eChapters

Hypothesis testing enables researchers to determine whether apparent climatic or agricultural differences are statistically meaningful. Parametric tests are appropriate when data satisfy assumptions such as normality and homogeneity, whereas non-parametric tests are useful for irregular, ranked or non-normally distributed observations. This chapter discusses commonly used procedures, assumptions, selection criteria and interpretation. Applications include comparing weather conditions, evaluating crop responses, detecting rainfall or temperature trends and assessing environmental change. Methods such as t-tests, Mann-Whitney, Wilcoxon, Kruskal-Wallis and Mann-Kendall tests are relevant to agroclimatic research. Appropriate test selection improves analytical reliability and supports evidence-based decisions concerning climate variability, crop performance and agricultural adaptation.

This chapter provides an insight into the genotypic and phenotypic correlations between plant traits. It incorporates the study of genotypic and phenotypic path analysis and the understanding of genetic variability, all illustrated through practical examples in R, relevant to plant breeding research.

Path Analysis

Path analysis explains not only the direct impact of one character on another but also indirect effects mediated through other variables in the system. The approach is similar to the analysis of variance and is sometimes referred to as the analysis of correlation coefficients. A notable feature of path coefficients is that they are standardized partial regression coefficients, devoid of units. This standardization allows for the direct effects of different variables to be compared and ranked based on their magnitude. This approach was first applied in plant studies by Dewey and Lu in 1959, particularly to examine the factors influencing seed yield.

Path Coefficients

In the computation of path coefficients, a path diagram is translated into a series of simultaneous equations. These equations reveal the direct and indirect contributions of causal variables to the outcome. For example, in the field of plant breeding: consider the yield of forage (Y) being influenced by different variables. These could include the leaf length (X1), leaf width (X2), and number of leaves per plant (X3).

An amine reacts with a carboxylic acid to form an amide. Similarly, the amino group  on one amino acid molecule reacts with the carboxyl group of another amino acid  to form a compound called peptide. A peptide bond is an amide bond that forms when the –COO- group of one amino acid reacts with the -NH₃+ group of another amino acid. The resulting compounds are called peptides. Even after this there is a reactive amino group and a carboxyl group in the peptide. If these groups react further a poly peptide can form and later a polymer called protein can form.

India is recovering from the euphoria of the Green Revolution and battling the residual effects of the extensively used chemical fertilizers and pesticides in the country’s soils. The decade from 1980 to 1990 alone saw the area under pesticides in India, increased a whopping 20-fold, from six million hectares to 125 million hectares. After a high annual consumption of nearly 75000 MT reached in the early ’90s, interventions in the form of Integrated Pest Management (IPM) practices have only now started to show a declining trend in the use of pesticides in India. Interestingly, India’s consumption of pesticides per hectare is low (0.288 kg/ha) when compared with world averages—0.5 kg/ha against Korea’s 6.60 kg/ha and Japan’s 12.0 kg/ha. According to the pesticides industry statistics, India spends US $3/ha on pesticides compared with US $24/ha spent by Philippines, US $255/ha spent by South Korea and US $633/ha by Japan. Yet, despite a comparatively low use of pesticides in India, the contamination of food products in the country is alarming. About 20 per cent of Indian food products contain pesticide residues above tolerance level compared to only 2 per cent globally. No detectable residues are found in only 49 per cent Indian food products compared to 80 per cent globally. A pesticide is any substance or mixture of substances intended for preventing, destroying, repelling or mitigating any pest. Though often misunderstood to refer only to insecticides, the term pesticide also applies to herbicides, fungicides and various other substances used to control pests.

Pesticides and their metabolites have received particular attention in the last few years in environmental trace organic analysis because they are regularly detected in food products, surface/ground waters and soil strata throughout the world as consequence of their widespread use for agricultural and nonagricultural purposes. So it is the need of the hour to study the levels of pesticides residues in plants, water and soil and their fate in environment after its degradation.

It would be necessary to work out tolerance limits of pesticides residues in/on crops, soil and water and the efforts, therefore, are directed towards various residue analytical methods like TLC, GLC and HPLC etc. which are suitable for the purpose.

Introduction

To keep pace with the ever-increasing demand for crop yield by the exploding population, use of chemical fertilizers and pesticides in agricultural production has become indispensable.  Production cost of agriculture has skyrocketed owing to the abandoning of green, organic farmyard manure and use of chemicals. However, the problems associated with chemical pesticides are abundant. The excessive application of chemical fertilizers causes soil sealing, fertility diminishing and residual problems. The leftover chemical fertilizers and pesticides have seriously affected the quality of agricultural products, people’s health and caused environmental pollution.  The over use of fertilizers has also damaged the soil’s original micro-ecological balance and deteriorated the diseases spread by soil.  While some pesticides must be abandoned because of their unacceptable non-target effect, there will always be a need in agriculture for safe and selective chemicals to limit the effects of pests.  More significantly, it is becoming increasingly more difficult and expensive to find new kinds of synthetic chemical pesticides.  Implications of chemical pesticides in ecological, environmental and human health problems have increased public awareness and concern regarding the continued use of agrichemicals that are damaging to human or  environmental health thereby obviating the search for effective alternative approaches which have minimal deleterious effects, more environmentally friendly, and will contribute to the goal of sustainability in agriculture.  In this line Plant growth-promoting rhizobacteria (PGPR) present immense potential and promise as effective substitutes for chemicals.  PGPR enhance plant growth and survival, control soil-borne fungi, and induces systemic resistance to phytopathogens and is used as inoculants for biofertilization, phytostimulation and biocontrol.

Phenol is normally a benzene ring containing an –OH group, and hence an aromatic alcohol. The term phenolic refers to similar aromatic compounds with one or more -OH groups. Phenolics constitute one of the most widespread classes of secondary metabolites. Commonly talked about class of compounds like anthocyanins, flavonoids, lignins, tannins, coumarins and chalcones are all phenolic substances. Phenolics are water insoluble substances. However, the water solubility increases with the increase in the number of -OH groups. Phenolics absorb electromagnetic radiation strongly. Many of the phenolics absorb in the visible part of the spectrum (Ex. anthocyanins) and are coloured. Phenolics are produced in plants by 1. Shikimate pathway through phenylalanine (C6.C3)  and 2. Acetate/ malonate pathway.

In organic chemistry, phenols, sometimes called phenolics, are a class of chemical compounds consisting of a hydroxyl group (—OH) bonded directly to an aromatic hydrocarbon group. The simplest of the class is phenol, which is also called carbolic acid C₆H₅OH. Phenolic compounds are classified as simple phenols or polyphenols based on the number of phenol units in the molecule.

Phenols constitute a class of aromatic organic compounds having at least one hydroxyl group attached directly to the benzene ring.

Phospholipids are the most abundant lipids of biological membranes. They serve primarily as structural components of membranes and are never stored in large amounts. As the name of phospholipid implies, this group of lipids contains phosphorus in the form of phosphoric acid groups. The major phospholipids found in membranes are the phosphoglycerides (phosphatides) (Fig.1). Which have two fatty acid molecules esterified

Phosphorus is present in soil both in inorganic form and organic form. The inorganic P can be divided into different pools. The major active inorganic forms are: P bound to aluminium (Al-P), iron (Fe-P), calcium (Ca-P) and silicate minerals and relatively less active forms are occluded and reductant soluble forms of P. On the other hand, the principal organic P compounds present in soil are (i) inositol phosphate, (ii)phospholipids, (iii)nucleicacid and other unidentified esters and phosphoproteins.

22.1 Determination of Available Soil P

The availability of soil P to plant varies greatly depending upon the reaction, minerological composition and amount of the soil colloid. Very little P is present in the soil solution except in recently fertilized or sodic soils. The type of phosphate ions present in the soil solution depends on the soil pH. In soils of neutral to slightly alkaline pH, HPO₄^2-ion is the dominant form. In slightly or moderately acidic soils, both HPO^-and HPO^2-ions prevail. At strongly acidic soil HPO 244 24 ion tends to dominate, while above pH 9.0, the PO₄^3-ion becomes more important - than H₂PO₄ .

As the P is drawn from soil solution largely through diffusion by the plant, it is replenished from solid phase pool of available P. P fertilizer is added to recharge this pool.

Phosphorus (P) is a critical nutrient in crop production, due to its low bioavailability in soils (Feng et al., 2004). Phosphorus is the vital component of DNA, RNA, ATP and photosynthetic system and catalyses a number of biochemical reactions from the beginning of seedling growth through to the formation of grain and maturity. Many factors influence soil P availability like type of parent material from which the soil is derived, degree of weathering and climatic conditions. In addition to this, erosion, crop removal and phosphorus fertilization and soil phosphorus levels also affect P availability in soil. Rock phosphate is the key raw material used for manufacturing phosphatic fertilizers on which the food production depend.

We do not know when intercropping began nor why early civilizations fostered its use. Whether by design or accident, intercroppinq dominated early agriculture and is still practiced in many areas of the world. With the advent of “modern” agriculture, intercropping began disappearing from many areas. This shift was driven primarily by mechanization and specialization. Despite pressures to abandon intercropping, it has survived and flourished Inereasing interest in sustainability and environrnental concerns have drifted attention back to intercropping as a means of better utilization of resources while preserving the environment.
Through intercropping, farmers can achieve the full production of the main crop and also an additional yield (bonus) associated with an increased plant population of the second component. Hence, intercropping can increase incomes obtained by smallholder farmers in areas where labor is not shortage, through reduction of economic risk and market fluctuation resulting from growing a single crop which is more prone to natural hazards and helping the farmers in better utilization of land by having more than one crop produced per unit area. Though all intercrops produced higher productivity, the farmers could better use the appropriate population of component crops in intercropping systems in order to maximize yield of both crops as well as total productivity. It is, therefore, important to support intercropping systems with appropriate agronomic practices such as timely irrigation, pest protection and the likes to sustain the cropping system in the countries where labor is not problem for proper management in general even though sometimes sole cropping may became more productive.

MOST OF THE ENERGY FOR LIFE COMES FROM SUNLIGHT

Total rate of energy delivery from sun to earth (at the top of the atmosphere) = 175,000 terrawatts

Terrawatt = 10^12 watts

Rate of energy capture by plants from the sun = net primary productivity (NPP) = 100 terrawatts

Only ~ 0.06% of sunlight is captured

Captured in chemical bonds, especially in sugar

Small amounts of energy are available to specialized microorganisms from chemical reactions not linked to sunlight

It is estimated that 99% of the energy used by living cells comes from the sun

Incorporation of sunlight into chemical bonds occurs through the process of photosynthesis

“Invented” by cyanobacteria about 2 billion years ago

Photosynthesis is a very important parameter in plant physiological studies. It is the only process in nature which utilizes solar energy and converts it into chemical energy. It has a direct bearing on plant productivity. By understanding the process of photosynthesis, manipulation of productivity can be made possible.

1. Measurement of Photosynthesis Rate

Measurement of CO₂ uptake provides an alternate and direct method of measuring productivity, with important advantages over measurements of change in dry weight. It is instantaneous and non-destructive.

Infra Red Gas Analyzer (IRGA) is an equipment which is most widely used for the measurement of photosynthesis in situ in the field or in detached leaves under laboratory conditions. It is less time consuming and reliable. It can also be used for the measurement of rate of respiration and CO₂ compensation concentration (CO₂ CC), provided a little alteration is made in the chamber.

Introduction

Drought is the most important abiotic factor that adversely affect growth and crop production. Drought stress can altered the normal physiological processes that influence one or a combination of biological factors for yield and yield attributing traits (Ashraf, 2010). The abnormal metabolism due to stress may reduce plant growth (Claves et al., 2002). Production is limited by environmental stresses, according to different scholar estimates, only 10 per cent of the world’s arable land is free from stress, in general, a major factor in the difference between yield and potential performance, environmental stresses. Drought is one of the most common environmental stresses that almost 25 per cent of agricultural lands for agricultural farm products in the world are limited (Loresto, 1976; Chaves, 2002). Drought occurrence in India is also very frequent. Drought occurred in past 1967, 1968, 1969, 1972, 1974, 1979, 1987, 2002, 2009 and had considerable impact on food grain production. For example, the drought of 1966-67 reduced overall food grains production by 19%. The drought of 1972-73 reduced the food grains production from 108.95 million tonnes to 95 million tonnes, causing a loss of about $ 400 million $. The 1987 drought in India damaged 58.6 million ha of cropped area affecting 285 million people (Ray et al., 2015). Drought in 2002 has reduced food grains production to 174 million tonnes from 212 million tonnes resulting in decline of 3.2% GDP (Rathore et al., 2009; Ray et al., 2015).

The water deficit reduces crop yield due to decrease in photosynthetic area, decreased radiation use efficiency and harvest index (Earl and Davis, 2003). Drought stress affect the water balance and plant metabolisms. Plants under drought conditions use various changes to tolerate stress conditions and increase drought tolerance which includes changes in whole plant, tissue, at physiological and molecular levels. Appearance of a single or a combination of inherent changes determines the ability of the plant to stand under aridity conditions. Tolerant plant adjusts its water balance by osmotic adjustment, deep root systems and by transient leaf rolling.

The seed yield, along with the rate of application and uptake of nutrients, is used to determine the following parameters for nitrogen or other nutrients:

Partial Factor Productivity (PFP) (kg seed/kg N applied): Partial Factor Productivity (PFP) is a measure used in agriculture to assess the efficiency of nutrient use, particularly nitrogen or other essential nutrients, in crop production. It is calculated as the ratio of the seed yield to the rate of nutrient application. The formula for PFP is:

*A higher PFP value indicates greater efficiency, meaning that more crop yield is produced per unit of nutrient applied. This is desirable as it implies that the nutrient is being used more effectively by the crop.

Agronomic Efficiency (AE) (kg seed/kg N applied): Agronomic Efficiency is a measure used to evaluate the effectiveness of nutrient application in increasing crop yield. It specifically assesses the yield gain per unit of nutrient applied. The formula for AE is:

Introduction

Phenolic compounds have been shown to be of importance in regulation of plant growth, development and metabolism, therefore now they are not considered as passive by products of any catabolic or anabolic processes. Salicylic acid is one of them and it is a naturally occurring phenolic which has received much attention due to its association with economically important plant responses to disease and other stresses (Raskin, 1992; Borsani et al., 2001; Clarke et al., 2004). Centuries before medical scientists had identified numerous therapeutic effects of salicylates. Leaves and barks of willow tree were used by women as a pain reliever during child birth in 4th century B.C. It also cured aches and fevers. Due to a number of curative properties of willow bark, in 1828 Jahann Buchner, a scientist from Munich had isolated a small amount of silicin - a salicylic alcohol glucoside, the major salicylate in willow bark. In 1838, Rafaela Piria had given the name salicylic acid (SA), from the Latin salix, a willow tree. Further during 19th century SA and other salicylates, mainly methyl esters and glucosides easily convert to SA, isolated from a number of plants. Salicylic acid has an aromatic ring which bears a hydroxyl group or its functional derivative (Fig. 1).

INTRODUCTION

Iron in the terrain’s crust is more oxidized now than it was when life evolved. It has been hypothesized that dissolved ferrous iron could have been a convenient oxygen acceptor and that deposition of oxidized iron in sediments must have taken place before oxygen could have entered the atmosphere in significant quantities. Obviously, during early evolution on this planet, the essential elements are present only in reduced form. Today a number of elements are present only in a highly oxidized form and considerable energy must be expanded to reduce them to a form similar to that on early earth which plants can utilize.

Iron represents essential elements which are usually available in oxidized form but must be reduced, often using metabolic energy, before they can be utilized. For the first time, Gris (1844) observed yellowing of grapevine leaves in absence of iron in the nutrient solution in which these plants were growing. Later, iron was reported to be essential for diverse group of plants. Due to a great variation in iron requirement by different plant species, it is difficult to decide whether iron is a macro or micronutrient.

Through green revolution, we have developed high yielding varieties albeit with high nutrient requirements putting much more reliance on chemical fertilizers. The major challenge facing plant biology right now is to improve crop production and to feed an expanding world population. This is against a background of pressure on agricultural land use and climate change having negative impacts on growing conditions. The adverse effects of agriculture, and specifically fertilizer use, include damage to the environment, a large carbon footprint for the manufacture and use of agrochemicals, and the utilization of non-renewable resources. One solution is to increase the area of land for agriculture, as well as increasing production while maintaining the current rate of inputs; however, this is predicted to have substantial negative impacts on the environment (Tilman et al., 2002), is unsustainable in terms of phosphate use, and would have a huge economic footprint in terms of energy demands for nitrogenous fertilizer production. The challenge is to increase yield, decrease inputs, and improve resistance to abiotic and biotic stresses. Improving crop nutrient use efficiency ideally requires an understanding of the whole system, from the macro (agro-ecosystem) to the molecular level.

Introduction

The physiological disorder of a mineral nutrient is entirely contingent upon its function within the plant body. Inadequate or excessive supply of any essential element can result in metabolic disruptions, influencing the activities of enzymes, rates of metabolic reactions, and concentrations of metabolites. Alongside alterations in metabolic patterns, severe deficiencies of specific essential elements also give rise to distinctive effects in leaves, stems, roots, blossoms, and fruits.

A. Nitrogen

Functions: Nitrogen is essential for plants, playing crucial roles in protein synthesis, nucleic acid formation, and chlorophyll synthesis. It is a key component of enzymes, contributing to various metabolic processes. Nitrogen also supports root development, cell structure, and the synthesis of secondary metabolites. Striking a balance in nitrogen levels is vital for maintaining plant health and ensuring optimal growth and productivity. Effective nitrogen management is essential for sustainable agriculture and overall ecosystem well-being.

Introduction

The life cycle of a plant passes through biotic and abiotic stresses and plants are being attacked at different stages of growth by a number of disease causing organisms. These organism including bacteria, fungi, viruses, and nematodes attacks plants. These pathogens caused large crop losses and probably since the beginning of agriculture have contributed to human hunger and malnutrition. The control of plant diseases is thus of fundamental importance and is a major objective of plant breeding and pathology programme and agriculture chemical industry. Plants resists pathogens attack both with preformed defenses such as antimicrobial secondary compounds and by inducing defense responses (Hammond and Jones, 2000, Heath, 2000). Inducible defenses can be activated upon recognition of general elicitor such as bacterial flagellin and even host cell fragments released by pathogens damage (Gomez and Boller, 2000, Hammond and Jones, 2000). However, plants also involved sophisticated recognition systems to detect proteins produced during infection by specific races of pathogens (Martin et al., 2003).

Most food legumes have a long history of domestication almost as long as cereals, and during this time they have been subjected to conscious and unconscious selections for better adaptation to environmental condition as well as better seed yield. In general, crops during their ontogeny faces a number of abiotic stress viz., excessive and/or low soil water stress, soil salinity stress, high as well as low temperature stress. It has been well documented that crop yields would be greater in many cropping regions if more water were available. 
Availability of water for agriculture is being challenged increasingly because of growing demand for water from other sectors such as industry, urban use, and for social and environmental purposes. Water stress may conceivably arise either from an insufficient or from an excessive water activity in the plant’s environment. Many physiological characteristics are correlated with the water potential of mesophyll tissue but the correlations are species specific. There is a general hierarchy of sensitivities among general physiological activities. Most sensitive are cell expansion, cell wall synthesis, protochlorophyll formation, and nitrate reduction. Generally turgor pressure is still accepted as the best indicator of water stress in plants. The specific mechanism by which turgor regulate physiological function probably relate to cell walls and membranes. Cell membrane structure, and spatial arrangement of enzyme, transport channels, cellulose synthesis rosettes, and receptor proteins may be dependent on turgor pressure.

Plant hormones - They are defined as:

1. Small
2. Organic compounds;
3. Synthesized by the plant;
4. Active in low concentration (<10^-6);
5. Promote or inhibit growth and developmental responses;
6. Often show a separation of the site of production and the site of action (although this isn’t as clear a distinction as in animals).

Based on these criteria, would the following substances be considered hormones? Ca²⁺, sucrose, 2 4 - D, glycine, or K⁺?

The growth and productivity of crops depend on various factors, with the nutrient content of plant parts like leaves and stems playing a crucial role. These parts are often used as indicators to assess the nutrient status of plants. Each crop requires essential elements at specific concentrations during different growth stages, known as ‘critical levels’. When the nutrient content falls below these critical levels, plants may display symptoms of deficiency.

Nutrient requirements and availability can be evaluated through: i) plant diagnosis, ii) soil analysis, and iii) plant analysis using qualitative or quantitative methods. By conducting these tests, necessary nutrients can be identified and applied to crops to sustain growth and correct deficiencies. While rapid tissue tests offer quick solutions for nutritional problems, quantitative estimation of both plant and soil nutrient concentrations is more economical and provides a long-term strategy for managing nutritional issues. Implementing quantitative estimation allows for informed application of fertilizers, whether as basal or foliar, thus addressing deficiencies effectively and ensuring sustainable crop growth.

Different diagnostic tools are designed to avert nutrient deficiency or sufficiency and if properly used both loss of yield and quality of crop can be minimized. Among several diagnostic tools, nutrient analysis of standing crop seems to be an efficient method in arriving at the need-based fertilizer scheduling for various crops.

Nutrient uptake by plants indicates the actual accessibility of nutrients in soil to the plants. Also, concentration of certain heavy metals in plant indicates their solubility in soil which leads to poor crop quality.Although, different plant species and even different varieties of same species may differ in their nutrient requirements, the concentration of nutrient element in plant can act as guide to support the soil test result in assessing nutrient supplying capacity of a soil and as a tool for correcting any deficiency if carried out early enough to prevent yield loss. However, analysis of harvested or mature crop is like a post mortem as this information only can help in nutrient management planning in subsequent years.

Like soil testingplant analysis also suffers from some limitations. Amongthem, the most important are the risk of sampling error as well as the chances of incorrect interpretation of test report in recommending fertilizers. Selection of right plant part and right stage of crop growth are very crucial for successful plant analysis.

4.1 Sampling and Preparation for Analysis

The determination of nutritional need of crops is an important aspect of nutrient management of any plant analysis programme. The need of fruit plants for mineral nutrients differ from those of annual crop species in a number of ways, many of which are related to the perennial nature of tree crops. In perennial tree crops, there is a need to supply nutrients both for ultimate fruit production, the fruits and the vegetative organs, which persist from year to year. The need for leaf analysis in perennial horticultural crops and forest trees has proved its superiority over soil diagnostic methods. This is essentially because of their deeper root system and the fact that nutrients supplied in one year may have its effect on both the nutrition and crop production in following years. However, it is largely being used not as an alternative method to soil testing, but as a supplement to soil testing. Results of foliar analysis are usually interpreted using the critical nutrient level (CNL) approach. Accurate interpretation of foliar analysis using the CNL approach is possible only when sampling is restricted to the same growth stage at which standard reference values have been established (Beaufils, 1971, 1973). The general purposes of plant analyses are:

Accumulation of nutrient elements in plant tissues indicates the accessibility of the concerned elements from the soil to the plant. Although different plant species and even different varieties of the same species may vary in their nutrient requirements, composition of a part or of the whole plant may well be adopted as a guideline to support the soil-test results for factual assessment of soil’s nutrient supplying power.

The word cell was coined by Robert Hooke with the help of compound microscope. Cell is the basic unit of life. A plant cell has three distinct components a). Cell wall b). Protoplasm and c). Vacuole. Cell wall  and  vacuole are considered as non-living substances. The protoplasm which is living is  composed of 1. Cytoplasm and 2. Nucleus. The cytoplasm contains several organelles such as mitochondria, chloroplast, ribosomes, endoplasmic reticulum, golgi complex, lysosomes, plastids etc.

Plant hormones (also known as phytohormones) are chemicals that regulate plant growth, which are termed ‘plant growth substances’.

Plant hormones are signal molecules produced within the plant, and occur in extremely low concentrations. Hormones regulate cellular processes in targeted cells locally and, when moved to other locations, in other locations of the plant. Hormones also determine the formation of flower, stems, leaves, the shedding of leaves, and the development and ripening of fruit. Plants, unlike animals, lack glands that produce and secrete hormones. Instead, each cell is capable of producing hormones. Plant hormones shape the plant, affecting seed growth, time of flowering, the sex of flowers, senescence of leaves, and fruits. They affect which tissues grow upward and which grow downward, leaf formation and stem growth, fruit development and ripening, plant longevity, and even plant death. Hormones are vital to plant growth, and, lacking them, plants would be mostly a mass of undifferentiated cells. So they are also known as growth factors or growth hormones..

Phytohormones are found not only in higher plants, but in algae too, showing similar functions, and in microorganisms, like fungi and bacteria, but, in this case, they play no hormonal or other immediate physiological role in the producing organism and can, thus, be regarded as secondary metabolites.

Abstract

Microbes are endowed with a high and exploitable potential of being useful associates with their surrounding environment and host in case of symbiotic relationship. Most of the microbes live alone but many of them require association of other living system for its survival. Hence, the beneficial role of microbes is always correlated with growth promotion and survivability of other associated living system. Now it is established that microbes play an important and key role in plant growth and development, even its survivability in case of symbiotic mycorrhizal association with orchids. They are nothing but potential tool protecting plants from different adverse conditions like diseased state, environmental stress like cold temperature, drought, metal contamination, salt and acidic or alkaline stress.

Plant hormones (phytohormones) are chemicals that regulate plant growth and are termed as ‘plant growth substances’. Plant hormones are signal molecules produced within the plant, and are present in extremely low concentrations. Hormones regulate cellular processes in targeted cells. Hormones also determine the formation of flowers, stems, leaves, the shedding of leaves, and the development and ripening of fruit. Every cell is capable of producing hormones in plants. They shape the plant, affecting seed growth, time of flowering, the sex of flowers, senescence of leaves, and fruits. Plant hormones affect gene expression and transcription levels, cellular division, and growth.They direct which tissues grow upward and which grow downwards. Hormones are vital to plant growth. Hence, they are also known as growth factors or growth regulators.

Plant hormones and growth regulators are compounds that influence flowering, aging, root growth, prevention or promotion of stem elongation, prevention of leaf emergence and/or leaf fall and many other physiological processes. These substances produce major growth changes at a very low concentration.

Hormones are endogenously produced substances in plants while plant growth regulators may be synthetic compounds (i.e. IBA and Cycocel) that mimic naturally occurring plant hormones or they may be natural hormones that are extracted from plant tissue (e.g. IAA).

These growth regulating substances, most often, are applied as a spray to foliage or as a liquid drench to soil around a plant’s base. Generally, their effects are short-lived and they may need to be re-applied in order to achieve the desired effect.

Plant growth regulating substances are normally classified into five groups viz.: (i) Auxins, (ii) Gibberellins; (iii) Cytokinins; (iv) Ethylene; and (v) Abscisic acid.

For the most part, each group contains both naturally occurring hormones as well as synthetic substances. Physiological functions of each and every group of growth regulating substances are given below in brief:

Plants are responsible for highly useful molecular reactions. All the enzymatic  reactions  that  occur in the cell are  termed  as metabolic reactions.  They  take place within organisms in an orderly and regulated way.  They  are  the  metabolic pathways and the compounds  resulting from the process, namely,  metabolism are called  the metabolites. Metabolism in Greek means change. It is the set of life sustaining chemical transformations within the cells of living organisms. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to the environments around them.
 
Metabolism is a highly organized,   coordinated and purposeful enzymatic activity inside a cell. Metabolism has four functions: 1. To obtain energy from the environment, 2. To convert molecules into building blocks, 3. To convert the building blocks into proteins, lipids, sugars, nucleic acids and other cell components and 4. To synthesize and degrade organic molecules for specific needs of the cell.

7.1. Introduction

Like all other living organisms such as humans, animals, and microorganisms, plants also need elemental nutrients for their growth and development. They assemble the nutrients from soil, water and air. However, to obtain economical crop yield, nutrients are also supplied to the crops from external sources such as chemical fertilizers and manures and using biofertilizers. It is the present-day need to handle the soil fertility status in a more realistic and careful way to obtain maximum crop harvest. Under poor management practices, soil may become infertile and loose its importance in agricultural use. In modern days, huge food demand for the burgeoning human population does not permit to show luxury to use only fertile soil. Moderately fertile soil or even degraded soil should also be managed properly so that they may be used to grow crops. For this, plant nutrients status of the soil plays a significant role along with other soil properties. For sustainable soil fertility management, parameters such as crop to be raised, its nutrient demand at various growth stages, current nutrient status of the soil, amount of nutrient application based on the soil testing results etc are important to be considered. Balanced nutrition to the plants is the prerequisite to obtain maximum benefit. If nutrients supplied to the plants are low in quantity than their requirement, crop production is lowered down. Similarly, if the nutrients are provided in more amount in the soil or unbalanced way through fertilizer or manure applications, total crop yield is suffered. It is a very common example that excess of phosphorus leads to zinc deficiency in most crop plants and it has been observed that excess N is responsible for potassium starvation in potato. Again, excess of iron, manganese, zinc, copper shows plant toxicity. Addition of nutrients to soils in excess also causes environmental pollution when the excess nutrients are lost from soil by leaching, surface run-off and volatilization. Unscientific way of soil fertilization leads to increasing cost of cultivation and imparts adverse effect to the environment instead of doing any good. Therefore, one should have a clear knowledge on soil fertility to obtain a sustainable productivity.

In the realm of natural elements, there exist approximately one hundred and three distinct elements. Among them, nearly ninety elements are absorbed by plants. To differentiate essential elements from those that plants can assimilate but are not vital, Arnon (1954) established the following criteria:

1. The plant must be incapable of normal growth or completing its life cycle in the absence of the element

2. The element is specific and irreplaceable by another

3. The element directly participates in plant metabolism

By applying these criteria, molybdenum and chlorine are not deemed essential, even though they serve a functional role in plant metabolism. This is because they can be substituted by vanadium and halides, respectively. Subsequently, D. J. Nicholas refined the definition of essential elements, replacing the term “functional or metabolic nutrient” to encompass any mineral element that contributes to plant metabolism, regardless of whether its action is specific.

Plant nutrition is the study of the chemical elements and compounds that are necessary for plant growth, and also of their external supply and internal metabolism. The criteria for an element to be essential for plant growth:

In its absence the plant is unable to complete a normal life cycle; or

That the element is part of some essential plant constituent or metabolite.

Plant physiology is a sub-discipline of botany concerned with the functioning, or physiology of plants. Closely related fields include plant morphology (structure of plants), plant ecology (interactions with the environment), phytochemistry (biochemistry of plants), cell biology, genetic, biophysics and molecular biology. Fundamental processes such as photosynthesis, respiration, plant nutrition, plant hormone functions, tropism, nastic movements, photoperiodism, photo-morphogenesis, circadian rhythms, environmental stress physiology, seed germination, dormancy, stomata function and transpiration, both parts of plant water relations, are studied by plant physiologists. The field of plant physiology includes the study of all the internal activities of plants those chemical and physical processes associated with life as they occur in plants. This includes study at many levels of scale of size and time. At the smallest scale are molecular interactions of photosynthesis and internal diffusion of water, minerals, and nutrients. Major sub disciplines of plant physiology include phytochemistry (the study of the biochemistry of plants) and phytopathology (the study of disease in plants). The scope of plant physiology as a discipline may be divided into several major areas of research.

Basic LabTechniques - This laboratory is intended to:

(1) Provide an introduction to basic techniques used in biology labs

(2) provide some experience with the equipment employed in future labs

2.1 Microscopy

The compound light microscope is a veryimportant tool in the study of biology. Typical compound light microscopes allow specimens to be viewed at 400 to 1000 times their actual size (total magnification is determined by multiplying the objective lens magnification by the ocularlens magnification). Thelight microscopeis made up of a system of lenses aligned in such a way thatallows magnification, as well as improved resolution. The resolution obtainable is also dependent on contrastin the specimen. Contrast can be adjusted with the iris diaphragm, located below the condenser lens,and can also be enhanced by the addition of stains to the specimen.

Scientific drawings of specimens observed under the light microscope are often used to provide a record of what was viewed. Proper scientific drawings should be neatly drawn,with smooth lines, in pencil (they should never be in colour). More than one cellshould be drawn to illustrate the cellularassociation to the observer(e.g.found singly or as part of a tissue). Labels should be added using straight horizontal lines to the right side of the drawing, and care should be taken with singular and plural forms of structural terminology. To demonstrate differences in density of specific structures, use stippling rather than shading. A figure caption thatindicates the specimen viewed, how viewed, and the to right side of the drawing, and care should be taken with singular and plural forms of structural terminology. To demonstratedifferences in densityof specific structures, use stippling rather than shading. Afigure caption thatindicatesthe specimen viewed, how viewed, and the magnification of the drawing is always necessary.

Plant pigments impart colour to the different components like leaves, flowers, fruits etc. They in turn are responsible for the colour of raw food, we eat. Pigments like chlorophyll, anthocyanins, flavonoids, tannins, xanthones etc. are the different pigments that are present in plants. The primary function of pigments in plants is photosynthesis, which uses the green pigment chlorophyll along with several red and yellow pigments that help to capture as much light energy as possible. Other functions of pigments in plants include attracting insects to flowers to encourage pollination.

Biological pigments, also known simply as pigments or biochromes are substances produced by living organisms that have a colour resulting from selective colour absorption. Biological pigments include plant pigments and flower pigments. Many biological structures, such as skin, eyes, fur and hair contain pigments such as melanin in specialized cells called chromatophores.

Pigment colour differs from structural colour in that it is the same for all viewing angles, whereas structural colour is the result of selective reflection or iridescence, usually because of multilayer structures. For example, butterfly wings typically contain structural colour, although many butterflies have cells that contain pigment as well.

1. Chlorophylls

Chlorophyll can be regarded as a true representation of health of green plants. This presumption is based on the fact that chlorophyll is most commonly and immensely influenced by biotic and abiotic stress conditions in addition to events like pathogenic invasion, pollution, mineral deficiencies as well as mineral toxicity. This is the reason that estimation of chlorophyll is considered to be one of the most important parameters in plant physiological studies.

Eukaryotic plant cells possess many types of ‘reserves’, one of them is plastid. A plastid, that contains green colour is known as chloroplast and the green colouration of a chloroplast is mainly due to the presence of a pigment to which we call as chlorophyll. Normally, chlorophyll constitutes about 4% of chloroplast dry weight.

Chlorophyll ‘a’ and ‘b’ are the most abundantly found in all autotrophic higher plants. However, there are other chlorophylls also such as ‘c’, ‘d’, ‘e’, bacteriochlorophyll and bacterioviridin which have restricted presence in blue-green, brown and red algae.

A chlorophyll molecule contains ‘Tetrapyrrole’ skeleton formed into a ring with an atom of magnesium (Mg⁺⁺) in the centre. A so-called ‘Pyrrole’ molecule contains four carbon and one nitrogen atoms arranged in a ring. Four such pyrrols arranged in a ring form the ‘Head’ of chlorophyll molecule. Attached to this is ‘porphyrin ring’, at one point, is a ‘phytol’ tail- a long chain of linked carbon.

Introduction

In agriculture and public health sectors, a variety of pesticides are still in uses that are toxic chemicals and having broad-spectrum actions. They kill target species but also harm the ecosystem seriously by affecting desirable organisms, thus, badly impairing prey-predator relationship. Most of these pesticides are persistent or non-biodegradable and hence exhibit biological magnification by accumulating at higher concentration in the organism, which are on the top of the food chain. The other drawbacks of repeated use of pesticides are eradication of natural enemies of pests, increased level of pesticide residues in soil, water, food and fodder crops, resistance of pests to pesticides and resurgence of minor pests in addition to the environmental pollution. It is clear that once used pesticide may persist, somewhere causing serious harm to the mankind and his ecosystem.

The increasing incidence of pesticide harms is fueling the need for new pesticides, which are toxicologically safe, more selective and efficacious and environment-friendly. Now the natural compounds, thus, have increasingly become the focus of those interested in discovery of pesticides. Tens of thousands of secondary products of plants have been identified and there are estimates that hundreds of thousands of these compounds exist. There is growing evidence that most of these compounds are involved in the interaction of plants with other species-primarily the defense of the plants from plant pests. Thus, these secondary compounds represent a large reservoir of chemical structures with biological activity. This resource is largely untapped for use as pest management agents^3, 4. The extraction of such chemicals from plants and derivatives of potent compounds are being encouraged all over the world under the Integrated Pest Management (IPM) approaches. The natural compounds and their synthetic derivatives are more selective in action, completely biodegradable and environment-friendly. In short, natural ways of pests control have already been established and are receiving much attention these days.

Introduction

Tissue culture refers to the technique of growing cells, tissues, or organs under controlled, artificial conditions. This allows propagation of tissues from a small sample of cells/tissues under sterile conditions. Plant tissue culture is widely used for various purposes, including the production of disease-free plants, rapid multiplication of plants with desirable traits, genetic modification, conservation of rare or endangered species, etc. Tissue culture is a valuable technique because it enables consistent and large-scale production of plants, ensures genetic uniformity, and allows manipulation of plant biology at cellular level. In this chapter, we will discuss about the major types of tissue culture techniques and their advantages, disadvantages, as well as applications in brief.

Different Types of Tissue Culture

Callus culture involves induction and growing of unorganized, undifferentiated cell masses from an explant on a nutrient/culture medium. The part of plant used to induce callus is called explant which can be tissue, organ or part of a plant.

Organ culture is used to maintain or grow an entire organ or a part of organ in vitro. It preserves the structure and function of the organ for studies or transplantation.

Embryo culture involves isolating and growing embryos from seeds or ovules in a nutrient medium. It is used to bypass seed dormancy or rescue embryos from hybrid crosses that may not develop naturally.

Cell suspension culture involves growing dispersed cells or small cell clusters in a liquid medium under continuous shaking. This is used for large-scale production of cells, secondary metabolites, and studying cell biology..

1. Introduction

Viruses are a unique group of infectious agents. They are distinct in their simple, acellular organization; however, they are the connecting link between live and dead. Viruses are also the perfect example of obligate intracellular parasitism. Despite their simplicity, plant viruses are extremely important and drawn attention of researches because they can be used as model to study the disease establishment and progression mechanism, reproduction inside the host and trilateral host-virus-vector relationships. Their small genome also gave liberty to extensively understand the genome evolution caused by the genetic exchange or recombination. As a consequence, this will help in the development of facile methods for management and control of new emerging viruses and their strains.

This chapter is written for the beginners and students of virology subject to provide the fundamental knowledge about the origin, history of plant virology, the general features of plant viruses, their structure, shape and size, mode of spread and development of their management strategies. Besides this, the new development of non-conventional methods for developing virus-resistance in plants has also been explained for enhancing the quality and production of commercial crops in the country.

Plant–water relations concern how plants control the hydration of their cells, including the collection of water from the soil, its transport within the plant and its loss by evaporation from the leaves. Flow of water through plant and soil over macroscopic distances is driven by gradients in hydrostatic pressure. Over microscopic distances it is driven by gradients in water potential. Evaporation of water from leaves is primarily controlled by stomata, and if not made good by the flow of water from soil through the plant to the leaves, results in the plants wilting. Plant water deficit is initiated as the crop demand for water exceeds the supply. The capacity of plants to meet the demand and thus avoid water deficit depends on their “hydraulic machinery.” This machinery involves firstly the reduction of net radiation by canopy albedo, thus reflecting part of the energy load on the plant. Secondly, it determines the ability to transport sufficient amount of water from the soil to the atmosphere via the stomata in order to provide for transpiration, transpirational cooling and carbon assimilation. Water is transported by way the soil-plant-atmosphere continuum and it is largely controlled by the resistances in the continuum as determined by root, stem, leaf, stomata and cuticular hydraulic resistances. The gross effects of deficient and of excessive soil moisture on plant growth are well known, but controversy has existed for many years around the question whether the so-called “‘available moisture” is equally available for plant growth or available only with such increasing difficulty that plant growth functions are retarded before the wilting point is reached. Various measurable aspects of plant growth do not respond in the same manner to increasing moisture stress. Crops will respond to irrigations, although measured soil moisture stress is quite low. Problems of relating plant growth to soil moisture stress conditions varying with both time and soil depth are considered. Soil factors affecting density or depth are reviewed and several ways weather factors influence soil, -moisture-plant-growth relations summarized.

INTRODUCTION

The purpose of writing this chapter is to develop a comprehensive understanding of the role of functions of water in plant growth and development. Water is essential to life on earth as the living organisms contain 80-90 per cent water. A typical crop or grassland will transpire approximately 500 ml of water per 10 g of dry matter produced. Water has a tremendous effect on the environment near the earth, which on regional basis we call ‘climate’. Ecological importance of water is due to its physiological importance because water affects the plant growth through physiological processes. All metabolic activities in the plant cell or tissue depend on water status of the plant. For example, in a maturing seed, respiration rate is highest as it moves towards maturation stage, water content decreases and hence rate of respiration slow down. At the harvesting stage, when the water content is 10-20%, the respiration rates become negligible. Now in a stored seed if the water content will be high it will result into higher respiration, thus release energy, which will increase the temperature and will finally destroy the seed.

The response of plants to air pollution can be understood by analyzing the physiological and biochemical parameters of plants.

Physiological Parameters

The epidermal cells are the first to interact with the air pollutants and also lack chloroplast. Epidermal cells hence cannot remove excess sulphur through the production and release of H2S. Damage to plants by air pollutants depends upon the amount of pollutants entering the cells and their reactivity with cellular constituents. Plants regulate the entry of gaseous molecules through stomatal movement thereby affecting the photosynthesis and transpiration. Response of plants to gaseous pollutants varies from species to species. This is due to differences in the stomatal conductance, aperture size and permeability of plasma membrane (Yunus et al., 1996).

23.1 Forms of Soil K

Ignoring potassium (K) in soilorganism, total K in soilmaybe classified as (i) water soluble K, (ii) readily exchangeable K (exchangeable K), (iii) slowly exchangeable K (non- exchangeable or fixedK) and (iv) mineral or lattice K. Thedifferentforms are in dynamic equilibrium with one another.