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The paddy grain contains a rough outer covering called husk. It accounts for about one-fifth to one - fourth of the weight of paddy. The inner kernel, called brown rice or dehusked rice, again contains some soft outer layers, jointly called bran. It accounts for about 6-8% of the brown rice weight, including the small germ (1-2% by weight) located in one corner. Rice milling is the process of removing the husk and a part of the bran from paddy in order to produce edible rice. Rice milling system ranges from the home-scale to the large, complex modern rice-processing installations. They include hand-pounding equipment, single hullers, emery sheller-cum-huller mills, emery sheller-cum-cone polisher mills and the modern rubber – roller rice mills. Rice milling industry does not only mill rice but it also carries many other essential functions, such as cleaning and grading, drying, storage, quality control etc. for the production of better quality rice. All these processes are discussed in this paper.

Unlike other food grains, rice is mostly consumed as cooked whole grain, Milling technology is therefore geared to obtain maximum outturn of milled rice and to reduce breakage to the minimum. The single huller mills are by and large located in villages or in localities where paddy is custom milled for produces and they still handle the bulk of the country’s production. The large-capacity rice mills located in urban or semi-urban areas for commercial milling are of ½ to 4 tones per hour capacity and handle the rest of the paddy milled. Some battery hullers are still in operation as large commercial mills, specially for milling parboiled paddy.

Introduction

In view of the accepted importance of analysis, the workload on soil, plant and water testing laboratories has increased considerably in recent years. Therefore, analytical methods have needed to be accelerated through the automation of instruments. Almost all instruments either contain inbuilt computers or can interface directly with micro processors, thereby simplifying instrument operation and providing versatility for the analyst. Most operations can be performed through keyboard commands. This type of instrument automation enables:

For Indian foods

Food processing industries are the fastest growing in India. India is the largest producer of milk, bananas, mangoes, guavas, papaya, ginger and okra. It is the second largest producer of wheat, rice, fruits, vegetables, tea, sugarcane and cashew nut. It is the third largest producer of cereals, coconut, lettuce, chicory, nutmeg, mace, cardamom and pepper at the global level (Highlights of Agriculture Census, 2010-11, http://pib.nic.in/newsite/PrintRelease.aspx?relid=132799). Most part of the income is spent on foods. It is important to establish and nurture mutually beneficial relationships with global food processing, food retail and related supply chain organizations. This will in turn help in the realization of significant business growth opportunities in India, through newer technologies, innovations and ways of value additions. The geographical location of India helps in the export of items to other countries. It is connected to Europe, Middle East and Africa from the western coast and to Japan, Singapore, Thailand, Malaysia, Korea, Australia and New Zealand from the eastern coast. Food processing is a priority sector for the Indian Government, especially in recent times with “Make in India” initiative.The country is considered as one of the most favourable markets because of the easy and affordable credit and other fiscal incentives. The total consumption of food and beverages in India is US$ 369 billion which is expected to increase to US$1.142 trillion and the output in the food processing sector might increase to US$ 958 billion by 2025. This offers a vast market opportunity by the Indian food processing, food retail, transport, logistics and related infrastructure sectors to players in the food processing value chain. The market for plant and machinery in the food processing sector is estimated in the year 2024-25 to be USD 51.41 billion as compared to the current value of USD 17.3 billion (2016-17).

Introduction There are multiple methods or trapping technologies available for pest management in agriculture. Some of the method discussed in literature are described here. Insect pests in an agricultural field can cause damage to the crops by infecting the crops with diseases and thus may affect adverse impact on its quality. Nowadays, farmers set up insect traps like sticky papers that comes in different colours such as yellow, green and blue to monitor the number of pests. Different insects are specifically/ particularly attracted to the colours of the sticky paper commonly such as yellow or blue (Espinoza et al?, 2016).

In addition to the conventional treatment methods i.e., surgery, chemotherapy and radiotherapy, there are some adjuvant targeted therapies which block the growth of cancer by altering the individually expressed specific molecules responsible for tumor cell proliferation, survival, metastasis or microenvironment. The majorly studied adjuvant therapies include use of hormones, tyrosine kinase receptors, anti-cyclooxygenases, anti-tumor suppressor gene p53 and epithelial-mesenchymal transition inhibition.

The main aim of hormonal therapy (Table 2) is to inhibit the hormone induced stimulation of carcinoma cells, which could be achieved either by ovariohysterectomy or different treatments like use of specific estrogen receptor modulators (SERMS), aromatase inhibitors for suppression of estrogen synthesis etc. A commonly used estrogen receptor (ER) antagonist drug tamoxifen for treatment of ER positive breast cancer in women, has also been tested against CMTs. However, it is not a viable treatment option in dogs due to associated side effects. Ovariohysterectomy is considered as a better and practical solution. The use of hormonal therapy in CMTs is based on the evidence of hormone dependency of these tumors as well as lessons learnt from hormonal therapy outcomes from human breast cancer. This therapy significantly ameliorates the recurrence of breast cancers and prolongs the survival rates in women having breast cancers positive for hormone receptors. However, the results of the canine investigations, which are all retrospective and non-randomized, are contradictory. Detailed research and prospective randomized trials, where effect of OHE is studied in context of hormone receptor status, are required to determine the role of hormonal therapy in CMTs.

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.

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.

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.

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

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

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.

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

• 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

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

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.

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.

Abstract

The conventional methods of pathogen identification have often depended on identification of disease symptoms, isolation and culturing of the organisms, and identification by morphology and biochemical tests. The major limitations of these culture based morphological approaches, however, are the reliance on the ability of the organism to be cultured, the time consuming nature and requirement of extensive taxonomic expertise. Furthermore, diagnosis of plant diseases can be even more difficult with asymptomatically infected propagative materials such as tree grafting stocks or potato tubers. The use of molecular methods can circumvent many of these shortcomings. Accordingly, there have been significant developments in the area of molecular detection of plant pathogens in the last three decades. The polymerase chain reaction (PCR) which revolutionised molecular diagnostics and biological sciences. In the last decade the range of targets that can be diagnosed using diagnostic PCR have grown tremendously. The very flexibility and application specific variations in the basic theme of the system have allowed the development of many PCR variants adapted to wide range of applications. Furthermore, diagnostic PCR has been greatly improved by the introduction of the second generation PCR, known as the Real time PCR where closed-tube fluorescence detection and quantification during PCR amplification (in real time) is possible eliminating the need for laborious post-PCR sample processing steps which greatly reduces the risk of carryover contamination. Using Real Time PCR, it is possible not only to detect the presence or absence ofthe target pathogen, but it is also possible to quantify the amount present in the sample allowing the quantitative assessment of the number of the pathogen in the sample. Enumerating the pathogen upon detection is crucial to estimate the potential risks with respect to disease development and provides a useful basis for diseases management decisions. Crops can be attacked by many pathogens which, in addition, often occur in complexes. Therefore, many disease diagnostic applications require simultaneous detection and quantification of several targets. Methodological limitations, however, are in many cases the reason for developing simplex or assays designed for only few targets. The DNA Microarray technology, originally designed to study gene expression and generate single nucleotide polymorphism (SNP) profiles, is currently a new and emerging pathogen diagnostic technology, which in theory, offers a platform for unlimited multiplexing capability. It is viewed as a technology that fundamentally alters molecular diagnostics. The fast growing databases generated by genomics and biosystematics research provides unique opportunity for the design of more versatile, high-throughput, sensitive and specific molecular assays which will address the major limitations of the current technologies and benefit plant pathology.

ABSTRACT

Central Plantation Crops Research Institute at Kasaragod maintains largest collection of coconut germplasm accessions representing different geographical regions. So far, morphological and isozyme markers were employed for germplasm characterization. To overcome the difficulties associated with the morphological markers, DNA based molecular markers are presently employed for germplasm characterization. In the present study, Inter Simple Sequence Repeat (ISSR) markers are utilized to estimate the genetic diversity among South East Asian germplasm accessions. Nineteen ISSR primers were used to amplify 8 germplasm accessions (4 palms per accession referred as population). The PCR products were electrophoresed in 1.80 % agarose gels. Binary data were analyzed using the software POPGENE ver. 1.32. Dendrogram was constructed based on Nei’s unbiased measure of genetic distance. Nineteen ISSR primers detected a total of 85 polymorphic markers across 32 individuals belonging to eight populations. The average genetic distance among the eight populations ranged from 0.7908 to 0.9327 with a mean of 0.8540. Of the 28 pair wise comparisons the accessions Laguna Tall and Kongthienyong Tall (KTYT) showed the highest genetic identity (0.9327). The lowest identity (0.7908) was between San Roman Tall (SNRT) and Philippines Dalig Tall (PDLT). The Shannon’s index ranged from 0.1615 to 0.299. Diversity parameters viz. number of effective alleles, gene diversity, number of polymorphic markers were calculated for each population. The dendrogram constructed based on the genetic distance revealed clustering of Kongthienyong Tall (KTYT) and Laguna Tall (LAGT) while Philippines Dalig Tall (PDLT) was positioned separately. In the genetic improvement programmes the diverse accessions can be used in hybridization for increased heterosis.

ABSTRACT

Purine Nucleoside Phosphorylase (PNP) is an enzyme that functions in the purine salvage pathway by catalyzing the phosphorolysis of purine nucleoside thereby releasing the purine bases and phosphorylated sugar. Interest in PNP as a drug target arises from its role in T-cell proliferation and T-cell mediated autoimmune diseases. Recently, we have isolated the compound, coixol, from the plant Scoparia dulcis L. and its three-dimensional structure has been elucidated. As the structure of the coixol mimics the structure of PNP inhibitors, we have undertaken the molecular modeling studies of this compound with Human PNP, as a screening test for further in vivo studies. Generally PNP inhibitors have been synthesized with a ribose sugar moiety attached to them. As the plant Scoparia dulcis L. contains glucose and rhamnose (six membered ring), these sugar moieties are also included along with ribose in the presen study. In order to understand the binding mode and interactions of the isolated compound attached with different sugar groups, we have carried out the docking studies with Human PNP. The interactions between the ligand molecules and active site residues of Human PNP are similar to those of solved complexes and the energy values are also comparable, which clearly indicate that these ligands may act as inhibitors.

Summary

Molecular evolution is the process of evolution at the scale of DNA, RNA, and Protein. Molecular evolution emerged as a scientific field in the 1960s as researchers from molecular biology, evolutionary biology, and population genetics sought to understand recent discoveries on the structure and function of nucleic acids and protein. It covers two broad areas of study : the evolution of macromolecules, and reconstruction of the evolutionary history of genes and organisms. The evolution of macromolecules refer to the characterization of the changes in the genetic material (DNA or RNA sequences) and its products (Proteins of RNA molecules) during evolutionary process, and to the rates and patterns with which such changes occur, and also the mechanism responsible for such changes. The second area also known as “molecular phylogenetics”, deals with the evolutionary history of organisms and macromolecules as inferred from molecular data and the methodology of tree reconstruction.

Summary

Molecular farming is the large scale production of pharmaceutically important and commercially valuable proteins in plants and animals. Molecular farming in plants has the potential to provide an inexpensive and convenient system in the production of unlimited quantities of recombinant proteins for use as therapeutics, diagnostics, vaccines, antibodies, plasma proteins, cytokines and growth factors. Plants are also being used for the production of oils, starches, plastics, enzymes for food processing and other uses and spider silk etc. However, quality and safety of the final product and wider effects of molecular farming on health and environment need to be addressed. The benefits of molecular farming should not be outweighed by risks to human health and environment.

4.1 Introduction

Many important traits such as yield, quality and some forms of disease resistance are controlled by many genes and are known as quantitative traits or characters (also called ‘metric’,‘polygenic,’ ‘multifactorial’ or ‘complex’ traits). The regions within genomes that contain genes associated with a particular quantitative trait are known as quantitative trait loci (QTLs). The identification of QTLs based only on conventional phenotypic evaluation is not possible. A major breakthrough in the characterization of quantitative traits that created opportunities to select for QTLs was initiated by the development of DNA (also called molecular) markers in the 1980s.

One of the main uses of DNA markers in agri-horticultural research has been in the construction of linkage maps for diverse crop species. Linkage maps have been utilised for identifying chromosomal regions that contain genes controlling simple traits (controlled by a single gene) and quantitative traits using QTL analysis. The process of constructing linkage maps and conducting QTL analysis–to identify genomic regions associated with traits–is known as QTL mapping (also called ‘genetic,’ ‘gene’ or ‘genome’ mapping). DNA markers that are tightly linked to agronomically important genes (called gene ‘tagging’) may be used as molecular tools for marker-assisted selection (MAS) in plant breeding. MAS involves using the presence/absence of a marker as a substitute for or to assist in phenotypic selection, in a way which may make it more efficient, effective, reliable and cost-effective compared to the more conventional plant breeding methods. The use of DNA markers in plant (and animal) breeding has opened a new realm in agriculture and horticulture called ‘molecular breeding’.