eChapters

8.1 The purpose of erosion research

The need for research

A soil conservation programme needs to be based on factual information about rates and quantities of erosion. For example some land obviously needs to be protected by mechanical works such as channel terraces, some land equally obviously does not need any protection, and a great deal of land lies somewhere between the two extremes. At some point the terraces become unnecessary or uneconomic, but a logical decision on where to draw the line can only be made if data are available on how much soil erosion is occurring and how much it would be reduced by terraces. Similarly, the effect of channel terraces should be compared with the effect of alternative measures, and the effect should also be measured on the different soils and crops which are likely to be encountered.

Nowadays there are excellent opportunities for research workers to exchange the results of their work. The national and iniernational journals are packed with accounts and results of research reports in their proceedings (as listed in Further reading). Some of the reported research results can be usefully applied in countries other than where the research was done, but care is required in any transfer of technology. If the local conditions of soil, climate, or land use, are different, the results may not apply. However, research in other situations can often serve as a pilot trial to show which factors should be studied locally. Even when local conditions are so different that the results do not apply at all, the techniques and apparatus developed by other workers can still be helpful.

9.1 Planning land use

Modern techniques such as mechanization, better crop varieties, and the scientific use of fertilizers can transform agriculture, but before they can be effective the use of the land has to be right. No techniques will make it possible to grow a good crop if the soil conditions are unsuitable for that crop, and no conservation works can prevent erosion when the basic cause is trying to grow crops on land which is really unsuitable for arable farming (plate 9.1). The object of land use planning is to determine the characteristics of land, its possibilities, and its problems, and try to match these to a form of land use which will be sustainable and economically productive.

9.7.1 Some planning principles

An often quoted definition is that ‘planning is the conscious process of selecting and developing the best course of action to accomplish an objective’. In the case of Land Use Planning the objective is the efficient intensive use of land resources.

It is difficult to imagine any field of human activity where some form of planning is not essential to achieve the objective. Consider going on holiday. Certainly it is possible to come home from work one evening, throw some clothes into a suitcase, go to the railway station or airport and buy a ticket to the first holiday resort which comes to mind. Some fortunate people may indeed enjoy so unplanned a holiday but for most of us it would be disappointing to find oneself in a mountain holiday resort without climbing boots, or on a sunny beach with only winter clothing in the suit case. No, one is more likely to achieve the objective of a happy holiday by a planned approach and this means going through a logical sequence of steps, i.e.

10.1 Different practices for different purposes

There are so many different practices used in erosion control that to describe them needs some form of grouping. For a long time mechanical protection was used to describe all the methods which involved earth moving, such as digging drains, building banks, levelling sloping land, and so on. Anything else was lumped together under biological methods for want of a better title.

This is appropriate for large mechanized farms where the approach is to use machines to do the earth-moving and follow up with improved farming methods. But this division does not suit the concept of erosion control through better land husbandry supported by mechanical protection, and the division is artificial when we start talking about progressive terracing using grass strips or live hedges.

An approach more suited to today’s thinking is to group methods and techniques according to their main objective. All have an element of saving soil loss, but an important difference is the handling of surface runoff. This chapter identifies three kinds of water management objective and two types of soil management on sloping land.

11.1 The farmer’s point of view

In the last chapter possible conservation practices were reviewed in groups according to their purpose in terms of influencing runoff or soil loss. Now, looking at ways of limiting soil degradation by improved land husbandry, the primary consideration is to look at the alternatives from the farmer’s point of view. In fact we need to be very wary of manual-type recommendations. A better approach is to offer a menu of alternatives, and the role of the professional is to help the farmer choose what is appropriate for his or her circumstances. A recent review of technologies acceptable to resource-poor farmers points out that combining practices into a farming system must take account not only of the physical factors such as soil and climate, but equally the available resource inputs, especially cash and labour, and the farmer’s objectives (STOCKING 1993).

The objectives of a commercial farmer are usually to maximize yield and income, but the subsistence farmer is likely to be more interested in improving food security by reducing the risk of failure, or improving the return on inputs of seed, fertilizer and labour, or improving the quality of life by reducing drudgery, particularly relevant in the case of women farmers.

We need a new approach to the farmer when recommending changes to farming practice. Instead of recommending practices because they will reduce erosion, we should show how they can lead to increased production. For example, practices which lead to better soil structure, more organic matter, or more moisture-holding capacity should be put forward because they improve yield, not because they reduce the soil erodibility. Increasing infiltration from better ground cover or the use of contour farming or ridging can result in better crops as well as reducing soil loss. Improved crop management could include more use of fertilizer and manures or crop rotations. These practices will make more sense to the farmer if they are recommended as leading to better production, which he can instinctively appreciate as desirable, rather than because they will reduce soil erosion which is likely to be a less important objective.

12.1 The nature of gully erosion

Gully erosion is spectacular and widespread, and so it is often used by conservationists as a characteristic symptom of erosion. As a result there is a danger of its importance being over-emphasized. Certainly it is most important as a source of sediment in streams, but in terms of damage to agricultural land or reduction of agricultural production, it is usually not very important for the simple reason that most land subject to severe gully erosion is of little agricultural significance. The really spectacular erosion so popular in non-technical reports shows large areas cut up by deep interconnecting gullies, but this situation is usually found in semi-arid climates unsuitable for any serious agriculture, or on soils which have such adverse chemical or physical properties that their potential production is very low. Added to this is the fact that gully control is always difficult and expensive, so the cost of reclamation usually exceeds the value of the land. Certainly in the sense of reducing the amount of eroded soil choking the dams and rivers it may be highly desirable to do something about gully erosion, but it is very much a case of prevention being better than cure. Limited resources in manpower, money and materials can usually be better employed in preventing future gullies than in curing existing ones.

The worldwide occurrence and recognition is well demonstrated in the variety of names: in English and American - gully, in Egypt - wadi, in South Africa - donga, in French-speaking lands - ravine, in India - nulla, in South America - carcava, or arroyo, and many others. The definition is the same in any case, a steep-sided eroding watercourse which is subject to intermittent flash floods. They are more common in semi-arid climates with infertile soils and sparse vegetation, but some spectacular examples are found in tropical forests in deep soils with dense vegetation.

Damage to arable land tends to attract most attention but degradation of non-arable land can also have serious effects, whether economic, or social, or on the food supply. In dry seasons, loss of grazing capacity is a common and serious problem, forest land may suffer through over-exploitation, roads can cause much damage particularly on steep land. In this chapter we will look at the more important erosion problems on non-arable land.

13.1 Erosion on grazing land

On well-managed high-yielding pasture it is unlikely that there will be any erosion, for the ground will have a good uniform cover. But land which is not arable because it is too poor, too infertile, too stony, or too arid, and is only described as grazing land because it is unfit for more intensive use, is a very different matter. Again, erosion control can be directly and precisely equated to improved management - anything leading to a better water balance and a better ground cover will lead to reduced erosion.

14.1 Changes in policy and strategy

14.1.1 Policy changes

In the discussion on land use planning we suggested that the ideal pattern of development is to establish a long-term national or regional policy, which leads to medium-term strategies, and short-term tactical operations. In the real world a curious situation is arising in that the adoption of the new land husbandry approach is growing so fast that the practitioners have moved ahead of the politicians and opinion formers, with the result that the implementation of strategies by Non-Government Organisations, aid agencies, and senior field officers, is helping to shape new policies.

There is always the problem that national policies ought to be long term, but are created by politicians usually working within a short time frame to the next election. Fortunately, the land husbandry approach allows planners at all levels from farmers to governments to appreciate the long-term issues.

The new approach was mentioned in section 9.2.1 in connection with land use planning. It is summed up in the slogan From soil conservation to land husbandry, and two reviews using that title list the main points as the need for:

1.1 INTRODUCTION

This volume is concerned with the chemistry of soil processes. These are rather arbitrarily divided and discussed in the first part of this book in terms of mass flow and diffusion, precipitation, cation, anion and ligand exchange, adsorption, translocation of metals, and oxidation and reduction. The way in which these processes operate to determine the fate of different substances added to soils is described in the remaining part of the book. In this initial chapter an attempt is made to show how the individual chemical processes described later combine with physical and biological processes to give soils their ability to support plant life, and to accept the detritus of the world and to convert it to harmless constituents of the soil mass.

2.1 INTRODUCTION

Mass flow and diffusion are processes which cause the redistribution of many components within the soil profile. They are usually investigated because they cause a redistribution of materials such as fertilizers and pesticides which are added to the soil, or because of the need to reduce salt concentrations to levels safe for crop growth. This has given an economic incentive to the investigations, but the processes are also basic to our understanding of the development of soil properties. For example, diffusion is the main process for the movement of gases into and out of the soil, which in turn affects many soil properties (Chapter 7), and mass flow of water is an important cause of the formation of horizons in soil profiles (Chapter 8). Hence there are both academic and economic reasons for attempting to understand the way the processes operate in soils.

Over the last few years our understanding has increased considerably. It is the purpose here to give the principles which have been evolved in this recent work, and to discuss their application. It will also be shown that many problems remain to be solved.

Diffusion means a spreading out, and is caused by random thermal motion, as is the Brownian movement of colloidal particles observable under the microscope. In unstirred liquids, which are our main concern in this chapter, all the molecules and ions of the solvent and solute have this random movement (molecules and ions in gases and some solids behave similarly). As a result of this motion, which occurs randomly in all directions, any irregularities in the concentration of a solution or mixture of gases eventually disappear.

3.1 INTRODUCTION

The chemistry of the soil is much more complex than can be represented simply by precipitation, adsorption, or exchange processes. The complexity arises from the time scale of soil chemical reactions in which the structure and dimensions, the extent and distribution of pores, and the content and mobility of water in them, interact immensely with the reaction chemistry. The fourth process adding to this complexity is the dissolution of native and reprecipitated soil constituents by percolating water containing solutes accumulated by natural processes or added by man. The fifth complicating factor compounding the time scale is that very often the resultants of soil chemical reactions are large complex molecules, occasionally polymeric, made up of several constituent groups or atoms. It is by no means clear which of the four processes participate in a chemical reaction and in which order. That a process reoccurs during a prolonged reaction is very likely.

Such complexities explain why no single model related rigorously to the retention and release of cations and anions, can provide a basis for a laboratory procedure to test and compare the chemical properties of soils. In this chapter, some of the soil reactions that are important to plant nutrition and pedological processes are discussed, principally those leading to relatively simple compounds accumulating in soil.

4.1 INTRODUCTION

All soil components contribute in some measure to cation exchange. The source, extent, and quality of the contribution of each to the cation exchange capacity is varied and complex. Ocasionally, reactions between components alter the extent and quality of cation exchange. Also, in some this is strongly influenced by the pH of the soil-water complex, and the electrolyte content of the soil solution. Indeed, when ‘simple and rapid’ methods, empirical or allegedly fundamental in origin, appear in the literature, they must be viewed circumspectly. Mostly, they provide an incomplete, or a one-sided, picture of the phenomenon. To justify his invention, the experimenter usually provides correlations with other intrinsic soil properties (e.g. the concentration by weight and the mineralogy of the <2 jxm particles, the organic matter content, the surface area) or with the reaction of soil with its environment (e.g. plant growth and composition). However convincing such statistical parameters might be for the population of soils investigated, they do not help elucidate, and may indeed mask, the true extent and quality of cation exchange.

This chapter deals with current views on the sources, extent and quality of cation exchange, and with comprehensive methods for evaluating these. The relationship between the properties thus observed and values obtained from simple and rapid procedures is considered.

5.1 INTRODUCTION

One of the generalizations that can be made about soils is that the particles of which they are composed together have a nett negative charge. There are exceptions: for example, some iron- and aluminium-rich tropical soils can attain a positive charge at low enough pH, but such cases are rare. It is nonetheless a fact that most anions are held strongly by the soil complex, and it is the purpose of this chapter to look at some of the reasons why this is so. Historically, the impetus to research in this area has largely been the practical necessity to understand the behaviour of applied phosphate fertilizer, and it is some indication of the complexity of the problems involved that, even after decades of effort by soil chemists and agronomists, this understanding is still far from complete. The reason for this is partly that the soil surfaces themselves are, as has been described by Greenland and Mott (1978) in the companion volume, the product of a ‘dirty’ environment. This generally means that phosphate added to the system has to exchange on sorption with an inadequately characterized suite of anions presorbed on ill-defined surfaces. There are also in the case of phosphate, possibilities of simultaneous precipitation. Faced with these problems, the trend in the literature over the past ten years or so has been to investigate in detail the physical chemistry of the sorption of anions onto simple surfaces which are fairly well understood, in the expectation that this will lead to ultimate comprehension of behaviour in the natural system. The results of many relevant experiments have only recently been published, and so some parts of the account are still at the discussion stage in the literature. This is especially true of phosphate, which looks destined to be a joker in the anion pack for some time to come.

6.1 INTRODUCTION

This chapter is concerned with the interactions which retain mobile chemical species in the soil environment. Emphasis is centred on the binding of small organic chemicals to soil particles of colloidal dimensions, and on the associations between polymeric materials and inorganic colloids which strongly influence the physical and chemical behaviour of soils. These interactions are also involved in the retention by soil of water, discussed by Farmer (1978) in the companion volume to this book, and in ion and ligand exchange reactions, and in mass flow and diffusion discussed in preceding chapters.

The term colloidal refers to particles and discontinuities of matter (e.g. pore spaces or thin films) of dimensions in the range of 1 nm to 1 jxm (IUPAC, 1972). For such finely divided systems the properties of the interfaces are very important because these largely control the behaviour of the colloidal systems. The term phase is used to describe the homogeneous parts of a system and an interface or surface is the boundary region between any two phases; the relevant interfaces are solid/gas, solid/liquid, liquid/liquid, and liquid/vapour. Where none of the solid, liquid, or vapour phases in a system are finely divided the ratios of the interfacial areas to the bulk volumes of the phases are small, and the effects of the interface between neighbouring phases can be neglected.

The most extensive surfaces in soils are contained in domains and micro- aggregates of colloidal particles (cf. Greenland and Hayes, 1978; Greenland and Mott, 1978), These surfaces are accessible from the pore spaces between solid particles. Under normal field conditions these spaces remain filled with water. Thus, although modern fertilizers, and chemicals for the control of plant growth, pests, and diseases are applied to soils as solids, liquids, and gases, most of the interactions with the soil colloidal constituents take place at the solid/liquid interface. We shall be primarily concerned here with uptake from the liquid phase by solid soil components, although interactions at the solid/gas interface can sometimes be important.

7.1 INTRODUCTION

An understanding of the processes of oxidation and reduction in soils and the associated changes and practical implications requires a knowledge firstly of soil respiration and the movement of O₂ and CO₂ in soils, and secondly an appreciation of the significance of the changes which occur when, as a result of the use of all the O₂ in a given zone of the soil, respiration changes from aerobic to anaerobic. This results in marked changes in the biochemistry of the system. A basic knowledge is therefore needed of the microbiology and biochemistry of aerobic and anaerobic respiration and of the physics of gas movement, as well as of the chemistry of the system.

8.1 INTRODUCTION

The development of a soil profile involves the mobilization of major and minor elements and their subsequent deposition elsewhere in the profile or removal in the drainage water. For a full understanding of these processes we need to know what are the forms and reactivities of the soil constituents, the nature and mode of action of the mobilizing agents, the forms in which the mobilized material is transported—whether colloidal or in true solution, whether in ionic or complex form, whether alone or in association with other soil constituents—as well as its stability towards oxidation and reduction, microbial action, pH, and sorption and coprecipitation. The availability of micronutrients to plants is presumably governed by factors such as these. The current concern with problems of soil contamination has brought to the attention of soil chemists numerous toxic metals that were previously regarded as essentially the province of the geochemist.

It is probably true to say that no one of the factors listed above can be considered in isolation, but so far as any one factor is of dominant importance, this is nature of the mobilizing species; this determines the form in which the metal is transported, and its ultimate fate in the soil or in the drainage water.

This chapter is an attempt to summarize our present knowledge of the processes responsible for the mobilization and immobilization of metals in soils.

9.1 INTRODUCTION

The annual production of organic carbon by photosynthesis on land is about 6x 10¹⁰ tonnes (Table 9.1), most of which eventually decomposes on or in the top 50 cm of the soil. This organic matter can be in lumps as big as a mature oak tree (say 0.5xl0²m³) or as small as a bacterium (0.5 x 10~¹⁸m³). It can be in material as resistant to decay as oil palm nuts, which persist for years in soil in the humid tropics, or as transient as mammalian protein. Yet in the long run, no fraction of the organic matter in plants and animals can withstand decomposition to carbon dioxide and water. If this were not so, any completely resistant fraction would by now cover the surface of the earth. Although under normal conditions organic matter does not accumulate indefinitely in soil, exceptions can occur, as, for example, when a soil becomes permanently waterlogged. When a geologically stable surface has been under the same vegetation for a long time, the soil approaches steady state conditions, with the annual losses of organic matter balancing the annual input. Thereafter the organic matter content of the soil remains constant, until the next vegetational change or geological catastrophe. This process, in which losses and gains proceed simultaneously, is described as turnover and may be defined (for carbon) as ‘the flux of carbon through the organic carbon in a given sample of soil’. Turnover time is then the amount of carbon in the soil system (or part of that system) divided by the annual input of carbon into the system (or part of that system). Turnover and turnover time will be discussed more fully in Section 9.2.5.

10.1 INTRODUCTION

The fate of plant nutrients in fertilizers added to soils is to be: (1) taken up by crops; (2) retained by the soil; (3) removed in solution in drainage water; (4) lost as a gas; or (5) removed by erosion. These five processes are discussed in this chapter. The purpose of using fertilizers is to increase crop growth and they fail in this unless they are taken up by plants. Table 10.1 gives FAO (1972) data which show that large fertilizer use is restricted to the developed countries which use 65 times the amount used per hectare in developing countries. Within the group of ‘developed’ countries most of North-West Europe uses much fertilizer; outside of Europe large use per hectare is confined to a few countries such as Japan and USA. It is in the developed countries where much fertilizer is applied that efficient uptake of plant nutrients is already important to national economies, and where nutrients lost from agriculture cause eutrophication of natural waters and are regarded as pollutants.

11.1 INTRODUCTION

The heavy metals which, by definition, are elements having a density greater than five in their elemental form, comprise some 38 elements. However, the term usually, and here, refers to twelve metals that are used and discharged by industry, i.e. Cd, Cr, Co, Cu, Fe, Hg, Mn, Mo, Ni, Pb, Sn, Zn. Most of the present discussion will centre on those metals that may represent potential hazards to plants or animals; these are Cd, Cu, Hg, Ni, Pb, and Zn.

The heavy metals are widely distributed in the environment, in soils, in plants and animals and in most of their tissues. The concentrations of individual metals in living tissue are ordinarily very low and must be maintained within narrow limits to permit the optimum biological performance of most organisms. Some heavy metals are essential in trace amounts, namely Co, Cu, Fe, Mn, Mo, Zn for plants and, in addition, Cr, Ni, Sn for animals; Cd, Hg, and Pb, have not been shown to be essential for either plants or animals. Deficiencies of the essential metals have been frequently reported and substantial benefits have arisen from correcting these by addition to the soil and subsequent transfer from soil to plant is for most increasing concern about the entry into soil of some heavy metals and the possible adverse effects that they might have on plants and animals and, in turn, on human health. The main sources of these heavy metals are: (i) urban industrial aerosols, created by combustion of fuels, metal ore refining and other industrial processes; (ii) liquid and solid wastes from animals and man; (iii) mining wastes; or (iv) industrial and agricultural chemicals. Although in some circumstances there are direct atmospheric inputs to plants, addition to the soil and subsequent transfer from soil to plant is for most heavy metals the major route of entry into the living tissues of plants, animals, and man. The fate of heavy metals added to soils, including their mobility and reactions in the soil and their subsequent uptake and distribution in plants, is therefore of critical importance in relation to man’s health.

1.1 Introduction

The word ‘horticulture’ was first used in 1600’s, and is derived from two Latin words, ‘hortus’(garden) and ‘cultûra’(cultivation), and it means ‘the culture (cultivation) of garden plants’. Relf (1992) defined “horticulture as an applied science and art of growing fruits, vegetables, herbs and spices, nuts, tubers, aromatic and medicinal plants, plantation crops, mushrooms and ornamental plants which include shrubs, flowering plants and turfs stimulating minds, spirits and emotions of individuals, enriching health and wellness of communities, and linking human beings to nature and its landscaped exteriors for wellness and wellbeing”. Fruits and vegetables are nourishing and protective foods. It has been recognized that fruits are a rich source of antioxidants which protect us from dreadful diseases. Vegetables and fruits contain vitamin E, K, and  carotene in addition to minerals like zinc, copper and manganese. To meet the ever-increasing demand of the country for fruits, vegetables, tubers, spices, flowers, ornamentals etc., we must strive hard to deliver better cultivars in as many aspects as possible to the society so that human beings will be in sound health physically as well as mentally. To achieve this goal plant breeding in general, and horticultural plant breeding in particular will come to our help.

2.1 Introduction

Dear students, you shall be taught plant biotechnology during the third semester in the course ‘Elementary Plant Biotechnology’. But, for understanding of non-conventional breeding methods/techniques you should acquire some knowledge of basic plant biotechnology. Hence, in this chapter plant biotechnology is introduced to you in brief.

2.2 Definition

The term ‘biotechnology’ stems from fusion of ‘biology’ and ‘technology’. It was coined by Karl Ereky, a Hungarian agricultural engineer, in the beginning of 20th century. According to him, all processes used to yield finished products from raw materials with the help of living organism come under biotechnology. It may be defined in number of ways. However, in simple terms, biotechnology may be defined as ‘the controlled use of biological agents, such as microorganisms, or cellular components, for beneficial use’ (U.S. National Science Foundation).

3.1 Introduction

Genetics deals with genes and cytogenetics with chromosomes that harbour genes. On the other hand, plant breeding strives to upgrade the genotypes of crop plants. So, the plant breeding methods should be based on genetic principles. Dear students, you should have clear understanding of genetics in broad sense so that you can appreciate the applicability of breeding methods. As I have already pointed out that you have been taught the course ‘Principles of Genetics and Cytogenetics’ in the first semester, only a brief discussion is followed for your review and better understanding.

3.2 Character

When we call ‘character’ or ‘trait’ in genetics, we mean any morphological, anatomical, biochemical or behavioural feature of an organism. For instance, flower colour, blooming period, leaf size, size of guard cells in stomata, vitamin C content, disease resistance etc. A single gene or a number of genes may govern the development of a character and, often it is influenced by the environment. Characters may be qualitative or quantitative.

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’.

5.1 Introduction

The development of quantitative trait loci (QTL) mapping methods to identify genes or QTLs controlling quantitative traits was a landmark achievement in plant genetics research in the late 1980s. Since then literally thousands of research papers have reported the identification of genes or QTLs for important traits across a diverse range of plant species. This wealth of genetic information was built on the foundation of decades of research in crop molecular genetics and genomics.

The selection and enrichment of QTLs within breeding material was the inevitable next step from QTL discovery to application, and there have been numerous reports of successful tracking of genes and QTLs within breeding programmes. DNA (or molecular) markers have enabled selection of major genes or QTLs for critical or important traits in a process called marker-assisted selection (MAS), which has revolutionized plant breeding. DNA markers are used as tools by breeders to improve the accuracy or efficiency of selection as well cost and time efficiency. Apart from MAS, DNA markers have numerous applications including DNA fingerprinting, genetic diversity analysis and parental characterization.

Recent developments in genotyping platforms and systems to implement molecular breeding schemes offer new tools for modern plant breeders. Single nucleotide polymorphism (SNP) markers are biallelic, co-dominant markers which are abundant in the genome. Insertion-deletion (Indel) markers are also prevalent and can be screened using high-throughput genotyping platforms. These platforms are cost-efficient, can handle large sample sizes and provide fast data turn-around time. The availability of genome sequences and genomic resources continues to provide a wealth of SNP and Indel markers which will undoubtedly be the marker type of choice for decades to come.

The availability of high-throughput SNP platforms in conjunction with advances in computational methods has also led to the molecular dissection of traits using genome-wide association studies (GWASs) across diversity panels and the development of genomics-based molecular breeding strategies. Association mapping (AM) has now emerged as a standard method for gene and QTL discovery for major crops.

6.1 Introduction

The process by which living beings give rise to the progeny of similar kind is called reproduction. Reproduction allows both multiplication and maintenance of a genotype/line/cultivar/species. So, the process of reproduction is also called propagation, and the plant part used for this purpose is called propagule. The way progeny originate is known as mode of reproduction (also called breeding system or reproductive system). The mode of reproduction of a crop determines its genetic composition which, in turn, is the deciding factor to develop suitable breeding methods. Knowledge of mode of reproduction is also essential for its artificial manipulation to breed improved types. The methods to be adopted for multiplication and maintenance of improved cultivars are also governed by the mode of reproduction. Especially in undertaking breeding investigations with new plants the nature of reproduction must be known before efficient breeding plans can be developed. The mode of reproduction has been well established for most of our important crop species.

6.2 Mode of Reproduction

Mode reproduction in crop plants may be sexual or asexual. In sexual reproduction (also called amphimixis), specialized reproductive cells called gametes are formed by the process of gametogenesis. Fusion of the male and female gametes leads to the development of an embryo and eventually the seed. In asexual reproduction, fusion of the male and female gametes does not occur, and new plants arise from unfertilized gametes (but not from zygote), or from specialized vegetative organs such as rhizome, tuber, bulb, corm, runner, sucker, stolon, bulbil etc., or by various artificial means of propagation such as rooting of stem and root cuttings, layering, grafting, gootee, etc., or tissue culturing.

7.1 Introduction

Breeding plans are based on controlled mating (i.e., mating between selected strains) and selfing of selected strains or a combination of both. Continued selfing is practised to isolate purelines and inbreds. On the other hand, crossing (hybridization) is necessary to produce hybrids and synthetics. In crossing, self-pollination is prevented in the female parent. Male sterility and self-incompatibility easily exclude self-pollination, and so they are used in hybrid seed production.

7.2 Male Sterility

Koelreuter (1763) for the first time reported male sterility in flowering plants. Male sterility is a reproductive deficiency of some plants in which male organs in bisexual flowers become defunct. It relates particularly to nonviable pollen grains that are formed through a chain of vital processes during microsporogenesis. These processes are so delicately balanced under genetic control of many loci that mutation of any one locus may lead to the formation of non-functional microspores, and hence male sterility. In male sterility, pollen grains are non-functional (inactive); but the female gametes (egg cells) are normally functional.

8.1 Introduction

In pre-historic times, people lived as hunters and gatherers. Then, gradually they began to produce the crops they ate on piece of land, and farming was born. Wild plants have certain traits that keep them protected and productive without human intervention. However, most of them are not desired for food or other use by humans. By spontaneous mutagenesis and hybridization, occasionally variant plants were found that lacked some of the undesired traits, such as bitter taste, thorns, or had particularly attractive features, such as larger fruits and more regular tuber shape. Consequently, as time passes such variation was picked up by humans by selection of such variants, keeping and advancing them. Thus, plant domestication is the process of bringing wild species under human management. In other words, plant domestication is the process by which genetic changes (shifts) in wild plants are brought about through a selection process imposed by humans. It is a method of plant breeding in the sense that, when successful, it provides domestic types that are superior to ones previously available.

Pre-historic man domesticated virtually all of our present-day crops. But, domestication of wild species continues even today and is likely to continue for a long time in the future. For example, in many countries there is an increasing emphasis on bringing forest trees producing timber, etc. under human management. A similar trend is seen for medicinal plants and plants producing specific compounds of interest, e.g., hydrocarbons, oils, etc. Kala jeera (Bunium persicum), a perennial spice, was domesticated during 1990s in Himachal Pradesh; it is being cultivated as an orchard crop. One important aspect of domestication at present is the use of particular genes from wild relatives in the improvement of cultivated species. When a plant breeder transfers one or a few desirable genes from a wild relative to a cultivated type, he is, in a sense, domesticating the wild species in part.

9.1 Introduction

The sum total of genes in a plant species is called as plant genetic resources (also called germplasm, gene pool, or genetic stock). In other words, plant genetic resources refer to a whole library of different alleles of a plant (crop) species. Germplasm is the lifeblood of plant breeding without which breeding is impossible to conduct. It is the genetic material that can be used to perpetuate a species or population. It not only has reproductive value, but through genetic manipulation (plant breeding), germplasm can be improved for better performance of the crop. Germplasm provides the materials (parents) used to initiate breeding programme. Sometimes, what a plant breeder does is to evaluate plant genetic resources and make a selection out of existing biological variation. Promising genotypes that are adapted to the production region are then released for cultivation by the farmers. Other times, a plant breeder generates new variability by using different methods such as hybridization, mutagenesis and more recently gene transfer. This base population is then subjected to appropriate selection methods, leading to the identification and further evaluation of promising genotypes for release as cultivars. When a plant breeder needs to improve crop plants, he has to find a source of germplasm that would supply the genes needed to undertake the plant breeding programme. To facilitate the use of genetic resources (germplasm), germplasm (gene) banks are given the responsibility of collecting, evaluating, cataloguing, storing and managing large numbers of germplasm. This strategy allows a plant breeder ready and quick access to genetic resources when he needs it. The fact that Sir Otto Frankel coined the term ‘genetic resources’ only in 1968 shows that the plant breeders, though aware of the gradual loss of germplasm, failed to recognize the urgency of protecting the genetic resources of crop plants prior to a point of no return.

10.1 Introduction

Plant breeders come across two categories of characters (traits) for improvement, namely, qualitative characters and quantitative characters. Red vs white flower, round vs wrinkled seed, determinate plant growth vs indeterminate plant growth etc. are examples of qualitative trait differences. There is no overlapping of characters and no confusion during classification. Such trait differences are usually governed by one or two gene pairs, each with large effect that can be measured even in the presence of segregation at other loci and even in the presence of effects of environmental factors. These characters are very less influenced by the environmental factors.

On the other hand, most of the traits of economic importance like yield of fruits of vegetable and fruit crops, yield of vegetative parts in fodder crops, yield of lint in cotton, yield of grains in cereals, pulses, oilseeds etc., plant height, days to maturity etc. are examples of quantitative characters. Variation observed for such traits is continuous. Again, there is overlapping of trait differences. So, one cannot assign individuals to a specific class unambiguously. Such characters are influenced by environmental factors, such that phenotypes are not same when grown over locations and/or seasons.

When different plants/lines of a species exhibit trait differences, it is called variation. Variation is essential for any improvement in a crop. It may be present in the population to be improved or else it may be created by different means such as hybridization, mutation, polyploidy, domestication, plant introduction, somaclonal variation, genetic engineering etc. Now, we shall discuss the types and estimation of variation.

11.1 Introduction

In chapter 10, we have discussed the different types of variation, namely, genetic, environmental and genotype × environment interaction variations. We have also learnt how to estimate the phenotypic variance and its components including genotypic (also called genetic), environmental and g × e interaction variances from trial data. Now in this chapter, we shall discuss on the genetic components of polygenic (quantitative) variation and its implications on breeding strategies.

11.2 Genetic Components of Polygenic Variation

In this chapter whenever we call genetic variation, we mean polygenic (quantitative) variation, and we know that variation is usually measured in term of variance. However, variation, variability and variance are almost used synonymously. The genetic variance has been classified into different components by various workers. Fisher (1918) divided genetic variance into three components: additive, dominance and epistatic (interaction) variances. Wright (1935) classified genetic variance into two components: additive variance and non-additive variance (dominance and epistatic variances). Mather (1949) classified genetic variance into two components: heritable fixable variance (additive variance and additive × additive epistatic variance) and heritable non-fixable variance (dominance variance, and additive × dominance and dominance × dominance epistatic variances). Later, Hayman and Mather further divided the epistatic variance into three categories: additive × additive, additive × dominance and dominance × dominance.

12.1 Introduction

Allowing certain plants from the population to reproduce, while barring others, comprises selection. This permission for reproduction may be granted by nature or by the plant breeder. In the other words, both nature and breeder exert selection pressure. Natural selection operates through differences of fertility among the adult individuals of parent generation as well as through differences of viability among the individuals of offspring generation. Artificial selection, i.e., the selection from action of the plant breeder in the choice of parents, produces its change of gene frequency by separating the adult individuals of parent generation into two groups, viz., the selected and the discarded, that differ in gene frequency. So, selection simply implies the retaining of desirable types or culling of unwanted or undesirable types.

13.1 Introduction

F₁ plants produced by crossing two parents with contrasting characters are called hybrids. Hybrids generally exhibit increased vigour and fitness over the parents. This phenomenon is called hybrid vigour or heterosis. Thus, heterosis is the phenomenon in which the hybrid of two genetically dissimilar parents shows increased vigour at least over the mid-parental value. Heterosis is just the reverse of inbreeding depression, which results after selfing the plants of the cross-pollinated crops. Kolreuter (1761-66) was the first to report hybrid vigour in the hybrids of tobacco, Datura, etc. Most of the early plant hybridizers including Mendel (1865) had noticed this phenomenon. Shull (1914) coined the term heterosis from two Greek words, hetero (different) and osis (condition), to replace his own earlier word ‘stimulus of heterozygosis’. In current usage, heterosis and hybrid vigour are used as synonyms and interchangeable.

13.2 Types of Heterosis

Depending on the nature, origin, adaptability, reproducibility and non-reproducibility, heterosis can be categorized into two: (1) euheterosis (true heterosis) and (2) pseudo-heterosis (false heterosis, i.e., luxuriance).

14.1 Introduction

The mating or crossing of genetically dissimilar individuals is called hybridization. Hybridization results in recombination that in turn widens the spectrum of variation among individuals. So, the reason for genetic diversity in progenies of crosses is the formation of new combinations of genes. This newly created variability is then channelized into development of better cultivars.

The importance of pure line selection as a method of breeding started decreasing when plant breeders felt that the genetic variability existing in the land races of self-pollinated crops had been almost completely exploited and there was little chance for further improvement in these crops by using pure line breeding. Therefore, no option was left for plant breeders except to cross diverse individuals and combine together desirable characters in a single genotype from two or more parents. The planned hybridization which could avoid self-pollination and chance cross-pollination, soon became the main feature of almost all plant breeding programmes.

15.1 Introduction

Plant breeding aims at developing genetically improved crop cultivars with economic benefits for small-scale and commercial farmers. Population growth, dwindling agricultural land and global climate change present increasing risk to crop production. Consequently, plant breeding aims to constantly develop crop cultivars with improved yield and quality and tolerant to drought, diseases and pests. Use of genetically improved crop cultivars and better management practices are among the best strategies to increase food production and meet a projected doubling of food demand in the next 40 years. Both the public and private plant breeding sectors face several constraints, including a shortage of professional plant breeders and breeding technicians, limited budget, inadequate facilities and lack of access to information. Successful plant breeding requires adequate infrastructural investment, in addition to the actual breeding activities. The benefits of plant breeding research and development can only be realized on a long-term basis because of the inherent nature of the crops and the eminent breeding procedures involved. Plant breeding involves two main activities, i.e., pre-breeding/ germplasm enhancement and cultivar development per se. These interdependent activities are the controlling factors that determine the pace at which cultivars are released timeously and consistently to farmers. The two phases, in turn, depend upon various factors, e.g., breeding goals, genetics and agronomy of the crop, breeder’s long-term objectives, availability of testing facilities and national cultivar-registration requirements. Despite these factors, there are certain clear steps and breeding procedures found in any conventional breeding programme. These include choice of parents, making crosses among chosen parents, and selection from recombined parents followed by extensive field testing of the candidate cultivars. Maintenance, multiplication and distribution of the seed are the ultimate stages of a breeding programme. Systematically outlined conventional breeding procedures, timeframes and estimated breeding generations are essential to objectively consider the ultimate timescales required to release new and improved cultivars of all crops. The information may assist plant breeding- students, educators, researchers, project advisors, administrators and funding agencies. Dear students, in this chapter we outline the timeframes of conventional breeding procedures of clonally (also called vegetatively) propagated, self-fertilizing (also called self-pollinated) and cross-fertilizing (also called cross-pollinated) crops.

16.1 Introduction

Plant introduction is the process of introducing plants from their growing locality to a new locality. Introduction of plants from a foreign country is called foreign introduction or exotic collection. Introduction from one state to another within a country is called indigenous collection or indigenous introduction. With introduction, the process of acclimatization is associated. Acclimatization is the adaptation or adjustment of an individual plant or population of plants under the changed climate for a number of generations. Plant introduction is an oldest method of plant breeding. It is used in self-pollinated, cross-pollinated and asexually propagated crops. The material of seed-propagated crops is introduced in the form of seed and that of vegetatively propagated crops in the form of cuttings or propagules. The introduced material may be a new crop, a wild relative or a new cultivar of a crop already grown in the area. There are five important sources of plant collection, namely, (1) centres of diversity, (2) gene banks, (3) gene sanctuaries, (4) seed companies, and (5) farmers’ fields.

17.1 Introduction

Self-pollinated vegetable, spice and ornamental crops may be heterogeneous. It is exemplified by landrace cultivars. They may have originated from single plant selections but have been grown over a long period of time. Landrace cultivars are a mixture of genotypes, perhaps because of breeders’ lack of appreciation of selection techniques to produce a pure line, spontaneous mutations, chance hybridization, or a combination of factors. Natural selection in landraces has resulted in a cultivar that is well adapted to the local environment. Depending on amount of human selection, differences among genotypes in a landrace cultivar may be small and inconspicuous. On the other hand, a lack of human intervention may mean that differences among plants in a landrace cultivar will be conspicuous. After years of self-pollination, individual plants are homozygous. Selection of such individuals would result in a true-to-type reproduction of their phenotype within the limitations imposed by the environment.

18.1 Introduction

The genetic variability present in populations of self-pollinated vegetable, spice and ornamental crops is rapidly exhausted by pureline selection. For further improvement, genetic variability must be created. This is generally achieved by hybridization. After the cross has been made, F₁ is grown and seeds set on it are harvested. This makes the seed source for raising F₂ population, and so on. The segregating populations from crosses are handled according to a suitable method. The three basic methods available for this purpose are: (1) pedigree method, (2) bulk method, and (3) backcross method. There are also certain modifications of these methods.

18.2 Pedigree Method

Pedigree method is developed from the pureline system and widely used method of plant breeding for self-pollinated crops. A main difference between pedigree selection and mass selection or pureline selection is that hybridization is used to create variability for the base population in case of the former, whereas in mass and pureline selections variability is naturally present in the base populations. The pedigree method was first described by H.H. Lowe (1927). This method predominated the crop improvement programme throughout the world until 1980s. Pedigree method is common in horticultural crops, especially where readily identifiable qualitative traits are involved. Vegetable crops in which pedigree system is used include tomato, cucumber, pepper, pea, lettuce, snap and field beans, all self-pollinated crops. In general, selection is done on F₂ plants. Yield is important in many horticultural plants, but quality is equally or even more important. Quality may be associated with identifiable traits, making the pedigree system ideal for self-pollinated vegetable crops.

19.1 Introduction

In self-pollinated crops, the methods of selection aim at improving individual plants. On the other hand, in cross-pollinated crops they aim at improving a population of plants. A population is a large group of interbreeding individuals. Hence, selection is called population improvement in cross-pollinated crops. Selection in self-pollinated crops results in isolation of pure breeding lines which is the end product. But in cross-pollinated crops, it results in an improved population which is used as the commercial cultivar. Improved inbred lines (also called inbreds) for producing hybrids can be obtained from such populations. Again, like many rounds of selection being practised in different inbreeding generations in self-pollinated crops we are also practising many rounds of selection in cross-pollinated crops. But, unlike self-pollinated crops selection in cross-pollinated crops is followed by intermating to develop a new population before starting another round of selection. One cycle of selection consists of selection of individual/family and intermating of the selected units. Such cycle is repeated till we get the improved population. This method of practising the cycles of selection and recombination in a population is called recurrent selection or population improvement. Frey (1983) prefers the use of recurrent selection for closed populations where no new germplasm is added to the population during selection. Population improvement was used for a group of breeding techniques where all aspects are similar to recurrent selection but with the provision of adding new sources of germplasm whenever feasible. It is only a matter of coincidence that past history of application of recurrent selection has been limited to closed populations, but its basic aim has always been the accumulation of favourable genes, without any restriction on the migration of new genes during the course of selection. Apart from a slight nuance, population improvement and recurrent selection are two titles of the same principle and procedure of manipulating the genetic potential of populations. Recurrent selection can also be applied in self-pollinated crops.

20.1 Introduction

A hybrid cultivar (also called hybrid) is the F₁ progeny of a planned cross between inbreds, cultivars, clones or populations. Depending upon the breeding approach, the hybrid cultivar may involve two or more parents. A critical requirement of hybrid production is that the parents are divergent. This divergence is the cause of superior performance of hybrids. The outstanding performance of crops is due to the exploitation of the phenomenon of heterosis (hybrid vigour) which is high when parents are divergent. Much of what we know about heterosis breeding (also called hybrid breeding) came from the work on maize hybrid cultivar development. However, commercial hybrids are now available in many crops including self-pollinated crops.

21.1 Introduction

There are a number of field, vegetable, fruit and ornamental crops that are cultivated using asexual or vegetative parts such as stems, roots, modified flower etc. This is a heterogeneous group of plants and can be further categorized into four groups for ease in understanding the breeding methods applied to them. They are:

Group 1: Flowerless or Sterile

This group either does not bear flowers or if bears, they are sterile and do not set seed, e.g., ginger, mango ginger, turmeric, garlic, betel, many yams, etc.

Group 2: Apomicts

Apomixis has been reported in over 300 genera. But stable apomixis has been reported only in a few cultivated plants like meadow grass, citrus, mango, raspberry, etc.

Group 3: Flowers but Seed-Set Rare

In this group flowering takes place under specific situations but seed-set is limited, e.g., potato, sweet potato, sugarcane, etc.

22.1 Introduction

Mutations are sudden heritable changes in the genotype of an organism. De Vries (1900) for the first time used the term mutation (mutare in Latin means ‘to change’) for the appearance of new types in evening primrose (Oenothera) plant. In 1901 he put forth the idea of producing mutations artificially for use in crop improvement. Alberto Pirovano (1922) was first to use X-rays and ultraviolet rays for inducing mutations in plants, but his work remained unknown. So, Muller (1927) became the first known to induce mutation in Drosophila fly using X-rays. Though Stadler (1928) had started working simultaneously on barley and maize and induced mutations, he was late in reporting mutation due to longer life cycle of these plants compared to Drosophila. Mutation may be gene mutation (the result of change in the nuclear gene or plasma gene) or chromosomal mutation (change in chromosome number, structure or chromosomal aberrations of various types).

23.1 Introduction

An organism or individual having more than two basic sets of chromosomes is called polyploid and the condition is known as polyploidy. Polyploidy is an important tool to increase genetic diversity by altering the chromosome number (2x) and consequently the number of genes within a single cell. Polyploidy has been one of the important mechanisms in the evolution of many cultivated crop plants.

23.2 Types of Polyploidy

23.2.1 Autopolyploidy

The condition that arises due to multiplication of the same chromosomes of a single species is known as autopolyploidy (also called ‘simple polyploidy’ or ‘single species polyploidy’). Autopolyploids have generally larger leaves, stem and other vegetative parts and flower, fruit and seeds than their normal diploids.

24.1 Introduction

When crosses are made between two different species of a genus or between two different genera, they are known as distant hybridization (also called wide hybridization). It includes both interspecific and intergeneric hybridization. Thomas Fairchild (1717) was the first man to do distant hybridization. He produced a hybrid between two species of Dianthus, viz., D. caryophyllus and D. barbatus (Carnation and Sweet William). Intergeneric hybrid produced by Karpechenko, a Russian scientist, in 1928 is Raphanobarssica. It is the amphidiploid of cross between radish (Raphanus sativus) and cabbage (Brassica oleracea var. capitata). Unfortunately, it had roots like cabbage and leaves like radish. Triticale was produced by Rimpau in 1890 itself. It is an amphidiploid obtained from a cross between wheat and rye (Triticum and Secale). Another example is Saccharum nobilisation involving Saccharum officinarum, S. barberi, S. sinensis, S. spontaneum. Wide hybridization has been used in the genetic improvement of some crops. It is an effective means of transferring desirable genes into cultivated plants from related species and genera.

25.1 Introduction

The method of selection in which a gene/QTL (Quantitative Trait Locus) is selected on the basis of the genotype of the molecular marker (also called DNA marker) linked to this gene/QTL is known as marker-assisted selection (also called marker-aided selection). The idea of marker-assisted selection (MAS) was first advocated by Tanksley (1983). MAS can be used in combination with the conventional breeding methods or novel breeding schemes could be devised to take full advantage of the marker data. MAS has been widely used for introgression of the desired genes and QTLs using backcross programmes.

25.2 Marker-Assisted Backcrossing (MABC)

The backcross programme based on molecular marker is usually called marker-assisted backcrossing (MABC). MABC has three activities: (a) foreground selection, (b) background selection and (c) recombinant selection.

25.2.1 Foreground Selection

The use of molecular marker to select the gene/QTL being introgressed is known as foreground selection. The objective of foreground selection is to select the target gene, i.e., the gene being introgressed, without phenotypic evaluation for the trait governed by the target gene. Foreground selection for a gene/QTL will be highly desirable in a variety of situation, some of which are listed below:

26.1 Introduction

We have already discussed the basics of tissue culture techniques in Chapter 2. Plant tissue culture techniques in combination with recombinant-DNA technology are essential requirements for development of transgenic plants (will be discussed in next chapter). However, tissue culture techniques like anther, pollen, ovule and meristem culture can themselves be used for improvement of different traits or as an aid to conventional breeding methods. In recent years, isolated microspore culture has been preferred as a breeding tool and an experiment system for various genetic manipulations. Besides, using protoplast fusion and hybrid embryo rescue, distant hybridization has been successfully achieved in many crops. Protoplast fusion technique can be used for the transfer of cytoplasmic male sterility from one species to another in very short duration. Somaclonal variation generated during tissue culture can also be utilized for recovery of variants showing disease resistance or other desirable characters.

27.1 Introduction

Crop improvement depends on genetic variation present in nature or created by hybridization followed by segregation and recombination. Again, gene transfers are possible only from the lines and species that are sexually compatible with the concerned species. Interspecific gene transfers pose many problems, including the loss of F₁ hybrids during embryo development due to abortion of the endosperm in the developing hybrid seeds. Embryo rescue technique was developed to rescue such interspecific hybrid embryos, and it has been widely used for this purpose. It is to be mentioned that embryo rescue can be used only in such cases where sexual hybridization is successful in producing zygotes that begin to develop into embryos.

Besides, the technique of somatic hybridization by protoplast fusion was developed to enable gene transfer from the species that do not produce zygotes on hybridization. This method has been extensively used and some useful lines have been derived. But this method is limited to utilization of genes present in plant species. Again, the results of somatic hybridization are unpredictable since many somatic hybrids fail to regenerate complete plants and the transfer of specific genes or groups of genes depends entirely on chance.

The recombinant DNA technology (also called genetic engineering) has permitted the transfer of genes from any organism into any organism. Besides, chemically synthesized genes can be transferred and integrated into genomes of various organisms to enable the expression of these genes. A gene transferred into an organism by genetic engineering is called a transgene. 

28.1 Introduction

The stress that is caused by biological agents or factors such as diseases, insect-pests and parasitic weeds is called biotic stress. The term disease can be broken into two words: “dis” (means negative, reverse or opposite) and “ease” (means comfort, or freedom from pain or discomfort). Hence, plant disease can be defined as any harmful alteration from the normal functioning of physiological processes. Diseases may be bacterial, fungal or viral. A wide range of insects infests various crop plants. The extent of damage caused to crop plants by various organisms is usually in the order fungi > bacteria > viruses > nematodes = insects. But the relative importance of these organisms varies to a great deal in different crops. Breeding of cultivars resistant to diseases and/or insect-pests is the cheapest, safest and most dependable means of limiting the losses due to them. Resistant cultivars form an important component of integrated management of diseases and insect-pests.

28.2 Breeding for Resistance to Biotic Stresses-Diseases

Agrios (1970) has defined disease as: “Disease is a series of invisible and visible responses of plant cells and tissues to a pathogenic microorganism or an environmental factor that result in adverse changes in form, function or integrity of plant and may lead to partial impairment or death of the plant or its parts.” The organism causing disease is called pathogen, while the plant affected by the disease is called host.

The principles underlying breeding for resistance to diseases are much the same as for other characters, except for one important difference, i.e., the diseases caused by pathogens are the product of interaction between two genetic systems, that of the host and that of the parasite. Both systems are capable of variation and evolution and affect the interaction between host and pathogen. Here the breeder is required to deal with the heritable traits of both the host plant and the pathogens invading it.

29.1 Introduction

An environmental factor that interferes with the complete expression of genotypic potential of a crop is called stress. The stresses may be biotic (pathogens, insect-pests, etc.) or abiotic. The main abiotic stresses are drought, mineral deficiency/toxicity and heat or cold. The losses due to abiotic stresses can be minimized by:

Crop management: The degree of stress can be reduced by suitable agronomic/soil management practices, e.g., irrigation to relieve drought stress, soil amendments to reduce salinity.

Development of resistant cultivars: This offers the cheapest, easiest to apply and most eco-friendly approach to reduce losses due to any stress.

Indirect breeding: Evaluation of materials under stress often helps in identification of a resistant line that may become an important commercial cultivar.

???????Direct breeding: It is deliberate breeding of materials for stress resistance. When a genetically variable material is grown under the stress environment, selection can be based on survival, yield and other traits contributing to stress resistance.

Mangroves Definition

A mangrove is tree, shrub, palm or ground fern, generally exceeding one and a half meter in height that normally grows above mean sea level in the intertidal zone of marine coastal environment and estuarine regions of the tropical and subtropical coastlines (Duke 1992). The mangrove is also defined as assemblages of salt tolerant trees and shrubs. Mangroves are taxonomically heterogenous and more related to environment than terrestrial or aquatic plants.

The term ‘mangroves’ is used to define both a group of plants and a community. To avoid confusion, Macnae (1968) proposed the term ‘mangal’ for the mangrove forest community, and the term ‘mangroves’ for the plants. Other terms for the mangrove forest community are coastal woodland, oceanic rainforest, intertidal forest, tidal forest, blue carbon forest, mangrove forest, and mangrove swamp.

Generally, mangrove species are grouped into two types: Exclusive and Non-Exclusive. The exclusive species are limited to the mangrove habitat, and they are also referred to as strict mangroves, obligate mangroves or true mangroves. The non-exclusive species are mainly distributed in a terrestrial or aquatic habitat, but they also occur in the mangrove habitats and they are referred to as semi-mangroves, back mangroves or mangrove associates. Tansley and Fristch (1905) are the first to introduce the criteria to classify mangrove species into true mangroves and mangrove associates. Tomlinson (1986) used rigid criteria to distinguish true mangroves from mangrove associates. In his criteria, true mangroves possess all or most of the following features:

Origin and diversification of Mangroves

Mangroves are quite old, possibly arising just after the first angiosperms (Duke 1992). Based on the fossil evidence and recent molecular studies, it is believed that mangroves originated along the shorelines of ancient Tethys Sea and there was a dispersal along the Tethys seaway westward into the Atlantic and further into the east Pacific (long before the closure of the Panama Isthmus) and eastward into South east Asia and Australia during the Late Cretaceous or early Eocene around 80 million years ago (Duke 2006). Nypa seems to be earliest fossil evidence. However, prior to closure of Tethys sea, around 40-55 million years ago, the mangrove genera - Nypa, Acrostichum, Rhizophora, Avicennia, Pelliciera, Sonneratia, Bruguiera, Ceriops, Heritiera, and Aegiceras - were present around shoreline (Duke 2017). The closure of Tethys Seaway by the mid-Tertiary (34-50 Million years ago) by northward movement of African landmass, created a physical barrier that completely terminated the Atlantic East Pacific (AEP) and Indo-West Pacific (IWP) exchange route, and resulted in subsequent diversifications within the AEP and IWP regions influenced by region-specific events (Ellison et al. 1999; Duke 2006). The plate tectonics and other vicariant events like Pleistocene sea level rise are attributed to the current distribution pattern and disjunct distributions of species within genera. Duke (2017) hypothesised two separate westward dispersal routes in AEP: (i) a southern path along the coasts of West Africa, South America and, (ii) a northern path along the North American east coast, whereas he hypothesised two isolated pathways in IWP towards eastward dispersal: (i) a northern path along the coast to the Middle East, Southeast Asia and, (ii) a southern path along the coasts of East Africa, India, and Australia. Further he noted that collision of India and Australia with Middle East and Southeast Asia respectively, resulted complication in dispersal route. Based on the available records it is presumed that diversification of mangrove plants has largely been driven by three key processes of speciation viz., Allopatric speciation, Peripatric speciation and Parapatric speciation (Duke 2017).

Distribution of Mangroves in India

Mangrove forests in India are found along the coastline of 9 States and 4 Union Territories (Fig. 5). The mangrove habitats are broadly classified into three namely, Deltaic (Eastern Coast Mangroves), Estuarine & Backwater (Western Coast Mangroves) and Insular mangroves (A & N Islands) (Mandal and Naskar 2008). India has a total mangrove cover of 4975 km²; of which, 57% is present along the east coast (Bay of Bengal); 31% along the west coast (Arabian Sea) and the remaining 12% in the Andaman and Nicobar Islands (FSI 2019).