eChapters

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.