living organisms or cells to environmental sample usually gives an information on toxicity, genotoxicity, estrogenicity etc. of the whole mixture of chemical compounds. According to the technical principle, methods of biological monitoring can be classified to bioassays, biosensors, immunoassays, and ecological methods. Besides being sensitive only to the bioavailable fraction of pollutants, biotests also have the power to assess the integrated effect of interacting chemical compounds and to detect the compounds, which are toxic only due to bioactivation.

9.1. Molecular breeding and marker assisted selection

Using conventional breeding, developing new varieties takes atleast 15-20 years.

Molecular breeding shortened the time to 7-10 years.

One of the tools for faster variety development is Marker Assisted Selection (MAS).

MAS-refers to use of DNA markers to assist phenotypic screening.

Plants that possess particular genes or quantitative trait loci (QTL) may be identified based on their genotype rather than their phenotype.

Introduction

Diagnosis of cancer has always been challenging. There is no single diagnostic test to confirm the cancer. A detailed evaluation of the patient comprises of history, physical examination and various diagnostic tests.

Most common steps in the diagnosis involve physical examination, imaging tests, laboratory tests, biopsy etc. Other than these there are several other battery of tests that are followed in modern diagnostics. The main aim of the diagnosis is to determine what type of cancer and more importantly the stage and the grade. Early detection of cancer provides cure or better chances of survival in any patient. It improves the prognosis of cancer and potentiate the effect of targeted therapy. There are several moderndiagnostic techniques like 2D and 3D imaging using PET positron emission tomography, MRI, Computed Tomography (CT), X Rayimaging and ultrasound scanning. The diagnosis of tumor involves several steps.

Introduction
Maize (Zea mays L.) is the second most widely crop grown globally after wheat, with 205 million hectares under cultivation. The area cultivated under maize is steadily increasing and expected to overtake that of wheat by 2030 (Erenstein et al., 2022). With production exceeding 1.2 billion metric tons, maize surpasses the production of other highly cultivated cereals like wheat and rice mainly due to its higher yields (Erenstein et al., 2022). Maize is cultivated in the Americas, Africa, and Asia, for multiple end-uses (Nuss and Tanumihardjo, 2010). It is a staple food in several countries across Africa and Latin America, and in a few countries in Asia, with an overall contribution of 15-20% of daily calorific needs (Shiferaw et al., 2011).
The global maize yield tripled from the 1960s with the average yield rising from 2 tons/ha to the current 5.8 tons/ha, mainly due to the adoption of highyielding hybrid cultivars and complementary input use (Erenstein et al., 2022). Maize is naturally an outcrossing species and inbreeding is unnatural. When maize is subjected to inbreeding and the resulting inbred lines from genetically distant backgrounds are crossed, hybrid vigor or heterosis is realized (Springer and Stupar, 2007). Hence, the development of the homozygous inbred lines is a very important step in hybrid maize breeding.
In the well-evolved maize breeding programs, the germplasm is well characterized into different heterotic groups where the hybrids developed by crossing inbred lines from different heterotic groups exhibit high heterosis (Ertiro et al., 2017a; Sang et al., 2022). For the development of inbred lines, maize breeders develop F1 populations by crossing two inbred lines within the same heterotic group (Prigge et al., 2011; Sang et al., 2022). Inbred lines are developed from the F1 population by recurrent self-pollination for 6-8 generations; this can take up to 3-4 years or even more, depending on the availability of off-season nurseries for generation advancement. The resulting inbred lines are highly homozygous (~98-99%), but not 100% homozygous. The doubled haploid (DH) technology emerged as a viable alternative to the time-consuming and resourceintensive recurrent selfing method to produce 100% homozygous inbred lines in just two crop seasons (Prasanna et al., 2012; Chaikam et al., 2019a).
In addition to significantly reducing the time taken to develop homozygous lines, the use of DH lines in maize breeding offers several other benefits: a) As DH lines are completely homozygous at all loci, they are stable and do not show further inbreeding depression; b) DH lines are also best suited for evaluating distinctness, uniformity and stability (DUS) criteria, thereby better facilitating plant variety registration and intellectual property protection (Röber et al., 2005); c) The use of DH lines facilitates selections on completely homozygous lines which is more reliable and effective compared to selections on segregating families with different levels of heterozygosity (Chaikam et al., 2019a); d) Use of DH lines also simplifies breeding operations like planting, managing the nurseries, seed shipments, record keeping, etc. as selfing nurseries spread over several generations are replaced by just two generations for DH line development (Prasanna, 2012; Röber et al.,

Cultivated plants in general including the spice crops observed today have been evolved through selections from their weedy and wild types. Apart from this, there had been another force which could bring the wild forms into cultivated forms named human intervention which is actually the process of domestication. Natural mutations and genetic recombination after selfing and crossing also played a significant role in the entire process. Whereas, natural forces take a long time to come into act, the techniques of plant breeding was devised and fine tuned throughout passing of times, essentially to accelerate the speed of evolution using these natural phenomenons. It was, therefore, mandatory for us to know the modes of reproduction and pollination to create variability in natural population and make all thise happen to what we see today in organised cultivated forms. Moreover, knowledge on reproduction of different plant species helps the breeder to choose the right breeding procedure to be used for crop improvement. Modes of reproduction help to evaluate the genetic constitution of crop plants by determining the extent of homozygosity or heterozygosity which, in turn, are unanimously applicable to any plant. To comprehend modes of reproduction in spice crops effectively, understanding about the floral biology is absolutely necessary. Plant reproduction, a process by which one species gives birth to its offsprings, may be of two types

Allele-Specific PCR

This diagnostic or cloning technique is used to identify or utilize single- nucleotide polymorphisms (SNPs) (single base differences in DNA). It requires prior knowledge of a DNA sequence, including differences between alleles, and uses primers whose 3' ends encompass the SNP. PCR amplification under stringent conditions is much less efficient in the presence of a mismatch between template and primer, so successful amplification with an SNP-specific primer signals presence of the specific SNP in a sequence.

Amplification Refractive Mutation System (ARMS) - PCR

In ARMS, the primer pair is designed so that one of the 3' ends coincides with a variant nucleotide in the target sequence. When the primer mismatches the template the frequency of extension is very low and consequently the effective number of sequence copies available for amplification is greatly reduced. ARMS PCR exploits a thermostable polymerase that lacks 3' exonuclease activity (usually Taq polymerase). Such enzymes extend primers bound to their target sequences very inefficiently when the 3' base is mismatched. Because the 3' exonuclease activity required for mismatch repair is not present, the extension of such primers in PCR is a rare event and amplification is retarded. However, once mismatch extension has occurred amplification proceeds normally from the newly synthesised target strand. Thus an important principle of ARMS is that non-matching (i.e. non-matching at only the 3' end of one primer) template may be amplified. The factors that contribute to this apparent ‘failure’ of ARMS are that when very high numbers of template molecules are added to the reaction, amplification is likely to proceed because the small proportion of mismatched primer extensions reach the sensitivity threshold of the reaction. Second, certain mismatches are extended more efficiently than others so that proportion extended in each PCR cycle varies.

During most of the years, there will be loss of agricultural production by at least 15 to 20 per cent per annum due to unfavourable weather situations. The farmers practicing agriculture expect uniform returns every year as the investment costs are much higher and cannot afford loss in production. Of late, the inter-seasonal and intra seasonal variations in weather are very frequent. The weather conditions observed were found to exceed even beyond known limits. Exceptional deviation from any one single weather parameter like air temperature, rainfall and wind can trigger considerable loss in production or sometimes even crop failure (Fig.12.1). Fig. 12.1: Components of a microclimate and its interlinkages Large scale weather modification is not practicable to a greater extent as uniform results cannot be expected under these conditions. There is need to explore cost effective management options that may significantly alter some weather parameter that is detrimental to crop production at field level by the farmers themselves. Therefore, microclimatic modification is an emerging technology to alter or change the unfavourable weather conditions detrimental to crop growth using cost effective and easily manageable techniques for minimizing the loss in crop production. The options for microclimatic modification have to be decided based on whether and the nature of weather aberrations. For example, dry spells are most common during rainy season in most of the arid and semi-arid regions. The farmers growing crops under rainfed conditions suffer considerable loss in production due to occurrence of dry spells as the crop experiences moisture stress. These dry spells may occur any time during the growing season. In such situations, the farmer needs to adopt a management option even before sowing a crop. Sometimes, the occurrence of weather aberration cannot be anticipated and the farmer has to prepare for adopting a management option based on weather forecast. Such measures are temporary and needs to be adopted to ward off the unfavourable weather conditions to a certain extent. Microclimatic modification can be a permanent, seasonal or temporary option depending upon the climate of the region. The crop microclimate refers to the climate just above and within the crop canopy and in the soil root zone that can be influenced by the day-today management practices. Microclimate modification is a measure to change or regulate the weather parameter at farm level. The microclimate management option also depends upon the nature and type of the soil as well.

Abstract

Tremendous hike inworld population has increased thrust on the limited resources which has considerably affected the viability of the food. The emerging challenge for policy makers and food scientists is to put forward viable solutions. Utilization of underutilized crops/plants that act as good sources of starch could be explored in a better way for the sustenance of the limited sources like food crops/plants. The demand for starch and the foods containing starch has been increasing continually. Since, the starch in its native form has certain limitations in its functional properties to be used for different applications. Therefore, it becomes important to explore certain technologies which could be used for modification of starch. Among different technologies gamma irradiation ensures food safety while inducing physicochemical changes of the components. Although, the chemical modifications have been used widely so far but the concerns related to the chemical residues left are diminishing their demand. Hence, the physical processes particularly the gamma irradiation process has emerged as an efficient alternative with some benefits over other process like eco-friendly, economical, reliable and safe for altering the physico-chemical and biological characteristics of the product. Gamma Irradiation of starch has been successfully employed for the achievement of some desired physico-chemical, biological and functional properties of the foods and other related items. In this chapter, valuable impact of gamma irradiation on the physico-chemical, biological and functional properties of starch has been summarized.

13.1 Biopolymer-Based Coatings with Antimicrobial Properties 13.1.1 Understanding Biopolymer-Based Coatings Biopolymer-based coatings are a game-changer in food packaging, offering natural, sustainable solutions for food safety. These coatings, derived from renewable sources, like polysaccharides (e.g., chitosan, starch, cellulose), proteins (casein, gelatin), and lipids (wax, shellac), have proven to be biodegradable and consumer-friendly alternatives to synthetic polymers. 13.1.2 Antimicrobial Properties and How They Work • Antimicrobial coatings are crucial in slowing down spoilage and extending the shelf life of perishable foods. They work by disrupting cell membranes, inhibiting cell processes, and creating oxidative stress in microbes. This is achieved through natural antimicrobials like essential oils (e.g., oregano, thyme, clove), plant extracts, and organic acids; inorganic agents like silver nanoparticles, zinc oxide, and titanium dioxide; and microbial-derived substances like nisin, lysozyme, and bacteriocins (Yu, Z et al ., 2022)

Studies have shown that modified atmosphere packaging (MAP), and controlled atmosphere storage have the ability to delay quality losses and thus extend shelf life of fresh or minimally processed or fresh-cut produce (Church 1994; Gil et al. 1996a, b; Lee et al. 1995). Modified atmosphere packaging of fruits can result in reduction of respiratory activity, delay in softening and ripening and a reduced incidence of various physiological disorders and pathogenic infestations (Artés 1993).

9.1. Introduction

In a fast-paced world, demand for pre-cooked, fresh-like, and convenient products without preservatives is increasing. This demand has triggered the need for better alternative packaging materials for food products like MAP (Modified Atmosphere Packaging), CAP (Controlled Atmosphere Packaging), edible packaging, biodegradable packaging, etc. Packaging plays a crucial role in transport, distribution, storage, retailing, and end-use, a means of ensuring safe delivery to the ultimate consumer in sound conditions at optimum cost. It performs the functions depicted in Fig.1 for both fresh as well as processed products (Opara et al., 2007; Opara, 2009).

Clsssification

Fracture of upper third humerus, shoulder dislocation and scapula has been grouped under highest level fracture. (Fig.1)

Purpose

To know the method of casting the highest level fracture by modified valeau sling application.

Requirement

Thick 8 layer cotton padding, adhesive gum, 6"-8" long bandage rolls.

Indication: Highest level fracture (femur fracture) (Fig. 1)

Treatment: Modified Velpeau Sling application

Requisite

Adhesive gum

Damage Cloth

Abstract

The agricultural scientists particularly those who are in advisory service, irrespective of specialization, are often approached by the farmers with diseased samples of their crops and sought advice on plant protection strategy. The strategy includes components of control measures, doses, mode and time of application. In the present article different steps of formulation of plant disease control strategy are discussed. To further elaborate the contents, examples from integrated management strategy of mango malformation disease is cited.

Keyword: Mango Malformation

Introduction

Mango malformation, disease was first time reported from Darbhanga District of Bihar State in 1891 by G. Watt. The disease is currently prevalent in almost all the mango growing country and is thus designated as the plant disease of International importance and previously considered to be a serious problem in the northern parts of the country, has now started to appear in central India too in severe form. It is well known, the mango malformation is the most serious disease, rendering mango cultivation non-lucrative in subcontinent and other regions of the world (Ahmad et al., 2002; Ploetz, 2001). Mango malformation caused by fungus Fusarium moniliforme var. Subglutinans, are proved (Freeman 1999; Zheng and Ploetz, 2002). Recently, these isolates were described as members of a new species, F. mangiferae Britz, Wingfield and Marasas sp nov. (Britz et al., 2002). The casual organism of mango malformation grows well at lower temperature and higher relative humidity. The disease is quite common in both grafted and the seedling plants (Kumar and Chakrabarti, 1997). The symptoms manifest as bunchy top (BT) in 4-5 month old seedlings in the nursery, vegetative malformation (VM) of twigs arising from axillary buds and malformation of inflorescence (MF). Normally floral malformation is more prevalent in bearing trees than vegetative malformation. Flowers in the malformed panicle are much enlarged and crowded with hypertrophied axes of the panicle. Malformed inflorescences/ panicle of different varieties were variable in respect of their shapes, sizes, growth and compactness, depending upon the cellular structure and physiology under environmental factors (Chakrabarti et al., 1990). Generally malformed inflorescences produce no fruit, or abort already stages (Schloser, 1971) and is directly responsible for reduction in yield (Kumar et al., 1993 and Singh et al., 1998). In the present study the incidence of Floral malformation on a large number of mango cultivars was recorded over a period of 5 years with a view to identify the entries of future resistant breeding programme.

17.1 Modules

• A module is a file containing python definitions and statements.

• A python module is (.py file) containing variables, class definitions, statement and function related to a particular task. The major feature of having module is that its content can be reused in other programs, without having to rewrite or recreate them.

• They are executed only the first time the module name is encounter in an import statement.

Type of modules:

• User defined modules

• Built-in modules

Ex.-array, math, numpy, sys, etc.

8.1. Documented ITKs on Moisture Conservation

The ITKs were documented under following specific categories

• Agronomic Measures
• Tillage
• Bunding & Terracing (Mech. & Vegetative barrier)
• Land Configuration
• Soil Amendment / Mulching
• Erosion Control & Runoff Diversion Structures
• Water Harvesting, Seepage Control & Ground Water Recharge

India is an agricultural country. The geographical area of India is about 328 mha out of which 147 mha of land under cultivation and 84-mha land is under irrigation. The population is increasing at an alarming rate that requires producing more food for the growing population. This problem can be solved either by increasing the land under irrigation or using different soil water conservation techniques. It is well known fact that during rainfall a considerable amount of water goes to sea due to high rate of runoff. It is highly needed to trap as much as water falling in the form of rainfall and recharge the groundwater so that it is made available for irrigation purposes.

Moisture plays by far the most important role in soils as regards vegetation. It is through the medium of water that the plants obtain their quota of mineral food vital for their growth. If water is gradually withheld from the soil, at a certain stage, the plant will begin to wilt and soon dry up. The soil may still contain some moisture but the plant is unable to make use of it. The minimum moisture in the soil below which wilting will take place is called the Wilting Coefficient and at one time great importance was attached to it. The determination of this Coefficient, however, is tedius. One must grow a number of plants and slowly watch them wilt and determine the moisture content at that point. Moisture content of the soil is determined by heating a weighed quantity of the sample in an oven kept at 100-110 ^oC. The moisture is expressed as percentage on the oven-dry soil.

Clouds play very important role on weather and climate. The formation of clouds takes place when water condenses in the sky. Clouds are visible accumulation of tiny water droplets and ice crystals in the Earth’s atmosphere. The moisture is always present in the atmosphere though it may not be visible. Clouds form when air becomes cooler until the water vapour present in it condenses to liquid form. The condensation over oceans occurs around solid particles like salt, dust, smoke etc. suspended in the atmosphere. The type of clouds depends upon temperature and wind. The clouds are classified based on physical appearance and the height at which clouds are formed (Fig. 7.1).

Term moisture stress is generally applied to the stomata opening and transpiration increases with time until they close due to high temperature.

5.1. Causes of moisture stress in plants

Main reason is extent of transpiration which is affected by leaf size and composition, size and distribution of stomata on leaf, atmospheric humidity, temperature, wind velocity and day length.

High atmospheric temperature due to intense sun and increased transpiration causes closure of stomata and wilting of leaves even, if soil moisture content is not limiting.

This deficit is made up during night due to decreased transpiration.

In plants, moisture content decreases either due to increased transpiration or reduction in absorption or both.

Abstract

Anantapur is the driest district of Andhra Pradesh and hence, agriculture conditions are very often precarious. Groundnut grows where other crops fail and thus it is the predominant crop of Anantapur district. Groundnut is grown in about 7.5 lakh ha in Anantapur district; however the average yields are low at 500 kg ha^-1. Among various available vegetation indices, normalised difference vegetation index (NDVI) is widely used for all reasons, which is a single numerical indicator of presence and condition of green vegetation. NDVI mapping at a regional scale helps to assess the spatial changes in the vigour of green vegetation and thus occurrence of any moisture stress. Climate tools have a great role in understanding the crop performance and estimating the yields. This study was taken up by using freely available MODIS data to understand NDVI in terms of abiotic stresses over Anantapur district and linking with the actual rainfall conditions, groundnut crop acreage and production. Results indicate that low groundnut yields in general could be related to NDVI-based stress measurements and rainfall quantum and distribution in the area however, with a few exceptions. It is hoped that by combining improved practices through IWM with climate-adapted crop varieties, rainfed farmers of Anantapur district can sustain their crop production under present climate variability and become resilient to future climate change.

Keywords: Climate, MODIS, NDVI, Anantapur, Groundnut, Integrated Watershed Management

Extraction of DNA from Tissue
(Using HiPurATM Multi-sample DNA Purification Kit)
Kit contents
Re-suspension buffer, Lysis solution, Prewash solution concentrate, Wash solution concentrate, Elution buffer, Proteinase K, HiElute Miniprep Spin Column (Capped), Collection tubes (uncapped), Collection tubes Dilute the prewash, wash solution and Proteinase K according to the kit.
Protocol
Prepare tissue
Weigh 25 mg of tissue, add approximately 3 ml of 0.8 per cent of normal saline. Homogenize the tissue with homogenizer or with mortar and pestle. Transfer the homogenized tissue with saline to a microcentrifuge tube. Centrifuge at 14000 rpm for 10 minutes. Discard the supernatant and use the pelleted tissue for further lysis.
Digest tissue
Add 180 μl of resuspension buffer and 20 μl of Proteinase K solution to the pelleted tissue in microcentrifuge tube. Mix by vortexing. Incubate the sample at 55oC until the tissue is completely digested (2-4 hours) in a shaking water bath. Vortex briefly after complete digestion.

MOLECULAR BREEDING

Molecular breeding is the application of molecular biology tools, often in plant breeding.

Genetic markers

Genetic marker is defined as a gene whose phenotypic expression is usually easily discerned, used to identify an individual or a cell that carries it, or as a probe to mark a nucleus, chromosomes or locus (King and Stansfield, 1990). Three broad classes of genetic markers are morphological markers, biochemical markers and DNA or molecular markers.
 
(1) Morphological markers

Morphological markers are based on the visually assessable traits viz., morphological and agronomic traits. However, they are limited in number.

MOLECULAR BREEDING

Molecular breeding is the application of molecular biology tools, often in plant breeding.

Genetic markers

Genetic marker is defined as a gene whose phenotypic expression is usually easily discerned, used to identify an individual or a cell that carries it, or as a probe to mark a nucleus, chromosomes or locus (King and Stansfield, 1990). Three broad classes of genetic markers are morphological markers, biochemical markers and DNA or molecular markers.

(1) Morphological markers

Morphological markers are based on the visually assessable traits viz., morphological and agronomic traits. However, they are limited in number.

Features of morphological markers

i.They are easy to identify, there is no need of any complex analysis. Trait of interest can be identified visually.

ii.Morphological markers are inherited qualitatively or quantitatively.

iii.Frequency of availability of morphological markers is less in number i.e., morphological markers may not be available for all the traits of interest.

iv.They are influenced by environment.

v.Since they are influenced by environment, they are unstable in inheritance.

vi.They are stage specific i.e., a particular marker will be useful to identify in a particular stage of plant and not any stage of the plant.

vii.They are influenced by genotype and developmental stages of the plant.

Besides drawbacks, the morphological markers are useful to the plant breeders for the selection purpose in certain situation.

Introduction
The most extensive diversity is found in the realms of plants and insects, encompassing over 1 million arthropod taxa, primarily comprising insects, which have been comprehensively described, along with more than 350,000 plant taxa. Notably, a substantial portion of the described insect species serve as either pollinators or herbivores. Over millions of years, insects and plants have coevolved, constantly adjusting and adapting to each other’s characteristics. Plants have developed numerous morphological and biochemical features to withstand damage from insects, while in response, insects have evolved a range of defensive and adaptive mechanisms. These mechanisms include behavioural, morphological, physiological, biochemical, and genetic traits, enabling them to either tolerate or adapt to the defensive traits of plants (Schmelz et al., 2006; Wu et al., 2007; Howe & Jander, 2008; War et al., 2018). Plant defenses against insect pests can be broadly categorized into two main types: antibiosis and antixenosis resistance. Antibiosis involves the direct impact of plant defensive traits on insect growth, development, and survival. In contrast, antixenosis defense relies on morphological or chemical factors that alter insect behaviour, deterring them from feeding and laying eggs on the plant. The trichomes, spines, cuticles, thorns, and lignified cell walls, are the morphological traits of defense that directly protect plants from insect pests. The biochemical defense mechanisms are typically activated in response to insect attacks and are characterized by their dynamic nature (War et al., 2018). Plant volatiles serve a significant function in the indirect defense of plants against insect herbivores. They accomplish this by either deterring the insect pests or by luring the pests’ natural adversaries. Among the various attributes associated with plant defense, chemical barriers, whether they are induced by stress or present constitutively, along with the nutritional composition of the plant, are regarded as particularly crucial for impeding insect growth and development (Peters & Constabel, 2002; War et al., 2019).
Chemical resistance entails the production of secondary metabolites, whether inherently present (constitutive) or induced as a response to a threat, to fortify the plant’s defense mechanisms (Figure 1). Constitutive defense metabolites, initially stored in an inactive state, referred to as phytoanticipins, become activated when herbivores attack. This activation is facilitated by the enzyme ß-glucosidase, which subsequently triggers the release of various aglycone metabolites possessing biocidal properties (Morant et al., 2008). Metabolites that are induced in response to herbivore activity are referred to as phytoalexins. These compounds encompass a variety of substances such as isoflavonoids, terpenoids, alkaloids, and more. They are recognized for their capacity to influence the growth and viability of herbivorous organisms (Walling, 2000). Furthermore, a notable role in imparting host-plant

Introduction

Livestock contribute directly to the livelihoods of nearly one billion of the world’s population. Livestock provide protein and minerals for human consumption, manure for crop production, and fibre and leather for industrial uses. Animals are also a source of draught power. Beyond their role of providing food and inputs for agriculture and industry, livestock provide security to farmers in developing countries, especially in emergencies such as crop failure. To many of the resource-poor, both smallholder farmers and landless livestock keepers, animals are a living bank, facilitating both income distribution and savings. In addition, by consuming crop residues and by-products, in addition to well-managed grazing, livestock production contributes positively to the environment, particularly in mixed crop-livestock production systems. Thus, livestock are an important source of income and employment that contribute to poverty alleviation and enhance the household food security of farmers.

INTRODUCTION

Molecular tools generally refer to molecular genetic tools. Although the first use of these tools began more than four decades ago, whenLewontin & Hubby (1966) used allozymes to find out the amount of genetic variation present in wild populations of Drosophila, the lack of expertise and high cost of these tools have prevented their widespread use among ecologists in general and behavioural ecologists in particular. But recently the accessibility and costs of these techniques have come down a lot and with the right kind of collaboration, lack of expertise is no longer an issue.

As was mentioned above, the Lewontin & Hubby’s (1966) investigation was done using allozymes. Although still an option, user-friendly neutral nucleotide markers are more preferred by investigators nowadays. The discovery of the polymerase chain reaction (PCR) in 1983 by Kary Mullis was the single landmark in this field, if one has to mention one. The use of molecular markers has totally revolutionized the field of ecology. It has provided ecologists the tool to ask questions, which were hitherto impossible to tackle and also to answer questions with much more precision and accuracy than was possible till now. It has toppled long held beliefs, sometimes, romantic ones, by ecologists.

Introduction
Infectious diseases in aquaculture are becoming increasingly important to address to support the growth and sustainability of the industry. This is especially true as many view farmed seafood production as a key solution for feeding the world’s growing population and reducing poverty in numerous countries (FAO, 2016). It is essential to establish biosecurity programs that effectively prevent, manage, and eliminate diseases within aquaculture operations. Biosecurity plays a critical role in safeguarding agriculture and aquaculture operations from the devastating effects of disease outbreaks. These programs are critical to safeguarding the health of aquatic species, protecting ecosystems, and ensuring the sustainability of the industry. At first, implementing biosecurity measures in aquaculture may seem like a simple concept. The well-known saying “prevention is better than cure” is especially relevant to aquaculture diseases, given the significant economic consequences of disease outbreaks. Effective biosecurity practices can help prevent these costly issues from arising. Biosecurity is a comprehensive and coordinated strategy that includes policies and regulations designed to assess and manage risks across various sectors, such as food safety, animal health, and plant health, while also addressing related environmental risks. Biosecurity measures focus on preventive practices such as quarantine, hygiene protocols, and environmental management.

Abstract

Nitrogen is the most essential nutrient for all plants and is also the major limiting factor in plant productivity. High yielding varieties of all crops are responsive to nitrogen but its ever-increasing use has shown detrimental impact on the environment along with extremely low use efficiency. Nitrogen use efficiency (NUE) in crop plants depends on various internal and external factors, which are dealt in detail. There has been a significant interest in genetic engineering of the crops to improve NUE. The use of biotechnological interventions by manipulating genes of the nitrogen utilization pathway to improve NUE has not been very successful. But transgenics/mutants with modified capacities for nitrate uptake, assimilation and remobilization have enhanced our understanding of the genetic control of NUE. In both cellular, and at whole plant level the mechanisms involved in N remobilization from the senescing organs towards the grain have recently gained importance but their understanding is still preliminary. Recent evidences have shown that grain filling during later stages of crop growth is supported by N recycling.

Although thousands of plant species exist on the earth, only those that were found to be useful for humans as food, feed, fiber, timber and other utility materials have been selected for domestication. When these plant species were affected by various biotic and abiotic causes, the necessity arose to determine the ways and means of protecting the valuable plants species and to understand the host plant defense mechanisms and pathogenic potential of the microbial pathogens causing enormous losses to the cultivators. All plant species have built-in resistance to most microbial plant pathogens existing in the environment. Susceptibility of plants to some of them is an exception, since they are endowed with genes which effectively nullify the possible adverse conditions created by the microorganism. Likewise, microbial pathogens possess genes for survival and pathogenicity to survive in the absence of susceptible plant species and to successfully establish infection in suitable plant species. The microbial pathogens have evolved highly specialized tactics to overcome the defense responses and to rapidly multiply in plants for their survival and perpetuation in a geographic location / ecosystem

Introduction
• Arrival of the nerve stimulus at the motor end plate result in reversal of the polarization of the sarcolemmal surfaces and the muscle gets activated
• This causes momentarily loss of potassium and sodium ions impermeability by the sarcolemma and Ca++ ions combined with calsequestrin in the sarcotubular system gets dissociated bringing Ca++ ion equilibrium with the sarcoplasm
• The junctional foot protein (JFP) and the L-type calcium channel (LTC) are the two big protein complexes responsible for the calcium release mechanism (Fig. 10.1)
• This leads to increase in level of Ca++ ion from nearly 0.10 mM to 10 mM
• Thus, troponin C, the calcium-binding site of the troponin complex becomes saturated bringing a structural modification resulting in interaction of actin with the MgATP2- on the H-meromyosin heads of the myosin molecule as the troponin I, the inhibitory protein, no more inhibits this interaction
• The interaction of actin with the MgATP2- intensely activate contractile ATP-ase near the bonding leading to break down of MgATP2- to MgADP– at a greater rate and liberating energy for inward (towards the sarcomere center) pulling of the actin filament
• This leads to breaking of bond between actin and myosin and thus, the myofibrillar part involved in above mentioned activity gets contracted

• General considerations

 • Polyacrylamide gel electrophoresis (PAGE)

 • SDS-polyacrylamide gel electrophoresis (SDS PAGE)

• Nucleic acid hybridization

 • Radio labelled probes

 • Biotin labelled probes

 • DNA finger printing

 • Polymerase chain reaction (PCR)

 • Reverse transcriptase polymerase chain reaction (RT PCR)

The shift from vegetative to reproductive phase in plants is the result of multiple gene cascades in response to photoperiodic and temperature dependent pathways, gibberellic acid pathway, vernalization pathway and autonomous pathway. The environmental cues are initially detected in the leaves and the mRNA of the flowering signal integrator FT gene, moving to the shoot apical meristem, acts as a long-distance signal for floral meristem identity. At SAM, FT-FD protein complex, based on signals from above said pathways in association with the signals from age-dependent and miRNA pathways, leads to the activation of master regulator gene of flowering AP1. The activation of genes involved in ABCDE model of floral organ differentiation, based on the directions of various cadastral genes lead to the development of floral organs. Thus, the sequential action of floral meristem identity genes, floral organ developmental genes, floral meristem size and organ number genes, floral organ pattern genes and cadastral genes leads to the flower development. This chapter sums up the gene interactions happening in leaf and SAM, leading to the development of a complete flower.

Introduction

Biochemical techniques are fundamental tools that allow scientists to investigate the molecular intricacies of biological systems, including DNA, RNA, and proteins. These techniques are essential for understanding cellular processes, genetic functions, and disease mechanisms. By employing biochemical methods, researchers can dissect complex biological systems at the molecular, cellular, and genomic levels, paving the way for advances in basic biology and therapeutic interventions.

Introduction to Molecular Biology Techniques Molecular biology is the domain of biology concerned with DNA replication, RNA synthesis (transcription), translation, and the role of proteins in cellular function, while molecular biology techniques are the keystones of modern biology, facilitating scientists to decode these molecular foundations of life. These molecular techniques aim to analyze and understand the structure, function, and interactions of biomolecules such as DNA, RNA, and proteins. These techniques facilitate an understanding of complex life processes such as gene expression, genetic variations, and cellular mechanisms. Researchers have used these molecular tools to unravel complex biological processes from genetic inheritance to cellular signaling pathways. The knowledge gained has been applied to solve challenges in various domains of biological science such as medicine, agriculture, and environmental science. During 1960’s methods to identify, isolate and manipulate molecular components were developed by molecular biologists. The field of molecular biology emerged in mid 20th century, driven by groundbreaking discoveries such as the deduction of the double-helix of DNA

Introduction

Nucleic acids, primarily DNA and RNA, are essential for the storage and expression of genetic information. Under physiological conditions, the amino and oxo tautomers of purines and pyrimidines predominate. Adenine a., guanine (G), cytosine c., thymine (T), and uracil (U) are the main building blocks of nucleic acids. Other building blocks include 5-methylcytosine, 5-hydroxymethylcytosine, pseudouridine, and N-methylated heterocycles. A -glycosidic bond connects D-ribose or 2-deoxy-D-ribose to the N-1 of a pyrimidine or the N-9 of a purine, with the syn conformers being the most common.

Nucleotides are the monomeric units of nucleic acids that contain a phosphate group attached to the sugar’s 3’ or 5’ hydroxyl. Extra phosphate groups form nucleoside diphosphates and triphosphates. These have high group transfer potential and help make covalent bonds. Cyclic phosphodiesters cAMP and cGMP act as second messengers. 3′ 5′ phosphodiester bonds link nucleotides to form polynucleotides, which have a directional 5′ and 3′ end. Four bases—A, G, C, and T—compose DNA, and hydrogen bonds (A to T, G to C) hold them together to form a double helix. Human DNA consists of approximately 3 billion base pairs organized into 23 chromosomes, encoding around 25,000 protein-coding genes and various non-coding RNAs (ncRNAs).

Introduction

Improvement of wheat grain quality depends on the knowledge of quality requirements of different end-use products and the genetic components controlling different quality traits. In previous chapters we have dealt in-depth with quality requirements of different end-use products and their genetic components. Depending upon the goal of quality improvement, different strategies are adopted to improve wheat quality. It depends upon the number of genes controlling the traits as well as the availability of the simple methods for phenotyping the traits especially during early segregating generations. In addition stability analysis of the traits across the environments is essential before we go for breeding. Constraints in time, cost, and sample availability usually necessitate the use of predictive tests during early generations, followed by milling and baking tests on advanced lines that have met a number of agronomic, disease and predictive quality criteria. Knowledge of germplasm lines having specific quality traits is needed to initiate breeding for the improvement of wheat grain quality for different end-use products. The quality requirements of different major end-use products are provided in the following table (Table 1).

Introduction

Food supply is a major concern in the near future as the human population touches 9 billion in 2050 and therefore, more food has to be produced. This has to be achieved in the face of climate change amounting to constant pressure of biotic and abiotic stresses. However, Swaminathan (2007) opined that science and technology can play a very important role in stimulating and sustaining an evergreen revolution leading to long-term increases in productivity without associated ecological harm. Rice is considered as global grain since it is consumed by more than half of the world population. In India rice supplies calorie requirement to more than 70 per cent of its population. This is evident from the fact that rice is cultivated in all the 30 states and 5 union territories of the Indian subcontinent of diverse ecologies ranging from below sea level to mountainous regions. Though India tops in rice acreage (43.61 mha) its productivity of 3.19 t/ha (rough rice) is far below world average of 4.12 t/ha and that of Asia’s average of 4.19 t/ha (Shobharani et al., 2010). This low productivity is mainly due to unfavourable ecologies of the varied ecosystems which, rice encounters during critical stages of its growth. Salinity and submergence are major abiotic stresses, next to drought, limiting rice production in South East Asia including India.

In India nearly 8 mha are salt affected of which 2 mha are coastal saline and 3.4 mha are sodic (Singh, 1994). Rice is predominant crop in these areas especially in vast stretches of eastern and western coasts of India. The presence of salts, in excess to plant growth, in the soil solution makes the soil detrimental to crop growth. The source of the excess salt may be from soil or irrigation water. The content and composition of salts (ions) in tandem with types of soil and weather conditions prevailing during the crop period decides the severity of salt stress. Similarly, f lash floods or short-term submergence regularly affect rice growing areas in South and Southeast Asia. Even more favorable irrigated areas experience flooding problems during the monsoon season. It is also prevalent in rainfed lowlands where most of the present day rice varieties do not survive complete submergence for more than a week. In India 30% of the rice growing area is prone to such menace resulting in severe yield losses (Neeraja et al., 2007).

Introduction

Over decades, improvement of domestic animal species has been done by selecting superior animals, mainly based on individual performance and their subsequent breeding to get progenies with higher production potential. Within the 20th century, understanding of inheritance of economic traits, factors influencing genetic potential and their interactions provided better criteria for selection and this has resulted into faster genetic gains. Several selection criteria which were composite ones based on the individuals as well as its relative performances were being used.

Introduction
Aquaculture has emerged as the fastest-growing sector in global agriculture. The total fish production worldwide includes both wild catches and aquaculture outputs. In recent years, fish production has consistently risen, reaching around 130.9 million tons, which accounts for 52% of the fish available for human consumption (FAO, 2024). Molecular breeding in fisheries and aquaculture utilizes cutting-edge genetic technologies to enhance favourable traits in aquatic species. This approach encompasses the application of molecular markers, genome-wide association studies (GWAS), and gene editing techniques to improve attributes such as growth rates, disease resistance, and resilience to environmental stressors. For example, marker-assisted selection (MAS) facilitates the identification and selection of superior broodstock by leveraging genetic markers associated with advantageous traits.

Introduction

Genetic programs in livestock have been extensively used to improve their productivity over the last 50 years. The traditional approach of breeding, based on quantitative genetics principle, has been very successful (Schaeffer, 2006), without knowledge of genes increasing or decreasing in herds. Effective progeny testing program and use of genetically proven bulls have made drastic genetic improvement in livestock populations. Further advances in computation for genetic merit have further added to improvement process. Livestock producers presently are focusing on overall development of livestock with improved health, production, reproduction and longevity and therefore, the traits are becoming the part of selection program (Decker et al., 2009). Advancement in molecular biology along with high-throughput genotyping has led to discovery of a number of single nucleotide polymorphisms (SNPs) in livestock (Van Tassell et al., 2008). SNP arrays covering the entire genome may explain most of the genetic variation in important traits of livestock (Meuwissen et al., 2001). These SNPs may act as molecular markers and be used as a substitute for phenotypic selection. This process, in a broad sense is known as molecular or marker-assisted breeding and describes selection strategies including marker-assisted selection (MAS) and genome wide selection (GWS) or genomic selection (GS).

Spectacular productivity gains have been achieved in wheat and rice in south and south-east Asia and also several other developing countries in Latin America and central Asia due to introduction of dwarfing genes in these two crops purely through conventional plant breeding approaches and these developments were christened as “Green Revolution” (Reynolds and Borlaug, 2006). The wheat breeding progrmme was being spearheaded by Norman Borlaug at CIMMYT (International Maize and Wheat Improvement Centre, Mexico) supported by Sanjay Rajaram and the rice breeding programme was under leadership of Gurdev Singh Khush at IRRI (International Rice Research Institute, Manila, Philippines) coinciding with these exciting developments during mid-sixties to mid-seventies. In recognition of these quantum jumps in yield of wheat and rice, Borlaug was awarded Nobel Peace Prize for Peace in 1970. Later on World Food Prize was instituted by joint efforts of Borlaug and his colleagues to honour Agricultural Scientists and others on pattern of Nobel Prize who had made significant contributions to sustainable food production and food and nutritional security globally. M. S. Swaminathan happened to be Director General, Indian Council of Agricultural Research when Green Revolution was taking roots in India and because of his enormous contributions to provide effective leadership to ensure that Green Revolution happened in India, M. S. Swaminathan is credited as “Father of Green Revolution in India” and he was the first recipient of World Food Prize in 1987 for spearheading the introduction of high-yielding wheat and rice varieties in India. G. S. Khush along with Henry Beachell received 1996 World Food Prize for achievements in enlarging and improving the global supply of rice during a time of exponential population growth and Sanjay Rajram was the 1914 World Food Prize recipient for his scientific research that led to huge increase in world wheat production.

ABSTRACT

Black pepper (Piper nigrum L.), known as the ‘King of Spices’ is an important export- oriented spice crop, valued for its medicinal and condimental properties. A perfect protocol for the rapid in vitro multiplication of this plant is available. However, systemic bacterial contamination is the single major constraint in the large scale in vitro production of plantlets. Based on morphological and biochemical characters, this bacterium was identified as Beijerinckia indica It grows profusely on nitrogen-free Jensen’s agar and solubilizes CaCO in the medium by acid production. It is resistant to a range of antibiotics and produces indole acetic acid. The bacterium is slow growing and has pH optima of 5.5 and temperature optima of 27oC. It has both endophytic as well as epiphytic association with the plant, the colonization being more in the stem and petiole. A single plasmid of 4.0 kb size was isolated from the bacterium and characterized. Competent cells of E. coli DH5a, transformed with this plasmid survived on Jensen’s nitrogen free agar, indicating its ability to fix atmospheric nitrogen. We stipulate that the nif genes are located on the plasmid of the bacterium. Since endophytic bacteria are known to stimulate plant growth through antagonistic activity against pathogens, production of growth promoting substances and inducing systemic resistance in several other agricultural crop species, the symbiotic association between Bejerinckia indica and black pepper could be further exploited through integrated nutrient management for improved growth and yield of this spice crop.

ABSTRACT

An effort was made to characterize twelve ber genotypes using RAPD markers. Of the twenty random decamer primers tested, 17 generated polymorphic bands, while rest of the primers showed monomorphic bands. The primers that amplified all the 12 genotypes were OPC-20, OPD-1, OPD-3 and OPD-4. The size of amplified DNA fragments varied from 0.56-4.26 kilobase pair. In total, 109 bands were obtained, of which 85 bands were polymorphic, while 24 bands were monomorphic. For the cultivars tested between 2-9 bands were obtained for each primer with an average of 5.45 bands per primer. The highest number of bands (9) were generated by OPA-4 and OPD-3. With un-weighted group method using arithmetic mean (UPGMA) cluster analysis, the twelve ber genotypes fell into four major clusters. The pair wise dissimilarities of ber genotypes showed that genotypes G-9 and G-8 were close to each other. Maximum dissimilarity was observed between the genotypes G-8 and G-12.

Molecular characterization involves the use of techniques that are available to analyze variation in plants and animals at the DNA level. Differences in gene sequences can be directly observed and described with a precision previously impossible to achieve. Many of the techniques that have been developed have already been used in evolutionary and taxonomic studies. They have immense value in studies of accessions identity and for the detection of novel useful variation in the plant germplasm. Molecular markers provide genetic information of direct value in key areas of conservation both ex situ and in situ. For ex situ conservation the key issues are:

ABSTRACT

The study was conducted to fingerprint and to analyze genetic diversity among 20 genotypes. of Psidium guajava and two species P. friedrichsthalianum and P. cattleianum using random amplified polymorphic DNA. Genomic DNA was isolated using modified CTAB method and polymerase chain reaction was carried out using standard protocols. In all 41 primers were used, 39 of which amplified 376 alleles with 347 polymorphic alleles. All the primers discriminated between two and more genotypes. Primers produced 2-16 alleles. The size of amplified DNA alleles ranged from 0.12-2.2 kilobase pairs. Polymorphic index content value was found to be maximum for primer OPB-12 (0.916). In the dendrogram all the 22 genotypes were grouped into two major clusters. Cluster 1 comprised of Spear Acid, Apple Colour and P. friedrichsthalianum, while Cluster 2 constituted rest of the 19 genotypes. Thus, RAPD markers detected a high level of polymorphism and can be used for breeding of improved guava varieties.

ABSTRACT

Piper colubrinum is a wild relative of the cultivated species of black pepper, Piper nigrum. The enzyme hydroxy methyl glutaryl Co A reductase which catalyses mevalonate synthesis, is the key enzyme in isoprenoid biosynthesis.This is the rate limiting step in the pathway which leads to the formation of sesquiterpene phytoalecins, a group of plant defense metabolites. Piper colubrinum is known to be tolerant to the dreaded disease called foot rot, incited by Phytophthora capsici. The hmgr gene is reported to confer resistance to fungal pathogens. Hence we made an attempt to isolate gene encoding this enzyme. cDNA was synthesised by reverse transcription from total RNA of P.colubrinum using oligo dt primers. Specific degenerate primers designed based on the conserved boxes among various plant species were used for amplifying hmgr gene from the cDNA. The 700 bp amplicon was cloned in pGEMT vector and sequenced with T7 primer. Multiple sequence alignment using clustal W 1.8 revealed homology of the cDNA fragment with hmgr genes in several other plant species. Maximum similarity was observed among P. colubrinum, Solanum xanthocarpum and Nicotiana tabacum. The cDNA library of P. colubrinum constructed in lTriplEx2 when screened with radiolabelled hmgr amplicon, yielded positive signals. Attempts are being made to isolate full length gene from these clones, which could be later used for imparting biotic stress tolerance to cultivated crop species.

Constituents of meat
i. Water- 75%
ii. Protein- 19%
iii. Soluble and non-protein substances- 3.5%
iv. Fat- 2.5%
• The muscle fibre is important unit of muscular tissue consisting of
a) Myofibrils- formed protein structures embedded in sarcoplasmic fluid
b) Sarcoplasmic reticulum- a fine system of tubules
c) Sarcolemma- a very thin membrane surrounding the myofibrils and around the exterior side of this membrane, the connective tissue is found
• 19% of protein in the muscle is muscle fibre (Table 11.1)
• α-alanine, glycine, glutamic acid and histidine are the major free amino acids present in the fresh muscle

INTRODUCTION

All plant species grown on this universe are attacked by insect-pests and diseases, resulting huge yield losses in agriculturally important species. Among diseases, extensive yield losses occurred due to soil borne fungal plant pathogens. Soil borne fungal pathogens infect roots or stem bases, their dispersal and survival stages are primarily confined to the soil. Although many soil pathogens may also produce air or water dispersed spores which results in long distance dispersal. Soil borne fungal diseases are specifically those diseases where the soil borne fungi has the capacity to survive in soil for long periods in the absence of their hosts, or survive in the soil outside of seed or host residues, but infection and symptom expression are confined to the subterranean organs of the plant. Soil borne fungi may be divided into two classes: i) The  soil inhabiting fungus which is characterized by its ability to survive indefinitely as saprophyte (e.g. Rhizoctonia, Sclerotium) and ii) The soil invading or root inhabiting fungus which is characterized by an expanding parasitic phase and a declining saprophytic phase after  the hosts death.