eBook Chapters

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.

Food is the basic requirement for maintaining the life process. Plants supply the bulk of foods required for human and animal. With limited cultivable area and ever increasing pressure of human population, the demand for food is constantly rising which can not be alone met by conventional plant breeding technologies. Novel techniques like plant genetic engineering are gaining momentum for production of superior plants or yield enhancement of a species.  It has been observed that the most commercially successful application of recombinant DNA technology is in genetic engineering of plants, which led development of multinational seed companies deriving monetary benefit from genetically modified crop and food products. From production of herbicide resistant or insect pest tolerant plants to alter the inherent quality composition of human food, plant genetic engineering has established firmly the commercial viability of recombinant DNA technology.

Introduction
Plant genetic engineering has revolutionized modern agriculture, enabling the development of crops that not only meet the demands of a growing global population but also address the challenges posed by climate change, pests, and diseases. As traditional breeding methods often face limitations in terms of time, precision, and scope, genetic engineering offers a powerful alternative. By directly manipulating plant genomes, scientists can introduce specific traits with greater accuracy and speed, leading to significant improvements in crop quality and productivity. This chapter explores the protocols and methodologies employed in plant genetic engineering aimed at enhancing the quality of crops, providing insights into the techniques that have transformed agricultural practices.
The importance of plant genetic engineering cannot be overstated. With the global population projected to reach nearly 10 billion by 2050, the agricultural sector must find ways to increase food production while ensuring sustainability and environmental conservation (Tilman et al., 2011). Conventional breeding methods, which rely on the natural variation present in plant populations, can be slow and imprecise. In contrast, genetic engineering allows for the targeted introduction of desirable traits, such as disease resistance, improved nutritional content, and enhanced stress tolerance (Gurian-Sherman, 2009). These advancements are crucial for maintaining food security in the face of growing environmental challenges.

Introduction

Tomato is one of the most important vegetable crops which is grown throughout the world. It is a rich source of minerals, vitamins and antioxidants and considered as a protective food. It is used in several forms ranging from raw to processed one and is widely used as one of the food ingredient. Its popularity is due to its versatility and the variety it lends to the human diet. Tomato leads all other vegetables in terms of total global production except potato which is often classified as starchy staple. India stands fourth in terms of global tomato production after China, USA and Turkey. The total production of tomato in India during 2007-08 was 10.26 million tones which accounted for 8.9 % of total vegetable production. Though concrete historical records of its first introduction into the country from its primary centre of diversity in South America do not exist, tomato is presumed to have been brought here during the second half of the 18^th century through Far Eastern countries. It is believed that tomato was introduced in India during British period in the year 1828 by Royal Agri -Horticultural Society, Calcutta. The story of tomato transformation from an exotic fruit to a popular dietary item and a major item of commerce all over the world is one of the most fascinating events in the saga of crop domestication. As recently as 1900, tomato was avoided in the belief that it was poisonous because of its known relation to the nightshades and other toxic members of the nightshade family. The tomatine is a predominant alkaloid mainly present in foliage and green fruits. However, at the stage of ripening, tomatine is degraded into an inert compound which is not toxic.

The National Bureau of Plant Genetic Resources, commonly known as NBPGR was established by the Indian Council of Agricultural Research (ICAR) in 1976 with its main campus at New Delhi. Being the nodal organization in India it has been given the national mandate to plan, conduct, promote and coordinate all activities concerning plant exploration and collection and also for safe conservation and distribution of both indigenous and introduced genetic variability in crop plants and their wild relatives. The Bureau is also vested with the authority to issue Import Permit and Phytosanitary Certificate and conduct quarantine checks on all seed materials and plant propagules (including transgenic material) introduced from abroad or exported for research purposes.

The world’s largest collection comprising 1117 entries is maintained at Turkmenistan (CIS). They exhibit great variability for fruit size and quality, skin color, resistance to abiotic and biotic stresses but most of them are temperate in nature and do not grow well in the Indian tropics. There is scope to use this material for breeding superior types.

There are several varieties adopted to both tropical and subtemperate climate. They are either evergreen on semi deciduous or deciduous types. The flowering habit, fruiting and flower physiology are altered with the habitat. The tropical climate with mild winter of south India, growth and flowering are continuous processes, while in the subtropical climate of north India the trees remain dormant during cold winter and flowers in the following spring and in temperate climate flowering occurs in summer.

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.

The aromatic plants are the valuable source for flavours, fragrances and other pharmaceutical products. The aromatic plants possess odoriferous and volatile substances, which occur in the form of essential oils, gum exudate, balsam and oleo-resin. The chemical nature of these aromatic substances may be due to a variety of complex chemical compounds. Natural essential oils comprising a complex mixture of aroma chemicals, which are difficult to reconstitute in the chemical industry, fetch very high prices. India has a long perfumery tradition that dates back to over 5,000 years in Indus Valley Civilization. In the excavation of Harrappa and Mohanjodaro, a water distillation still and receiver have been recorded, whose shape resemble to the deg and bhabka currently used by attaries (traditional perfumers) of Kannauj in India (Gupta and Chadha, 1995).
Aromatic plants are very important part of agriculture and have been grown in India for their fragrance and therapeutic use from ages. Presently, several aromatic plants are in use for medication have come from our ancestors, inhabiting in different countries. The recent advances made in chemical and instrumentation technology led to the identification and isolation of principal chemical compounds diversely used in medicines, food, cosmetics, toiletries, bouquets, aerosols, paints, varnishes, insecticides etc (Arya et al., 2021). However, the perfumery and allied industries consume much larger amount of the natural fragrant material. Many of the aromatic plants are valued for naturally occurring essential oils and the bulk of the produce finds use in perfumery and the food flavouring industries.

Plants are vital part of the world’s biological diversity and essential resource for human well being. Besides meeting our basic food and fibre requirement, many thousands of wild plants have immense economical and cultural importance and potential for providing food, medicine, fuel, clothing and shelter for vast number of people at the global  level. Traditional Chinese medicines use around 5000 plant species and about 7000 different plants are used in traditional medicines in India. Plants play an important role in maintaining basic ecosystem functions essential for survival of animal life. Thus, it is of vital importance to collect and conserve the plant genetic resources on a global basis. It is all the more important as several cases of genetic vulnerability of plants that are grown for food and other uses have been recorded (National Research Council, 1972, Granett et al., 1991). Genetic diversity in the germplasm of crop plants is an effective defense against genetic vulnerability. The genetic diversity is strategically used as modern plant breeding intervention to help increase stability and sustainability of food production using modern cultivars.

Introduction

Plant Genetic Resources (PGR) are uniquely placed within the overall ambit of biodiversity and play an important role in providing food, fuel, clothing, medicine and shelter for the whole mankind. The value of plant genetic resources or the plant germplasm can be visualized from the fact that Sir Joseph Banks, the Director of Kew Botanical Gardens accompanied Captain Cook on a plant collecting voyage. Plant genetic resources are going to occupy the centre stage in plant breeding and seed industry development in India as will be the case with other countries. However, despite the great importance of plant genetic resources in crop improvement programmes, there is ever increasing threat to the PGR due to degradation of their habitats, changes in ecology, cropping systems, modernization of agriculture, rapid replacement of locally adapted indigenous cultivars by modern high yielding varieties and the effect of massive urbanization. This calls for a sustained and scientific management of plant genetic resources. The issue of PGR management remains basically the same whether we are dealing with field crops, vegetable crops or perennials with slight changes in specific cases. For an effective management of PGR, all the CGIAR funded international agricultural research centres have independent units/divisions on PGR management. IPGRI is coordinating and strengthening the PGR management programmes at the international level. In India, National Bureau of Plant Genetic Resources, New Delhi is the nodal organization on PGR management. This article shall deal with the core components of PGR management in vegetable crops.

Plant genetic resources (PGR) are the genetic material of plants which are of value for present and future generations of humankind. Often used as a synonym to plant germplasm, it can be defined as a seed, a plant or plant part including cell cultures, genes and DNA sequences that are held in a repository or collected from wild as the case may be and that are useful in crop breeding, research or conservation because of genetic attributes. The term is used to describe a collection of genetic resources for an organism or genetic material which forms the physical basis of inherited qualities. In brief, germplasm is the sum total of the hereditary materials in a species. Germplasm is the foundation and lifeblood of plant breeding without which plant breeding activities cannot be conducted. Germplasm is the genetic material that can be used to perpetuate a species or a population. The base germplasm can be improved for better performance of the crop. In the initial stage of a breeding programme, breeder evaluates the available germplasm lines and makes a selection from them for further test and final release to the farmers. Later on, the germplasm serves as a source of the parental lines which are used to initiate another phase of the breeding programme. Besides, using the base germplasm, breeders generate new variability using a variety of breeding methods such as crossing parental lines and developing new lines, induced mutations and more recently gene transfer. This new variability is again subjected to appropriate selection methods leading to identification and further evaluation of new and promising genotypes for release as cultivars. Generally, germplasm includes following types:

Allard (1960) defines germplasm as “the sum total of the hereditary  materials in  species” The word germplasm in context of plants is now referred to as plant genetic resources i.e. PGR.PGR is a component of the world’s biological diversity. The term biological diversity is a vast and often undervalued resource. Biological diversity includes every form of life, from the smallest microbe to the largest beast. Biodiversity is the variety and variability of all plants, animals and microorganisms and the ecological complexes of which they are part. The earth’s biodiversity – its ecosystems, species and genes – are the product of over 3000 million years of evolution. Throughout this time, small changes have accumulated in populations, resulting in a multitude of living forms closely adapted to the physical conditions they face and to each other. They supply all our food, much of our raw materials and energy and many of our medicines. Intact eco-systems also play a central role in the functioning of biosphere. Plants are of crucial importance in stabilizing climate, protecting watersheds on soils and maintaining the chemical balance of the earth. When key species are lost, vital ecological services are disrupted (Zedan, 1995).

13.1. Germplasm

Also known as genetic resources or gene pool or genetic stock.

Sum total of hereditary material i.e. all the allele of various genes, present in a crop species and its wild relatives

Introduction

The objec tive of genomic research in any species is to sequence the whole genome and to decipher functions of all the different coding and non-coding seq,uences. The technology for large-scale DNA sequencing has enabled the scientists to undertake genome sequencing project in a realistic time scale. Since the time of first ‘large’ genome sequencing in bacteriophage λ in 1983, the projects on different groups have been completed. Eg. Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, Oryza sativa, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Pan troglodytes, Homo sapiens.

There are certain species which have been chosen for genome projects as model organisms. A model organism is a non-human species that is used to understand biological phenomena with a thought of gaining insight into the working of other organisms. They are chosen on the basis of their small genome in size, diploid genetics with a few chromosomes, rapid life cycle, easily transformed, well positioned in plant phylogeny, small stature for plant growth in a small space, large number of seeds produced, convenient for discovery of gene-trait discovery at low cost and speed and well investigated. They include,

• Monocots – Oryza sativa

• Dicots – Arabidopsis thaliana

• Temperate grasses – Brachypodium

Abstract

Plant Bioinformatics is a new and rapidly evolving field driven by the advances in ‘Omics’ technologies. This chapter is intended to help both beginners and experienced researchers to develop and apply bioinformatics tools to specific areas of plant genomics research. This chapter will also help plant biologists to access and implement comparative genomics studies of the plant genes of interest. Also discussed are the databases which house the data on plant genes and genomes. The chapter ends with a review of basic Perl Programming for sequence motif analysis beneficial for plant biologists.

Introduction

Ever since the discovery of DNA structure, the field of plant genomics has experienced a dramatic change in the ways scientific problems are approached. With the recent advances in High Throughput analysis clubbed with methods like Physical mapping of genes, RFLP, RAPD, large scale EST sequencing and mRNA protein profiling, there is an enormous amount of biological data available for various analysis. As the amount of data grows tremendously, there is a demand for developing tools and methods to effectively access these assembled data for analysis, modeling, visualization and prediction. In this chapter, we emphasize on some of the key concepts in bioinformatics, tools and databases relevant to plant genomics.

There is need to find better ways and solutions to mitigate future agricultural challenges toward increasing productivity across the crops and equip them with the desirable genes for resistance to biotic and abiotic stresses and to mitigate the impact of climate change and also to make them nutritionally superior. Here comes “Plant Genomics”—a newly evolved discipline of plant sciences—targeting to decode, characterize, and study the genetic composition, structures, organizations, functions, and interactions/networks of all plant genes in a genome-wide scale. Being evolved from plant molecular genetics, biology, and biotechnology, plant genomics represents the key sub- divisions of structural, functional, comparative, evolutionary, physiological, and genetical genomics. Its development and advances, however, are tightly interconnected with plant science sub-disciplines, such as proteomics, metabolomics, epigenomics, phenomics, metagenomics, transgenomics, breeding-assisted genomics, bioinformatics and system biology as well as modern instrumentation and robotics sciences.

Plant genomics is a recent convergence of many sciences. Simply stated “Genomics” is the new science that deals with the discovery and noting of all the sequences in the entire genome of a particular organism. The genome can be defined as the complete set of genes inside a cell. Genomics, is, therefore, the study of the genetic make-up of organisms. Determining the genomic sequence, however, is only the beginning of genomics. Once this is done, the genomic sequence is used to study the function of the numerous genes (functional genomics), to compare the genes in one organism with those of another (comparative genomics), or to generate the 3-D structure of one or more proteins from each protein family, thus offering clues to their function (structural genomics). In crop agriculture, the main purpose of the application of genomics is to gain a better understanding of the whole genome of plants. Agronomically important genes may be identified and targeted to produce more nutritious and safe food while at the same time preserving the environment. Genomics is an entry point for looking at the other ‘omics’ sciences. The information in the genes of an organism, its genotype, is largely responsible for the final physical makeup of the organism, referred to as the “phenotype”. However, the environment also has some influence on the phenotype. DNA in the genome is only one aspect of the complex mechanism that keeps an organism running – so decoding the DNA is one step towards understanding the process. However, by itself, it does not specify everything that happens within the organism. The basic flow of genetic information in a cell is as follows. The DNA is transcribed or copied into a form known as “RNA”. The complete set of RNA (also known as its transcriptome) is subject to some editing (cutting and pasting) to become messenger-RNA, which carries information to the ribosome, the protein factory of the cell, which then translates the message into protein.

The methods of plant germplasm preservation or conservation depend  upon type of germplasm i.e. seed or non-seed clonal materials. 

Storage of Seeds

According to the storage tolerance of seeds to low temperature and dry environments seeds are further divided into storable (orthodox) and non-storable (recalcitrant) types. The orthodox seeds are those seeds which are fully desiccation tolerant. These basically include small seeded grain crops and vegetables. They can be stored for a long time under low temperature and low humidity environment and are separately stored in long, medium and short term storage conditions in accordance with the purpose of storage.

The diversity collection and making it available for future use is one of the most important activities related to management to plant germplasm resources. The collection of plant germplasm from their natural habitat is broadly known as plant germplasm exploration. The main reasons for collecting germplasm of given gene pool in a given geographical location are as follows (Engels et al., 1995)

Marshall and Brown (1975) have considered the subject of optimal sampling strategies for use in the genetic conservation of crop plants. The theme of this paper has been relatively narrow. These authors have defined a strategy for populations under imminent threat of extinction applicable to particularly the traditional landraces of some major crops such as wheat, rice and barley on account of danger of replacement of the landraces on a very broad scale due to the spread of modern cultivars. According to Brown and Marshall (1995) the emphasis in collecting of crop genetic resources has  changed radically over the years. Instead of crisis-driven broad scale crop specific programmes, the collection of plant genetic resources now involves 3 important elements as given below :

Many types of containers are used for growing plants in nurseries. These are clay pots, plastic pots, fiber pots, wooden pots, etc. Generally, the type of container to be used for growing a plant depends upon the kind of plant, objective of growing, choice of grower, etc. With advancement of technology, the container-grown plants are widely adopted, practiced by the nurserymen. The advantages of container grown plants are they are not prone to damage during packaging and transport. These are widely used for many fruit and ornamental plants. The different types of container and their characteristic features are as follows.

• Clay pots: Well-baked earthenware pots are used for raising plants. These are available in different shapes and sizes. On the basis of shape and size; these are named by pela, parali, kundi, nand, khobada, etc. Porous nature of the clay pots permits aeration, and water movement. Pot made with clay soil and well-baked will last longer than those made with sand or loamy soils. Before using, these are dipped in water for some period to soak the water in the pot itself sufficiently. However, earthen pots are heavy in weight, possibilities of breakage during potting and repotting and hence are less durable.

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

Soil salinity is one of the most serious environmental issues that limit agricultural productivity. Most of the food crops belong to glycophytes and hence, they are not able to withstand salinity stress. Salt stress significantly affects the various morphological, biochemical and physiological processes of the plant which leads to poor plant growth. Therefore, there is an emergent need to find out mitigation strategies to cope with the deleterious impacts of salt stress. Plant breeding techniques, efficient resource management and genetic engineering have been employed to cope with salt stress but these were of limited success as salt tolerant trait is complex both genetically and physiologically. Therefore, using plant growth promoting bacteria seems to be a cost effective and sustainable approach for salinity stress management. Hence plant growth promoting bacteria could play a significant role in alleviating salt stress. This chapter endeavor to provide an overview of the various important mechanisms such as facilitation of nutrient uptake, production of phytohormones, ACC deaminase production and siderophore production employed by the plant growth promoting bacteria to enhance the plant growth under salinity stress.

Abstract

The concern of global food security is growing day by day as the agriculturally available land is reducing each day with the expansion of industrialization and urbanization. During the course of urban and industrial development, crop production is greatly affected by global warming, contamination of hazardous materials, salinity and drought. To combat against such adversities, scientists have taken several additives measurement like development of transgenic crops, application of indigenous plant growth promoting microbes etc. for sustainable agriculture. Use of plant growth promoting microbes is getting popular day-by-day as they occupy a privilege niche with the autochthonous flora of specific environment. For the expanse of food and shelter, the microbes supply a wide range of plant regulators (e.g. auxins, cytokinins, gibberellins, ABA, phenols, NH₃ etc.), antibiotics, alkaloids, steroids, terpenoids, diterpenes, enzymes (e.g. cellulases, lipases, proteinase, esterases etc.) etc. for overall development of the plant. Apart from growth promotion, it also protects the plants against pathogenic invasion creating a competition with pathogens for nutrition and habitat. In near future, formulation of different plant growth promoting bacteria (like alpha- Azorhizobium, Azospirillum, Ancylobacter, Rhizobium, Bradyrhizobium, Sinorhizobium, Novosphingobium sp., beta- Burkholderia sp., gamma- Acinetobacter, Aeromonas, Azotobacter, Enterobacter, Klebsiella, Pantoea, Pseudomonas, Stenotrophomonas sp. Proteobacteria, Bacillus sp., Paenibacillus sp. and Actinobacteria- Microbacterium sp. etc.) and fungus (Aspergillus, Trichoderma, Penicillium etc.) may reduce the use of pesticides and chemical fertilizer to promote greener ways of crop production.

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.

Abstract

The greatest challenge facing us in the coming years is to produce adequate amounts of basic necessities of food, feed, fibre, fuel and raw materials for the rapidly shrinking per capita agricultural land. One alternative is to make a sustainable use of existing marginal lands. In many regions of the tropics and sub-tropics, the need to use marginal low-input soils with usually inadequate nutrient(s) supply permits only very low or unreliable yields to be achieved. It is frequently not possible  to supply required amounts of mineral fertilizers or chemical pesticides because of the low purchasing power of the marginal farmers. In particular, it is not possible to compensate for the deficient nutrient supply and this constitutes a yield limiting factor. The role of soil microorganisms in sustainable productivity has been well construed. In recent years, root inhabiting (rhizozosphere) bacteria (rhizobacteria) is gaining importance.

Introduction

Plant growth in agricultural soils is inf luenced by a myriad of abiotic and biotic factors. As a routine practice growers normally use physical and chemical approaches to manage the soil environment to improve crop yields while the application of microbial products for this purpose is less common. An exception to this is the use of rhizobial inoculants for legumes to ensure efficient nitrogen fixation; a practice that has been occurring in North America for over 100 years (Smith, 1997). The region around the root, the rhizosphere, is relatively rich in nutrients, in expense of as much as 40% of plant photosynthates from the roots (Lynch and Whipps, 1991). Consequently, the rhizosphere supports large and active microbial populations capable of exerting beneficial, neutral, or detrimental effects on plant growth. The importance of rhizosphere microbial populations for maintenance of root health, nutrient uptake, and tolerance of environmental stress is now recognized (Bowen and Rovira, 1999; Cook, 2002). These beneficial microorganisms can be a significant component of management practices to achieve the attainable yield for in other words a crop yield limited only by the natural physical environment of the crop and its innate genetic potential (Cook, 2002).

The prospect of manipulating crop rhizosphere microbial populations by inoculation of beneficial bacteria to increase plant growth has shown considerable promise in laboratory and greenhouse studies however, responses have been variable in the field (Bowen and Rovira, 1999). The potential environmental benefits of this approach, leading to a reduction in the use of agricultural chemicals are fitting the sustainable management practices. Realizing the biological interactions occurring in the rhizosphere, recent progress are in need to fulfill the practical requirements of inoculant formulation and timely delivery which would increase the technology’s reliability in the field and facilitate its commercial development.

Plant Growth Promoting Rhizobacteria (PGPR) are root-colonizing bacteria that form symbiotic relationships with many plants. The name comes from the Greek rhiza, meaning root. Though parasitic varieties of rhizobacteria exist, the term usually refers to bacteria that form a relationship beneficial for both parties (mutualism). They are an important group of microorganisms used in biofertilizer. Biofertilization accounts for about 65% of the nitrogen supply to crops worldwide. The term PGPRs was first used by W. Kloepper in the late 1970s and has become commonly used in scientific literatures. PGPRs have different relationships with different species of host plants. The two major classes of relationships are rhizospheric and endophytic. Rhizospheric relationships consist of the PGPRs that colonize the surface of the root, or superficial intercellular spaces of the host plant, often forming root nodules. Endophytic relationships involve the PGPRs residing and growing within the host plant in the apoplastic space.Some common examples of PGPR genera exhibiting plant growth promoting activity are: Pseudomonas, Azospirillum, Azotobacter, Bacillus, Burkholdaria, Enterobacter, Rhizobium, Erwinia, Mycobacterium, Mesorhizobium, Flavobacterium, etc.An ideal PGPR should possess high rhizosphere competence, enhance plant growth capabilities, have a broad spectrum of action, be safe for the environment, be compatible with other rhizobacteria, and be tolerant to heat, UV radiation, and oxidizing agent.

Introduction

Lithosphere, including the earth’s crust, is helpful in providing the base or medium for sustenance of most life processes and forms, interwoven in fine network interdependencies within themselves and the environment surrounding them i.e. ecosystems. Terrestrial ecosystem contains an important dynamic living matrix termed soil, which is critical for agricultural production and food security. Soil forms the medium for growth and maintenance of a variety of plant species while the plant roots in the soil represent a four dimensional region in space and time of profuse activity relative to the bulk soil, revolving around pH, nutrient, redox potential, and exudate gradients changing as distance from the root increases (Marschner, 1995). The soil region adhering the plant roots is being strongly influenced by the presence of these roots and is characterized by high rates of microbial population and activity and referred as rhizosphere (the soil adhering to plant roots).

Unlike root-free soil, the rhizosphere around growing plants is a very dynamic environment that hosts a much higher number of microbes, in particular bacteria. Microbes interact with each other and with plants in symbiotic, associative, neutral or antagonistic ways. A plant colonized or penetrated by a microorganism can either result in asymptomatic or disease or form an association or symbiosis, depending on the cells’ perception of each other and how the environment affects that interaction. Microbes that penetrate and colonize plants have developed elaborate strategies to subvert plant defenses.

INTRODUCTION

Biological control involves the suppression of pests/organisms with other organisms.  It is an eco-friendly method for management of plant pathogens which can be done exploiting the fungi (Ampelomyces, Trichoderma, Coniothyrium, Candida etc.) or bacteria (Agrobacterium, Bacillus, Pseudomonas and Streptomyces) from rhizosphere,  as well as phylloplane and endophytes (Jayaraman and Verma, 2002). The rhizosphere microfloras are predominantly composed of gram negative pseudomonads.  The fluorescent pseudomonads constitute a large proportion of the rhizosphere microflora presumably due to their nutritional variability being able to use a large number of organic substances (Stolp and Gadkari, 1981). However earlier workers used fluorescent pseudomonads extensively they now prefer Bacillus sp. due to their spore forming ability and heat tolerance which make its formulation easier.

The rhizosphere is the narrow zone of soil surrounding the root that is under the immediate influence of the root system. This zone is rich in nutrients when compared with the bulk soil, due to the accumulation of a variety of organic compounds released from roots by exudation, secretion and deposition. Organic compounds released by plant roots include amino acids, fatty acids, nucleotides, organic acids, phenolics, plant growth regulators, putrescine, sterols, sugars and vitamins. Because these organic compounds can be used as carbon and energy source by microorganisms, microbial growth and activity is particularly intense in the rhizosphere.

Abstract

Rhizobia are soil bacteria that fix atmospheric dinitrogen after establishing symbiotic relationship inside the root nodules of legumes (Fabaceae). Plant Growth Promoting Rhizobacteria are the group of bacteria which thrive in the rhizosphere region and enhance the plant growth through direct & indirect mechanisms. Pulses are being inoculated with specific rhizobial strains to have better nodulation in India. The native rhizobial strains from the root nodules of legumes from different agroclimatic zones of Odisha was isolated, characterised and screened for PGP activities. Out of all eleven isolates showed similar characteristics with the family Rhizobiacae. Among them six isolates contained nif-gene and PGPR activity (B2, B4, B5, B6, B7 and B8) were applied to seeds, that helped in faster germination and better elongation of root and shoot. The observations were statistically significant.

Any substance or mixture of substances intended through physiological action, for accelerating or retarding the rate of growth or maturation, or otherwise altering the behaviour of plants or the produce thereof are known as plant growth regulators. It does not include plant nutrients, trace elements, nutritional chemicals, plant inoculants and soil amendments.

Plant hormones are organic compounds other than nutrients, synthesize by plants and regulate plant growth and development. They are active in very low concentrations, produced in certain parts of the plants and are usually transported to other parts where they elicit specific biochemical, physiological and morphological responses. They are also active in tissues where they are produced. The term plant growth regulator is usually used to denote a synthetic plant hormone, but most of the synthetic compounds with structures similar to those of the natural hormones have also been called hormones. For instance, the synthetic cytokinin, kinetin is considered a hormone.

Introduction

Plant growth regulators are defined as small, simple chemicals produced naturally by plants to regulate their growth and development and are essential for regulating their own growth. They act by controlling or modifying plant growth processes, such as formation of leaves and flowers and elongation of stems.

In modern forest nursery raising, the benefits of extending the use of plant hormones to regulate the growth of economically important plants have been established. There are two possible goals in inducing trees to form floral buds, in particular, female buds. The first is to achieve precocity. Precocious flowering in normally immature trees can provide advantages in breeding and seed production because it overcomes a substantial seed production delay intrinsic to late-maturing conifers. The second reason is the phase change from juvenile growth to mature growth. The induction of either precocity or increased male flower and female cone formation are generally the result of applied treatments. A few studies have focused on the intrinsic physiological differences between high and low producing clones.

Plant growth regulators are organic substances other than nutrient, which is required in minute quantity to modify the plant growth processes. PGR has very important role in fruit breeding which is used in every facet of crop improvement e.g. multiplication of hybrids/selection through asexual means or by micro propagation, breaking of seed dormancy, growth control, regulation of flowering, fruiting and induction of sterility in reproductive organs etc (Dhatt, 1985). Details of the various uses of plant growth regulators are given as under.

Growth

Growth means quantitative increase in the planwt body e.g., increases in the length of stem, roots, number of leaves, fresh and dry weight of fruits etc.

Development

It refers to the qualitative changes from the initiation of growth to the death of a plant or plant parts like seed germination, formation of flowers, fruits and seeds, emergence of buds, leaves and falling of leaves and fruits.

Plant hormone is an organic compound synthesized in one part of the plant body and translocated to another part where in very low concentration it causes a physiological response. However, this definition could not demarcate the vitamins and other growth influencing substances from hormones. For this reason, the term Phytohormone was introduced with included vitamins, growth hormones and flowering hormones. Phytohormone can be defined as an organic substance produced naturally in higher plants, controlling growth or other physiological functions at a site remote from its place of synthesis and active in minute amounts, whereas, an organic substance, which promotes growth, i.e., irreversible increase in height or volume, when applied in low concentration to the shoots of plant is known as growth hormone.

The plant hormones are naturally occurring as they are synthesized by the plant. On the other hand, there are several manufactured chemicals, which often resemble the hormones in physiological action and molecular structures, are called growth regulators. Generally, there are five classes of phytohormones.

The phytohormones universally present in all plants are classified as under:

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.

The quantitative increase in plant body such as increase in the length of stem and root, the number of leaves etc., is referred to as plant growth whereas, the qualitative changes such as germination of seed, formation of leaves, flowers and fruits, falling of leaves and fruits is referred as development. Utilization of these substances for proper development of the plant is regulated by certain chemical messengers called plant growth substances or plant growth regulators, which in minute amounts increase or decrease or modifies the physiological process in plants. Plant growth substances are the chemical other than nutrient which required in very small amount but without which plant can not complete their physiology.

The two sets of internal factors, viz., nutrition and hormone control the growth and development of the plant. The raw material required for growth is supplied by nutritional factors which include the minerals, organic substances the protein, carbohydrates, etc.

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:

Plant growth

Definition: The quantitative increase in plant body such as increase in the length of stem and root, the number of leaves etc., is referred to as plant growth.

Plant development

Definition: The qualitative changes such as germination of seed, formation of leaves, flowers and fruits, falling of leaves and fruits is referred as developement.

Phytohormones

Definition: These are the organic substance or hormones produced by plants which in low concentrations regulate plant physiological process. It is synthesized in one part of plant and translocated to other parts. These are endogenous substance means naturally occurring in the plant.

The quantitative increase in plant body such as increase in the length of stem and root, the number of leaves etc., is referred to as plant growth whereas, the qualitative changes such as germination of seed, formation of leaves, flowers and fruits, falling of leaves and fruits is referred as development. Utilization of these substances for proper development of the plant is regulated by certain chemical messengers called plant growth substances or plant growth regulators, which in minute amounts increase or decrease or modifies the physiological process in plants. Plant growth substances are the chemical other than nutrient which required in very small amount but without which plant can not complete their physiology.

The two sets of internal factors, viz., nutrition and hormone control the growth and development of the plant. The raw material required for growth is supplied by nutritional factors which include the minerals, organic substances the protein, carbohydrates, etc.

Phytohormones: These are the hormones produced by plants which in low concentrations regulate plant physiological process. These usually move within the plants from a site of production to a site of action.

Plant growth regulators: These are organic compounds other than nutrients, which in small amounts promote, inhibit or otherwise modify any physiological process in plant.

It may be defined as any organic compounds which are active at low concentrations (1-10 ml) in promoting, inhibiting or modifying growth and development in plants. The naturally occurring (endogenous) growth substances are commonly known as plant hormones, while the synthetic ones are called growth regulators.

Plant hormones: It is an organic compound synthesized in one part of plant and translocated to other parts, wherein very low concentration causes a physiological response.

The plant hormones are identified as promoters (auxins, gibberellin, and cytokinins), inhibitors (abscisic acid and ethylene) and other hypothetical growth substances (Florigen, death hormone, etc.).

Plant growth regulators are defined as chemicals other than nutrients and vitamins which regulate (or) modify the physiological process ofthe plant. A plant hormones or phytohormones are chemical substances which are naturally produced by plant in specific organs and are translocated from site of synthesis to the site of action. They bring about specific physiological response, even in very low concentration. The quantity of synthesis of these hormones differ from plant to plant, plant internal and external factors. They are readily absorbed and these chemicals move rapidly through the tissues when applied to different parts of the plant. A plant growth hormone may be termed as a plant growth regulator, but not vice - versa, since other than natural plant hormones, plant growth regulators are synthetically manufactured chemicals.

Plant growth regulators have a diverse chemical composition. Based on the general response the chemical mediates in the plant system, they are classified as growthpromoters and growth inhibitors/retardants. However, a particular growth regulator may be growth promoter at a lower concentration and growth inhibitor at higher concentration.

Plant growth regulators or phytohormones are organic substances produced naturally in higher plants, controlling growth or other physiological functions at a site remote from its place of production and active in minute amounts. Thimmann in1948 proposed the term Phytohormone as these hormones are synthesized in plants (Thimmann, 1963).

1. Introduction

In the field of sustainable agriculture our main aim to produce high quality, safe and affordable food for ever-increasing worldwide population. Today, global agriculture is at crossroads and this is the consequence of climatic change, increased population pressure and detrimental environmental impacts. Furthermore, agricultural growers and producers have the additional constraints of economic profitability and sustainability. During the last couple of decades excessive amounts of chemicals are used to improve plant health, productivity and for management of plant pathogens, which has disturbed the ecological balance of soil and has led to the depletion of nutrients. Therefore, there has been ever-increasing interest to develop new mechanisms to ensure food security through sustainable crop production system that will supply adequate nutrition without harming the agroecosystem. Plant growth in agricultural soil is influenced by many abiotic and biotic factors. There is a thin layer of soil immediately surrounding plant roots that is an extremely important and active area for root activity and metabolism which is known as rhizosphere.

Failure in timely diagnosis of diseases and other pests has often been responsible for devastating losses. Reducing crop losses by keeping pests at bay is crucial to food security. Plant clinic is an innovative paradigm which plays a vital role in assuring food security and ushering prosperity by providing timely diagnosis and rendering necessary advice to the growers, gardeners and other stakeholders for managing pest problem in India. Plant clinics are all about plant health. Though the major role of plant clinic lies in diagnostics and advisory, the activities of plant clinic extend beyond plant clinic, with emphasis on extension, working more closely with farmers and organizations involved in promoting food production. The role of plant clinics beyond diagnostics and advisory. These are:

The term “plant health” has two overlapping meanings. In the more specific meaning, plant health refers to plant quarantine, while in the less specific use, it covers all areas of plant protection, such as plant pest management, plant quarantine, and pesticide regulation and application.

Thiamann (1948) designated the plant hormones by the term ‘phytohormones’ in order to distinguish them from animal hormones. He defined a phytohormone as “an organic compound produced naturally in higher plants, controlling growth or other phy-siological functions at a site remote from its place of production and active in minute amounts.”

According to Johannes van Over-beek (1950), the plant hormones are defined as “organic compounds which regulate plant physiological process – regardless of whether these compounds are naturally occurring and/or synthetic; simulating and/or inhibitory; local activators or substances which act at a distance from the place where they are formed.”

When crops are grown in either intercropping or sequential cropping interaction between different component crops occurs which is essentially a response of one species to the environment as modified by the presence of another species is commonly referred to as interference or interaction.

The interaction are classified into three groups

1. Competitive interaction: One species may have greater ability to use the limiting factor and will gain at the expense of the other and this is called competitive interaction or when one or more growth factors are limiting, the species that is better equipped to use the limiting factor(s) will gain at the expense of the other and this is called competitive interaction.
2. Non competitive: If the crops are grown in association and the growth of either of the concerned species is not affected, such type of interaction is called non competitive interaction or if resources (growth factors) are present in adequate quantities, as a result of which, the growth of either of the concerned species is not affected, then it is non-competitive interaction or interference.
3. Complementary: If one species is able to help the other, it is known as complementary interaction or if the component species are able to exploit growth factors in different ways (temporal or spatial) or if one species is able to help the other in supply of factor (like legumes supplying part of N fixed by symbiosis to non-legumes), it is complementary interaction or interference and also referred to as Annidation.