eChapters

INTRODUCTION
Agroforestry is a land use option that increase livelihood security and reduce vulnerability to climate and environmental change. Agro-forestry has many potential, such as to enhance the overall (biomass) productivity, soil fertility improvement, soil conservation, nutrient cycling, micro-climate improvement, carbon sequestration, bio drainage, bio- energy and biofuel etc. There are many agroforestry systems practiced in India from time immemorial, but the potential of home gardens and their socio-economic significance is very well documented.   Home gardens represent land use systems involving deliberate management of multipurpose trees and shrubs in intimate association with annual and perennial agricultural crops  and livestock within the compounds of individual houses (Fernandes and Nair 1986). Home gardens can also be called as Multitier system or Multitier cropping. Home gardens are highly productive, sustainable and very practicable. Food production is primary function of most home gardens on sustenance basis.

INTRODUCTION

Promoting agroforestry is a major opportunity to deal with problems related to land-use and CO2-induced global warming (Albrecht and Kandji 2003). As per recent projections, the area of the world under agroforestry will increase substantially in the near future. Undoubtedly, this will have a great impact on the flux and long-term storage of carbon in the terrestrial biosphere (Dixon 1995). Several studies have shown that inclusion of trees in the agricultural landscapes often improves the productivity of systems while providing opportunities to create carbon sinks (Winjum et al. 1992; Dixon et al. 1993; Krankina and Dixon 1994; Dixon 1995). The amount of carbon sequestered largely depends on the structure and function of agroforestry systems - which to a great extent, are determined by environmental and socio-economic factors. Other factors influencing carbon storage in agroforestry systems include tree species and management system. The significance of agroforestry with regards to carbon sequestration and other CO2 mitigating effects is being widely recognized. There are sound reasons to believe that agroforestry can contribute significantly to carbon sequestration. It is important that research attention is focused on this aspect of agroforestry systems (Nair and Nair 2002).

INTRODUCTION

The ultimate objective of forest tree breeding is to develop fast growing high yielding genetically improved superior strains in order to replace the wild natural forest stands so as to obtain higher forest productivity per unit area and time. A breeding programme, in fact, involves purposeful management of genetic variability present in a taxon. The variation is regulated through controlled mating. This obviously, needs detailed information on the nature and extent of genetic variation on one hand and equally on the reproductive biology of the species. A clear understanding of phenological behaviour, time of anthesis, time and duration of stigma receptivity, fertilization, mode of pollination, seed development etc. is necessary for attempting crosses between genetically different forms which is invariably involved in the breeding programmes. Although, tree breeding work has been done to a great extent on the temperate species (Devey et al. 2002; Murat et al. 2006; Gotzenberger et al. 2007), no serious efforts were made in the past on tropical forest species including Jatropha (Jatropha curcas), presumably due to the consideration that similar breeding methods may perhaps, be applied to the tropical trees as well. This, however, is not applicable, as the phenological and reproductive features are typical different to each species. It was in this background that the present research article was planned to collect information on floral biology, breeding behaviour and hybridization programme in Jatropha for subsequent application in its genetic improvement.

INTRODUCTION

Total forest cover in India is 70.17 million ha or 21.34% of the total geographical area according to the State of Forest Report 2015. Of this, 8.59 million ha (2.61%) is very dense forest, 31.54 million ha (9.59%) is moderately dense and rest of 30.04 million ha (9.14%) is open. The trees outside forest (TOF) are estimated to cover 9.26 million ha area which constitutes about 2.82% of the total geographical area of the country.  Thus the total forest and tree cover of the country is 24.16% of the total geographical area. The estimates of total growing stock of forest and TOF are 4.195 billion m3 and 1.573 billion m3, respectively. The total growing stock of wood in the county is estimated to be at 5.678 billion m3 which implies an average growing stock of 72.63 m3 ha-1 in 79.42 million ha of forest and tree cover (FSI 2016).

INTRODUCTION

Medicinal and aromatic plants (MAPs) play a critical role in the healthcare provision of much of the world’s population, whether they are used to make a decoction in rural Africa, to extract an alkaloid in Switzerland or as a health food supplement in the United States. MAPs are important from several perspectives like preventive and curative treatments and are source of income to underprivileged or aboriginal people who collect these herbal plants from forests or cultivate on their field. The importance and value of traditional and indigenous herbal medicine was the subject of WHO’s campaign during the 70’s, which led to an appeal to all member countries to do their utmost to preserve their national heritage in the form of ethno-medicine and ethno-pharmacology and to re-include the use of known and tested medicinal plants and derivatives into their primary health care in rural areas, as well as an alternative when modern medicine is not available.  Out of more than 400 plants species used for production of medicine by the Indian herbal industry, fewer than 20 species are currently under cultivation in different parts of the country (Uniyal et al. 2000). According to the Department of Ayurveda, Yoga and Naturopathy, Unani, Siddha and Homoepathy (AYUSH), India has 5,662 varieties of medicinal plants and of these trading takes place in 460, while 178 are exported in huge quantities (over 100 metric tonnes per year) and about 70 per cent of India’s population use traditional medicines derived from numerous plant species (Niraj et al. 2002; Saigal et al. 2002). It is estimated that in developing countries, about 90 per cent of medicinal and aromatic plants are harvested from wild while cultivated lands account only for 10 per cent of the total medicinal plants in active trade (Karki 2002). The increasing demand calls for cultivation of these valuable healers on commercial basis. However, the available land cannot be brought directly under MAPs cultivation. There is need to identify the landuse systems, already in practice, which may provide condition congenial for better growth and development of medicinal and aromatic plants as they are naturally getting in the wild. Tree plantations, fruit orchards and home gardens seems to be the viable option for commercial cultivation. Out of these fruit orchards could be more potential land use. Fruit trees have long gestation period of 8-10 years and till canopy development, the interspaces can be conveniently used for cultivation of medicinal and aromatic crops to get additional income. Even at later stages of orchard development trees have minimal adverse affect on the growth and yields of a number of medicinal plants grown as intercrops compared to the yields in the open (Nair et al. 1989), in some instances there may be reduction of yield of MAPs and fruit component, but the combined returns from both the components are greater than from sole cultivation. This temporal scale is even more in case of shade loving medicinal and aromatic plants. Peasants prefer fruit trees on their farms (Raintree 1992; Franzel et al. 1996) with perspective of contribution to consumption (Salam et al. 2000) and income generation (Ayuk et al. 1999; Delobel et al. 1991). Thus, these components are well thought-out to be beneficial due to low labour input and comparatively high returns round the year. This chapter presents a brief review of growth, yield and economic viability of such tree-crop combinations and further explore their potential under fruit tree based horti-medicinal agroforestry systems.

INTRODUCTION

Nearly 60% of the population of the country is dependent on agriculture. Rainfed agriculture supports 40% of the population and 75% of the poorest of the poor in the country (Pant 2001). Therefore, maintenance of health of production base stands as a prime goal to be achieved for sustainable production, prosperity and posterity. Tree culture is highly necessitated for amelioration of climate, soil, production of firewood, fodder, timber, fibre, fruit, gum etc. Hence, agroforestry is a viable option particularly in the Indian context.

INTRODUCTION

Wood has been a source of fuel from time immemorial for human societies. It has been used directly as firewood and also as charcoal. The world today is energy deficient. Energy derived from fossil fuels is costly, unsustainable and its extensive use is polluting the environment. The much talked about phenomenon of ‘Global Warming’ has been ascribed to the higher accumulation of greenhouse gasses in the atmosphere released from the use of fossil fuels and also deforestation. Wood biomass is one of a range of renewable energy resources. It has an advantage over wind and solar energy, for example, as these cannot necessarily deliver power when required. Wood besides being renewable is also a clean and carbon-lean fuel and could play a valuable role in our contribution to climate change mitigation.

INTRODUCTION

Climate change is one of the most important global environmental challenges facing humanity with implications for food production, natural ecosystems, freshwater supply, health, habitat destruction biodiversity, etc. According to the latest scientific assessment, the earth’s climate system has demonstrably changed on both global and regional scales since the pre-industrial era. Since the very beginning of civilization, land resources have been under tremendous pressure for food and forest products. Anthropogenic activities have affected the biosphere through changes in the landuse and forest management activities, thus altering the natural balance of greenhouse gases in the atmosphere. The environmental security thus, has become a serious concern across the globe. The meteorological records have shown significant increase in the environmental temperature referred to as the global warming. Human activities have increased green house gases and raised global temperature by 0.50 C over the past 100 yr, which may increase by 1.4 to 5.8°C during the next century (Bhadwal and Singh 2002). Evidence of this global crisis include the rise in global sea levels by 3.4 mm yr-1 ((http://climate. nasa.gov/vital-signs/sea-level/) through the melting of the world’s snow peaks and glaciers, which poses a threat to millions living in coastal areas. A drastic effect on splitting of huge glacier in the Antarctica has already been registered, which has thrown a challenge to save the earth, lest the very survival of the mankind will be jeopardized. Each degree rise in temperature will displace the limits of tolerance of land species some 125 km towards the poles or 150 m vertically on mountains. The Inter-governmental Panel on Climate Change (IPCC) estimates that 20 to 30 per cent of plants and animals could be at risk of extinction if average global temperatures reach the projected levels (Hawkes et al., 2000).

INTRODUCTION

Carbon dioxide gas is fundamental to sustaining life on earth for two reasons (i) it is a source of C for photosynthesis, and (ii) it acts like blanket in atmosphere that keeps the earth warm. Molecular CO₂ absorbs short wave solar radiations and release them as long wave infra red radiations. An atmospheric concentration of 300 ppm is adequate to support life on earth. CO₂ accounts for about half of the greenhouse effect. The natural concentration of green house gases (GHGs) has been essential to life on earth, creating the average temperature of 15ºC. Without the naturally occurring green house effect, the average temperature would be minus 18ºC. CO₂ concentration has now reached 400 ppm. If present trends continue then CO₂ levels would reach 600 ppm in 2100 and 1300 ppm in 2200 and level off at 1800 ppm in the year 2400 (Harvey and Danney, 2000). With increasing CO₂ concentration the amount of solar radiation absorbed by atmosphere would increase and make earth warmer. The higher atmospheric temperature can affect global hydrological cycle and alter the distribution and productivity of terrestrial biota. This can have devastating consequences for human life as each 10C increase in temperature, vegetation zones may change dramatically, moving toward the poles by 200-300 km. Further, each 1ºC of global warming will also increase water evaporation, leading to about 2% greater mean global precipitation.

INTRODUCTION

Himachal Pradesh, the mountainous state is well known for its natural wealth. It is situated between 300 22’ 40"to 330 12’ 40" N latitude and 750 45’ 55" to 790 04’ 20" E longitude in the western Himalayas. The 12 districts viz., Bilaspur, Chamba, Hamirpur, Kangra, Kinnaur, Kullu, Lahaul & Spiti, Mandi, Sirmaur, Shimla, Solan, and Una of the state covered 10.5 per cent of the Indian Himalayan Region (IHR) and 1.69 per cent of country’s geographic area. State experienced high variation in an elevation and climatic conditions. An elevation of the stateranged from 350 to 6975 metres above mean sea level (amsl.) that increases from west to east and south to north.On the basis of elevation and slope,the state is divided into fourdistinct topographical regions: (1) Shiwalik Hills, (2) Mountains-Lesser Himalaya, Greater Himalaya and Trans Himalaya, (3) Valleys-Shiwalik dun valleys, fluvial, and glacio-fluvial valleys, and (4) Mountain Passes (Singh and Kumar, 2014). Whereas, physiographically, state is divided into four agro-ecological zones: the Shivaliks’ low, mid and high-hills; and the cold and dry or the alpine zone (Table 1). The 70% of the state area is steep to very steep, about 19% is moderate to moderately steep, and 11% is gentle to nearly level slopes.

INTRODUCTION

Soil is known to harbour an array of micro-organisms. The soil micro-organisms play vital roles in the half-hidden portion of the plant i.e., the rhizosphere, where they are invariably present and are stimulated by organic substrates supplied by the plant. These are known to form the mutualistic, symbiosis with photosynthetic plants and play a key role in increasing availability of plant nutrients, the improvement of their uptake, the production of plant growth regulators, plant protection against root pathogens etc. in both natural and man-modified eco-systems.

INTRODUCTION

Phytotoxin literally means “plant poison”; it may refer to any toxin produced by a plant. Phytotoxins generally have allelopathic effect. Allelo-chemicals when added/released to substratum may be directly or indirectly harmful or beneficial to the growth and development of the associated vegetation or to the source plant itself. The definition of allelopathy accepted by the International Allelopathic Society is; “any process involving secondary metabolites produced by plants, algae, bacteria and fungi that influence the growth and development of agricultural and biological systems” (Torres et al. 1996). Allelo-chemicals are defined as bio-communicators suggesting the possibility of active mixtures, because of the findings in which single compounds are not active or are not as active as a mixture (Macias et al. 1998). 

INTRODUCTION

The interactions of plant communities – natural or man-made, with their pests are invariably complex, and the complexity further increases with the diversity of the system. When a farmer adopts agroforestry instead of monocultures, the opportunities of relatively easy monitoring of the pest and their frequent disturbance through crop rotation, tillage and burning are traded against a greater stability of the system with an increased potential for self-regulation, which is however complex and more difficult to control. For this trade to be successful in reducing pest risks, agroforesters should not merely rely on increased diversity, but should attempt to integrate into their decisions the full range of traditional and scientific knowledge on the interactions between plant species, planting designs and management practices on one hand, and pests and their natural enemies on the other hand. This obviously requires collecting knowledge and organizing in more systematic way than up to now.

INTRODUCTION

The terms agro-forestry and farm forestry are used interchangeably in India with respect to the establishment and/or management of trees on farms for productive purposes. It also particularly recognizes the use of trees and shrubs on farms to support agricultural production, protect soil and water resources, enhance biodiversity, sequester carbon, and improve landscape values. Lundgren (1982) defined “Agroforestry as a collective name for land use systems and technologies where woody perennials are deliber-ately used on the same land unit as agricultural crops and/or animals, either in some form of spatial arrangement or temporal sequence. In agroforestry systems there are both economical and ecological interactions between the different components”. It has been proposed that including a tree component within the farming system, either on bunds and boundaries (sequentially with crops) or intercropped in an agroforestry type configuration, can lead to increased land productivity while diversifying the farming enterprise (Atta-Krah et al. 2004; Huxley 1999; Young 1989), and increase economic security for small farmers (Russell and Franzel 2004).

INTRODUCTION

The entire Himalayan region is vast and its diverse geographical grouping is unique and has complex ecosystem and occupies about 18% of the total geographical area of India. Indian Himalaya (27O 50' – 37O 06' N and 72O 30' – 97O 25' E) includes the parts of trans, north-west, west, central and east Himalaya and covers approximately an area of 4,19,873 Km2 with 2500 Km length and 240 Km width. The north-western Himalayas generally represent the Himalayan tract from Kumaon in Uttar Pradesh to Chitral in Gilgit. The Himalayan ranges situated in this region exhibit a diverse climate, topography, vegetation, ecology and land use pattern. The annual average rainfall varies from 8 cm in Ladakh to over 200 cm in some parts of Himachal Pradesh and Uttar Pradesh. The vegetation may vary from the scrub in the lower hills to arctic in the Greater Himalayas. The unique physiography, climatic conditions and soil characteristics of the area has resulted in a variety of habitats and a significant biological and cultural diversity. Along the altitudinal gradient (300-800 m.a.s.l) the vegetation varies from sub-tropical, temperate, sub-alpine to alpine types. It supports about 8000 species (47.06% of the total flowering plants of India) of which 30% are endemics, 10.2% trees, 8.44% wild edibles and over 15% medicinal (Samant and Dhar 1997).

Introduction

Biodiversity provides enormous direct economic benefits, an array of indirect essential services through natural ecosystems, and plays a prominent role in modulating ecosystem function and stability. It provide farming systems and taxa the means to recycle nutrient, reduce insect, pest and disease problems, control weed, maintain good water and soil conditions, handle climate stresses while producing commodities necessary for human survival. It is estimated that 1400 m ha of croplands and agro-ecosystem may provide ecosystem services worth US$ 92 ha-1 per year in pollination, biological control, and food production amounting to total US $ 128 x 109 per year (Costanza 1997). Moreover, Thrupp (1997) explained several benefits provided through conservation of biodiversity (Figure 1). The animal and plant diversity and the knowledge of associated management of these resources are the assets with the farmers which are important in marginal and difficult farm conditions. Higher diversity allows greater access to available resources, and hence increased net primary production and decreased nutrient losses. Diversity management can constitute a central part of livelihood management strategies of farmers and communities in different production system (Rege et al. 2003). The multifunctional services of biodiversity in amelioration of agro-ecosystems as given in Table 1 have also been emphasized by both the Millennium Ecosystem Assessment (2005) and the International Assessment of Agricultural Science and Technology for Development (2008). 

INTRODUCTION

Indigenous agroforestry systems exhibit a great intricacy with respect to their components where trees, shrubs, climbers and grasses are common. In the north-western Himalaya, farmers maintain naturally regenerating tree/shrub species, particularly on edges of terraced agriculture fields without any significant input of manpower. These systems are called as indigenous agroforestry system (Ram and Singh 1996; Vishvakarma et al. 1998, Thakur et al. 2004 and 2005). Shrubs have been meeting the fuel wood requirement of the local peasants from forest as well as village wasteland and field boundaries. Shrub dominated ecosystems extend from arctic to tropical region and occur over the entire moisture gradient from desert to wetland (Specth 1979; DI Castro 1981; West 1983). 

INTRODUCTION

Biodiversity  refers to varieties of life on the Earth including  animals, plants, microbes and genes within them, their habitats and ecosystems and all variations within a given ecosystem, biome or entire planet. Biodiversity is the basis of life on Earth, important for the functioning of ecosystems, provides us with products and services without which we cannot live. Consider our food range in India. It ranges from Indian bread (chapatti), rice and rice products and related curries and other varieties made out of different vegetables. These food items are made of wheat, paddy, maize, bajra, ragi, potato, tapioca, sweet potato,  yams and corns, pulses like pigeon pea, green and black gram, Bengal gram, soyabean, vegetables like tomato, brinjal, cucumber, pumpkin, drum stick, bitter gourd, snake gourd, bottle gourd and various gourds, French bean, amaranth and  so many leafy  vegetables, spices and condiments like chilly, cardamom, ginger, turmeric, pepper, nutmeg, clove, cinnamon, cumin, coriander, fenugreek etc. This is the diversity of food we have in India. Similarly, all other groups such as herbal medicine, ornamentals, timber and non-timber species are also very diverse.

INTRODUCTION

The latest Assessment Report (AR-5) of Intergovernmental Panel on Climate Change (IPCC) has concluded that warming of the climate system is unequivocal, and since the 1950s, many of the observed changes are unprecedented over decades to millennia. The report further pointed about the warming of atmosphere and ocean; shrinking of glaciers, sea level rise and more frequent and intense extreme weather events. The most critical information pertains to the increase of the concentrations of greenhouse gases. The report figures that human influence, primarily the burning of fossil fuels, has been the “extremely likely” dominant cause of global warming over the past several decades. Based on the scientific evidences, it is reported “warming by the end of the 21st century will lead to high to very high risk of severe, widespread, and irreversible impacts globally” (Edenhofer et al. 2015).

INTRODUCTION
 
A single teaspoon of soil has more organisms than the total number of people in this planet. Therefore measuring microbial population and their activity in soil is essential in order to measure the potential of a soil to mineralize nutrients. The rhizosphere is the biologically active zone of soil, where plant roots and microorganisms interact, and is of significant importance for plant performance as well as for nutrient cycling and ecosystem functioning (Singh et al. 2004; Marschner et al. 2004., Bhaduri et al. 2015). The structure of rhizosphere microbial communities is the result of complex interactions between plant genotype and fertilization (Aira et al. 2010).

INTRODUCTION

Resource, land use patterns and erosion of homrgardens biodiversity have been at the core of the debate on sustainable ecosystem management today. Homegardens are considered as a resource system of multiple functions and an important wheels of vehicle for biodiversity, environmental and ecological benefits, food security (either directly food grains, fruits, vegetables and root crops or indirectly improving soil conditions and there by promoting understory crop productivity especially on degraded sites), soil conservation potential, nutritional security, socio-cultural as well as mitigation of the impact of climate change and job creation in developing and under developed countries. While increasing human population, urbanization and pressure on the earth’s ecosystems, has resulted in the breakdown of these traditional agroforestry systems, accompanied by increasing economic, cultural, nutritional, and environmental problems, there is little awareness that homegardens are under similar threats.

1.1 DEFINITIONS
1. Forest
Forest is the homeland of trees. Because man must protect and maintain the life of the forest and because of this;  certain natural
calamities  and  bad  use  of  the  forest  constitute  severe danger to  the forest  and the  environment at large.  In  other to divert from these difficulties, man was bound to cultivate trees. This is silviculture. Silviculture then became a science and art.

2.1. GERMPLASM COLLECTION
a. Propagation techniques
There are four main propagation techniques that are used in plant reproduction for most plants, viz;
• Seed
• Cuttings
• Marcotting
• Grafting
Note: That not all plants can be propagated by all the four methods mention above.

3.0 INTRODUCTION

There are two main types of plant reproduction / multiplication that are used and these include sexual reproduction known as seed propagation / multiplication and the asexual reproduction known as vegetative propagation / multiplication. Propagation is most often by seeds produced by plants or by plant parts like vines, roots, tubers, suckers, etc. Propagation is the natural mechanism by which plants regenerate. Seed is the organ of reproduction in flowering plants.

3.1 SEXUAL REPRODUCTION OR SEED PROPAGATION TECHNIQUES

Seed is the organ of reproduction in flowering plants. Sexual reproduction is propagation by seeds. This is the main method by which plants reproduced in nature as most plants produce seeds except in species that have separate male and female plants; e.g. Njansang (Ricinodendron heudelotii) and Black fruit (Canarium schweinfurthii)

Seed multiplication seems to be the most practicable technique by the farmers. Example Agroforestry Species that are mostly propagated by seeds are Sweet Bush mango [Irvingia garbonensis], Bitter Bush mango [Irvingia wombolo], Bitter kola, Kola nitida, Kola acuminata, Njansang [Ricinodendron heudelotii].

4.1 THE NURSERY
We distinguish several types of nurseries among which we have Permanent nursery and Temporal or Seasonal nursery.
4.1.1 Permanent nursery
Permanent nursery is a large nursery destined to produce large number of plants for several years or in other words, the place is used for several years even if the plantation center is far. It is also called the central or industrial nursery. For example, the Cameroon Development Corporation [CDC] with head quarter in Limbe has its central nursery in Bota – Limbe. Here oil palm seedlings are being transported from the nursery in Limbe to the Bomboko area in Idenau Subdivision and Illoani in Ndian Division. A special management practices is being carried out in this type of nursery notably:
• Access road for vehicles accessible in all seasons ;
• Forecast annual rotation of surface area and annual production of plants;
• Forecast species with permanent shelter to serve for the protection of pots;
• Anticipated area for irrigation systems;
• Construct a shade, store, office and a guard’s room;
• Forecast methods of plant preservation for plants destined to be transported to far stations.

5.1 PRODUCTION METHODS OR DIFFERENT TYPES OF PLANTS PRODUCED IN THE NURSERY

The different types of plants produced in the nursery include plants in plastic bags, bare-root plants, stumps, pseudo estacas, root trainers, copper coated trainers and jiffy pellets.

The most common production techniques may not always be the best. Bare-root plants and pseudo estacas are easy to transport to the field, but their survival and growth are usually very poor. Plastic bags are cheap and easily available, but they result in coiled roots and are heavy to carry to the field. Root trainers, copper coated trainers and jiffy pellets are alternative systems which may have higher initial costs for the nursery. However, the farmer will receive the benefit of fast growth and high survival in the field

6.1 PROCESSES IN THE DOMESTICATION TECHNOLOGY

6.1.1 Introduction

The world Agroforestry centre Former international Centre for Research in Agro – forestry (ICRAF) and other home base orgainsation in their programme Africa Humid Tropics Regional programmed are the leader in the science and practice of integrating working trees on small farms and in rural landscapes. In this programme trees that ensure security in food nutrition income, health, shelter and energy and a regenerated environment are domesticated. The mission of this is to increase; diversify and stabilize income, food and health strategies from practicing agroforestry approaches in general domesticating indigenous trees and their products particular.

Definition of Agroforestry

Basically agro forestry is the integration of agriculture forestry and sometimes animal production. This is a measure to maintain soil fertility, stop desertification and soil degradation. Foresters and agriculturalist have long recognized the important of these approached which have been incorporated into forestry law of severe countries. This does not only involve the planting of certain trees in farms but also the protection of certain trees species which are not to be felled or damaged during farming.

Abstract

Indian agriculture made a rapid stride, converting the country from food scarcity to sufficiency. But challenges for the Indian agriculture in 21st century are much greater than before. The growing population has to be fed and surplus has to be produced with declining land, water and threat of climate change. Food and livelihood security of increasing population is a cause of concern and has received focused attention across the globe. Food security emphasizes access to sufficient, safe and nutritious food for an active and healthy life. Similarly, livelihood security has the emphasis on income and other resources to enable households to meet their fair needs.

The horticulture which includes fruits, vegetables, spices, flowers and medicinal and aromatic plants, has proved beyond doubt its potentiality for gainful diversification. Initiatives taken by Government and other stakeholders have impacted the development in terms of increased production, productivity and availability of horticultural crops. One of the significant developments is that horticulture has moved from rural confine to commercial production and this changing scenario has encouraged private sector investment in production system management. Now the horticulture sector contributes 29.65 per cent to agricultural GDP that has achieved a growth rate of 5-6 per cent during the decade. India has emerged as the second largest producer of fruits and vegetables and has first position in several horticultural crops. Production and export of flowers have increased manifold and the country has a major stake in global trade of spices and cashew nuts. Exports of medicinal plants, fruits and vegetables have also exhibited rising trend.

Abstract

Bioinformatics is a discipline combining biology, mathematics and the technology including computational tools and databases. It is one of the fast growing fields in the scientific community. This chapter is intended to provide an overview of the important databases of bioinformatics used for research in molecular biology, taxonomy, conservation biology, forensics and medicine and for the commercial applications in pharmaceutical industry and agricultural biotechnology. This chapter also describes various internet resources available in the field of Bioinformatics.

Introduction

Bioinformatics has emerged as one of the important scientific disciplines which revolutionized application of life sciences in our day to day life. A simple definition of bioinformatics is: “Bioinformatics is the use of computational techniques for the consolidation and analysis of large scale experimental biological data”. Hence, Bioinformatics has transformed the life science discipline from a purely wet lab-based science to a computationally assisted information science.

Application of bioinformatics in life science has multi facets right from gene discovery to drug design where the knowledge on sequence, structure and function of genes and proteins take the lead. The objectives of biological database generation are to: (i) organize the large scale experimental biological data for further investigation, (ii) make the biological data available globally and (iii) avoid duplication of experiments.

Abstract

Plant genetic resources constitute the chief component of agro-biodiversity and comprise of land races, modern cultivars and obsolete varieties, breeding lines, genetic stocks and wild species. They provide the basic materials to the plant breeders to utilize genetic variability for the development of high yielding cultivars with a broad genetic base. The utilization of these genetic resources, however, depends upon their efficient and adequate characterization and evaluation, which in turn entails efficient characterization standards and appropriate strategies.

Introduction

Analysis of trait data generated from characterization and evaluation of the genetic resources is used to understand and use diversity. Currently, a large number of distance measures are available for analyzing similarity/dissimilarity among accessions based on different traits representing different types of variables. The selection of the most appropriate distance measure for each trait is the prerequisite for diversity analysis. One of the approaches is to form clusters where accessions between clusters would be more diverse than the accessions within a cluster. The clustering algorithms require a distance/similarity matrix between the accessions which can be calculated depending upon the nature or type of traits such as morphological and agronomic traits and/or molecular markers.

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.

Abstract

In recent years there has been a world-wide shift in consumer choice and preferences for herbal drugs. Herbal drugs are crude preparations of various kinds of medicinal plants. It involves dried plant or any part such as leaf, stem, root, flower, or seed. According to WHO survey, about 70-80% of the world population particularly in the developing countries rely on non-conventional medicines mainly of herbal sources for their primary health care.^[1] Herbal medicines are being widely accepted for their safety, efficacy, cultural acceptability, better compatibility with the human body and lesser side effects. With the legal acceptance in many countries of the world as an alternative system of medicine, the growth rate of ayurvedic and herbal industry is estimated to be more than 30% for the last 25 years. 

Introduction

With an ever-increasing global inclination towards the consumption of herbal medicines, there is a growing need of raw materials and to identify the active principles that should be available in optimum quantities at the requisite time. Currently, the herbal medicine sector faces numerous challenges such as narrow genetic base, identification and authentication of species, chemical characterization of active compounds and identification of the target molecules. The pharmacologically active metabolites are produced in very low amounts by the plants and their chemical synthesis is expensive, hence there is a growing pressure of procuring these active metabolites from the wild leading to diminishing the populations, loss of genetic diversity and local extinctions. Domestic cultivation of medicinal plants offers an attractive alternative but not much information is available regarding the cultivation practices for many plants and also, there are issues related to storage practices, quality, safety and stability assessment that need to be addressed. Futher, the study of secondary metabolites and their enhancement is a bottleneck due to lack of knowledge about characterized biosynthetic pathways and enzymes in many plants and how their synthesis is regulated at molecular level. To address these challenges, new molecular tools and biotechnological approaches are much warranted. However, the rapidly changing pace of technology and development of high-throughput research, the field of plant biotechnology is beginning to suffer from data overload. All biotechnological efforts have involved empirical, labor-intensive and time-consuming methods. Bioinformatics is one such approach in which biology and information technology converge. It is an interdisciplinary scientific tool that facilitates both the analysis and integration of information from ‘omics’ technologies including genomics, transcriptomics, proteomics, metabolomics and phenomics. The present chapter highlights some of the important areas in bioinformatics which play a significant role and could also have immense impact in medicinal plants research.

Abstract

The completion of large number of genome sequencing projects has generated large volumes of raw sequence data. One of the fundamental tasks in bioinformatics is the creation of databases for data storage and development of tools for analysis. The first plant genome to be completed is that of Arabidopsis thaliana in 2000^[49]. This was followed by the rice genome and others. The availability of complete genomes has provided us with an opportunity to analyze them and understand plant biology in a holistic way. It has enhanced our understanding of factors affecting plant growth and development, abiotic and biotic stress, disease resistance, host pathogen interactions amongst others.

Abstract

Manipulation of a large number of genes is often required for the improvement of even the simplest character. Molecular marker trace valuable alleles in a segregating population and mapping them. Genome mapping has emerged as a powerful new approach for research in botany, agriculture and other related fields. Genome mapping methods help to locate specific DNA markers to delineate when one has reached particular gene of interest and forming a molecular map. DNA mapping encompasses a wide range of techniques useful for studying DNA at different levels of magnification. Genetic Linkage Mapping Using Molecular Markers, Development of Genetic Maps, Mapping populations and comparative genomics are elucidated.

Introduction

Understanding biology and genetics at molecular level has become very important for better understanding and manipulation of genome architecture. Molecular markers have contributed significantly in this respect and have been widely used in plant science in a number of ways including genetic fingerprinting, identification of duplicates and selecting core collections, determination of genetic distances, genome analysis, identification of markers associated with desirable breeding traits which are useful in marker assisted breeding, genomics and development of transgenics. Use of these markers also significantly reduce breeding time and cycles required for crop improvement. Molecular level understanding of the inheritance of agriculturally important traits creates new opportunities to streamline plant breeding.

Abstract

Development of reliable automated techniques for the identification and annotation of exon and intron regions in a gene has been an important area of research in the field of computational biology. Several classical approaches like probabilistic model, artificial intelligence and digital signal processing are already in use to cater to this challenging task. In this work, we propose a Support Vector Machine based kernel learning approach for detecting splice site patterns and their conservation across the species. Electron-Ion Interaction Potential (EIIP) values of nucleotides were used to map DNA character sequences to corresponding numeric sequences. Radial Basis Function (RBF) SVM kernel was trained with cross validation using these EIIP numeric sequences. This was then tested on test gene datasets of multiple species for detection of splice site pattern. Receiver Operating Characteristic (ROC) curves and various other statistical measures have been utilized for displaying the performance of the classifier. Results indicate an inter-species splice site conversion profile.

Abstract

Support Vector Machine (SVM) is a classification and regression prediction tool, widely employed in different fields of science and engineering. A review on some recent plant bioinformatics applications using SVM is made. Different soft wares for SVM are also explained. There is a growing amount of plant genomes data currently available from different sources. Recent advances made using SVM and Feature selection in plant bioinformatics are reviewed

Introduction

Recent developments in genomic and post-genomic research have generated a vast amount of biological data. This data is growing exponentially with the advancement of research technologies. Several plant genomes have been sequenced recently. For instance, the complete sequence of Arabidopsis thaliana and the draft sequence of rice are now available^[1]. Also, sequencing of several other plants including maize, tomato, sorghum, etc is in progress. Considering the amount and complexity of this data, it is impossible for an expert to analyze and compare the data manually. Thus, there is an increasing need for computational methods that can efficiently store, organize and interpret this large amount of data.

Abstract

The field of bioinformatics emerged as a tool to facilitate biological discoveries more than 10 years ago. The ability to capture, manage, process, analyze and interpret data became more important than ever. Bioinformatics in agricultural science has many complex aspects and problems that must be resolved due to the involvement of a wide variety of fields and subjects. Consequently, the establishment of interdisciplinary research areas is required, which should include collaboration among experimental and informatics researchers in different fields within industry, academia, and government. Thus, the Agricultural Bioinformatics Special Interest Group was established to promote interaction among researchers and provide an opportunity to report on bioinformatics studies in agricultural science: design and analysis of functional foods, scientific testing of food safety, breeding of agricultural organisms, development of environmental friendly agricultural chemicals, bioremediation and production of useful chemical materials using microorganisms, measuring and monitoring biodiversity, statistical genetics in resource ecology, and so on. The activities of the Agricultural Bioinformatics Special Interest Group include (1) Studies of applied bioinformatics in the agricultural science (2) Development of new research areas in agricultural science using bioinformatics (3) Practical application of bioinformatics technologies in the field of agricultural science (4) Development of new bioinformatics technologies characteristic of agricultural science.

Abstract

Mitochondrial (mt) genomic study may reveal significant insight into the molecular evolution and several other aspects of genome evolution such as gene rearrangements evolution, gene regulation, and replication mechanisms. Other questions such as patterns of gene expression, mechanism of evolution, genomic variation and its correlation with physiology, and other molecular and biochemical mechanisms can be addressed by the mt genomics. Rare genomic changes have attracted evolutionary biology community for providing homoplasy free evidence of phylogenetic relationships. Gene rearrangements are considered to be rare evolutionary events and are being used to reconstruct the phylogeny of diverse group of organisms. Mitochondrial gene rearrangements have been established as a hotspot for the phylogenetic and evolutionary analysis of closely as well as distantly related organisms. This evolutionary episode has significant contribution among animals as well as plants and serves as an important genomic evolutionary event for the analysis of mitogenomes on large scale.

Abstract

Spices are aromatic substances of plant origin which are commonly used for flavouring, seasoning and imparting aroma in foodstuffs. They are cultivated in an area of 5.98 million ha globally with a total production of 7.31 million tons. India is considered as the home of majority of these spices from ancient times and sizable area of the country is under spice cultivation. The latest statistics shows that the total cultivated area in India under spices is 2.89 million ha with a total production of 3.33 million tonnes. About 109 plants belonging to 31 families are recognized as spices useful as ingredients in food. Many of them have been demonstrated to mediate therapeutic benefits for wide spectra of diseases ranging from multiple sclerosis to colorectal cancer.

Introduction

Advances in molecular genetics in the last 20 years like rapid DNA amplification techniques using PCR, rapid sequencing methods and computational software programs have enabled the placement of molecular markers on to the maps of chromosomes of most major crop species and the subsequent tagging of genes of interest by their placement near those markers^[38]. Unfortunately very little or scanty molecular data of spices are available in the public domain (Table 12.1). ‘Orphan crops’ like spices which have not yet received the investment of research effort or funding can exploit comparative genomics and bioinformatics to assist research and crop improvement provided they are related to a well-characterized model plant species.

Abstract

The study of palm genomics can aid to understand the genetic and molecular knowhow of all biological processes in palms that are vital tothe palm species. This knowledge will allow the path for the fruitful exploitation of palms as biological resources in the development of new cultivars of improved quality and with shortened economic and environmental costs. This knowledge is also vital for the development of new diagnostic tools. Traits considered of primary interest are resistance to pathogens and abiotic stress, fruit quality and yield. Genomics and bioinformatics approaches helped in unraveling the genomes of economicpalsm like coconut, oilpalm and datepalm. The genome characteristics and tools for genome analysis are provided in the chapter. Due to the economic importance of cocoa, many scientific research studies (genome, EST, transcriptome) have been carried out in the past years in this crop also.

Introduction

Plantation crops constitute a large group of crops. The major plantation crops include coconut, arecanut, oil palm, cashew, tea, coffee and rubber; and the minor plantation crops include cocoa (Prapulla and Indira, 2014). India is the third largest producer of coconut and goes in front of the ninety coconut-producing countries of the world (Richard 2013). India is the largest producer and consumer of cashew nuts (Mohod et al., 2011.). India also occupies number one position in arecanut production (Dwivedi et al.,2008) besides being the largest tea producers in the world. While Coffee is the second largest traded commodity in the world, it has, in recent times become an extremely important foreign exchange (Prapulla and Indira, 2014).

Abstract

Microorganisms constituting the major fraction of the total biomass, are the main source of biodiversity in our planet and play an essential role in maintaining biogeochemical processes, which ultimately regulate the functioning of the Biosphere. Molecular ecological studies of microbial communities revealed that only a small fraction of total microbes in nature have been identified and characterized so far, since the majority of them are recalcitrant to cultivation. The emergence of ‘metagenomics’ have paved ways to the analysis and understanding of the genetic diversity, population structure, and ecology of complex microbial assemblages through culture – independent genomics-based approaches. The concept, metagenome, represents the total microbial genome in natural ecosystem consisting of genomes from both culturable microorganisms and viable but nonculturable bacteria. The construction and screening of metagenomic libraries in culturable bacteria constitute a valuable resource for obtaining novel microbial genes and products. Several novel enzymes and antibiotics have been identified through the metagenomic approach from many different microbial communities. This technology in the near future will provide breakthrough advances in the field of medicine, agriculture, energy production and bioremediation. This paper looks in to the various steps involved in metagenomic studies and how its potential can be utilized in the various aspects of agriculture to improve crop production and protection. The importance and role of bioinformatics in deciphering metagenomic data are also looked into.

Abstract

Our biological heritage, from genes to ecosystems, is threatened on a global scale. Biological species, the prime focus on biodiversity, provide all our basic requirements such as food, medicine, fuel and things for well being, make nature’s sustainability through purifying air and water, pollinating crops, etc. and motivate us at a deep emotional level. During the course of human civilization and consequent urbanization process biological species and environment have been degraded. It is estimated that about 20% of all species are expected to be lost within 30 years and 50% or more by the end of the 21^st century [36]. The current rates of species extinction are 1000–10,000 times higher than the background rate of 10-7 species per year inferred from fossil record. Today, we seem to be losing two to five species per hour from tropical forests alone. This amounts to a loss of 16 m population per year or 1800 populations per hour. This led to biodiversity crisis in the global level [23,26,35] and generated an outpouring of research on biodiversity for the last 25 years. As a result we could have a general understanding about the distribution of biodiversity, the proximate causes (habitat loss, habitat fragmentation, habitat degradation, invasive species, pollution, resource exploitation) contributing to its loss, sketches of the root causes of biodiversity loss, and the outlines of better management policies. Since the establishment of the convention on biological diversity in 1992, conservation of biodiversity has become a priority concern on the international agenda.

Abstract

There has been consistent narrowing down of gap in our knowledge about various ‘omics’ as the omics’ based disciplines are filled with valuable information emerging from research. During the last two decades, the practice of genetics has not only changed the broad horizons of medicine but also found its niche through “high-dimensional biology” there by allowing geneticists to reframe the good-old definition of gene from a locatable region of genome sequence involved in heritability to a locatable region of genome sequence associated with a functional region or a functor. Various other scientists viewed genetics ‘‘as the study of single genes and their effects’’ and genomics as ‘‘the study not just of single genes, but of the functions and interactions of all the genes in the genome.’’ We will cover the qualitative difference that bridges various disciplines casing Omics.

Abstract

Advances in genome sequencing technologies have made it possible to uncover the whole genome sequences of numerous organisms from microbes to higher eukaryotes. Haemophilus influenza, a free living bacterium, was the first complete genome to be sequenced in 1995 by a team headed by J. Craig Venter and Hamilton Smith at The Institute for Genomic Research (TIGR). Immediately after this, Mycoplasma genitalium, a bacterium responsible for reproductive-tract infections and well-known for having the shortest genome of all free-living organisms was sequenced. Subsequently, TIGR unearthed the genome sequences of many microbes like Methanococcus jannaschii, Archaeoglobus fulgidus, Helicobacter pylori, Borrelia burgdorferi etc. During the years 1996-2000, the complete genome sequences of several model organisms such as bacterium Escherichia coli K-12, baker’s yeast Saccharomyces cerevisiae, nematode Caenorhabditis elegans, fruit fly Drosophila melanogaster etc were published. Since then the complete genome sequences of many other eukaryotes have been released by the genome sequencing community.

1.1 Introduction

Like animals, plants are living beings and so require water and air for their survival. In addition, they need water for preparation of food by the process of photosynthesis. Majority of this water requirement of the crops is met from different forms of precipitation. However, when the water requirement is not fully met from precipitation, then growth of the crops is affected. This results in reduction of yield of the crops. The reduction in yield depends on the amount of scarcity of water requirement of the crops. It also depends on the stage of crop growth and also depends on the types of the crops. Generally all the crops are sensitive to water stress during reproductive stage. Water requirement of crops depend on many factors. It depends on the type of crops, irrigation schedules practiced, soil texture, position of groundwater table below effective root zone of the crop and management practice followed in crop cultivation. The pulses, oilseeds, vegetables etc. which are also otherwise termed as dry land crops need less water compared to rice which is a water loving crops and perennial crops like sugarcane, banana etc.

Water requirement of crops is partly met by the upward flux of groundwater. The capillary rise of shallow water table in the form of upward flux helps in meeting the water requirement of crops to some extent. The upward flux depends on the type of the soil, effective root zone depth of the crop, depth of water table below effective root zone depth of the crop and potential gradient of soil moisture suction. If the soil is heavy like clay, effective root zone depth of the crop is more (deep rooted crop) and position of ground water table is near to ground level (shallow water table), then the upward flux is more.

2.1 Introduction

Rain and snow are the two chief sources of water of the earth. In-situ conservation of rainwater helps the plants to meet some of their consumptive uses directly. Not all the amount of rainwater that falls at a point is conserved by the soil reservoir to support the plant growth. Some part of it flows over the soil surface as surface runoff and some seeps down as infiltration and finally adds to the under ground reservoir. Therefore, rain or snow, which is not used directly by the plants, becomes a potential source of either surface or ground water for irrigation. In areas with extreme low temperature, snow contributes major source of water supply wherever, in humid and sub humid regions, rain is the principal source. Precipitation, rain or snow, is the first stage of the continual cycle of water in its round from atmosphere to the earth and return by evaporation from water bodies, snow surfaces and land surfaces. The continual cycle of distribution of water is governed by the process called as hydrologic cycle. Thus, precipitation or atmospheric water is the first form of water above the earth’s surface, the second form being the surface water on earth and the third form is the subsurface water or underground water. The study of occurrence, distribution and circulation of precipitation through the unending hydrologic cycle forms the basic part of study of hydrology. As mentioned above, the part of precipitation that is not used by the plants in-situ flows over the soil surface as runoff and contributes to either surface or ground water supply.

3.1 Introduction

Water used for irrigation can be stored mainly in three sources i.e. soil reservoir, surface reservoir or groundwater reservoir. Accordingly the storage system can be defined as soil reservoir storage system, surface reservoir storage system or groundwater storage system. Each of these storage systems has its own merit and demerit. Some of the storage systems though economical but are not helpful to store the irrigation water for longer periods. On the other hand, some other storage systems are very costly, but the irrigation water can be stored there for a longer period. However, before adopting a particular storage system, economics of the system need to be calculated. The cost of installation of the system and the water stored in the storage system and its use as supplemental irrigation to the crops to increase the production in terms of monetary benefit need to be assessed and then the economics of the system should be computed. The storage system that gives maximum benefit-cost ratio and net present value should be adopted for storage of irrigation water. The different types of storage systems are discussed below.

4.1 Introduction

Discharge is also called as rate of flow. Discharge is defined as the volume of water flowing through a cross section in a unit time. It can be expressed as cubic metre per second (cumec), cubic feet per second (cusec), litre per sec (lps) etc. One cumec is equivalent to 35.5 cusecs or 1000 lps. The measurement of discharge is very important in everyday life starting from deciding the amount of irrigation to be supplied to a crop at a particular growth stage, or amount of water supply for domestic and industrial uses, for flood control and power generation etc. It plays a vital role in water resources planning. If a stage-discharge (also called as gauge-discharge) relationship for a particular gauging site is developed, then daily measurement of discharge in the gauging site is not required. Discharge can be estimated from the developed relationship of discharge versus stage if the measurement of stage is known.

5.1 Introduction

A reservoir that collects and harvests in-situ rainfall as well as runoff from the catchment area can be used for many purposes: the most important of which is the supply of water to crops as supplemental irrigation. The water of the reservoir can be used for domestic and industrial uses. It is also a good source for recreational use. Total water demand of the reservoir including irrigation to different crops in different seasons, domestic and other non agricultural uses are to be assessed. While estimating the crop water requirement and irrigation requirement, various crops to be grown in the service area of the reservoir, their water requirements, crop duration, extent of coverage and water management practices followed are to be taken into consideration. Multiplying the irrigation requirement with crop coverage area, volumetric irrigation water requirement of crop can be found out. Summation of irrigation requirement of all crops grown in service area of the reservoir gives total irrigation demand of the reservoir.

Small farm reservoirs are normally used for irrigation to crops as well as to meet the live stock water demand. Normally the large live stocks like horse, cattle require 20 thousand litres of water per head per year whereas the small live stocks like sheep, goat, pigs require 2 thousand litres of water per head per year. Adding the irrigation demand to the livestock demand, total water requirement of the reservoir is calculated. In addition to this, water used for industrial, domestic and other sectoral purposes are to be added to irrigation and livestock demand to estimate the total water demand of the reservoir.

6.1 Soil

The term ‘soil ’is defined in various ways depending on the general professional field in which it is used. However to an agriculturist, soil is the substance existing on the earth surface, which grows and develops plant life. For an engineer, soil is the unaggregated deposits of mineral and organic particles covering major part on the earth crust. It includes widely different materials like boulders, sand, gravel, clays and silts. Soil is produced by the weathering of solid rocks. The formation of soil is due to geologic cycle continuously taking place on surface of the earth. The geologic cycle comprises weathering or denudation, transportation, deposition and upheaval, again followed by the above mentioned processes. Weathering may be natural or artificial. In natural weathering, physical processes like temperature changes, flow of water, ice, wind and rain play the role. In artificial weathering animals especially human beings interference causes soil erosion and formation.