eChapters

Introduction

Barley is an important cereal crop grown all over the world and is used mainly for feed and malt purposes and little for human food. Barley is the world’s oldest grain, as evidenced by discoveries in ancient cities in the Middle East and North Africa. It has been cultivated for about 8,000 years, and today is the world’s fourth largest cereal crop. Considerable evidence is available that points to the role of barley as sustaining food source in the evolution of humans. Additionally, alcoholic beverages of various types and fermented foods prepared from barley are commonly referred to in the ancient literature. As other food crops (wheat, rice, corn and rye) became more abundant, barley was relegated to the status of “poor man’s bread”. In the United states, barley used as food is 1.5%, as animal feed 65% and in malt and alcohol production 30% (Newman and Newman, 2006). In 1991, barley used as food in European countries was even lower (0.3%) than the United States. In contrast, during the same time period food was the largest for barley in Morocco (61%), China (62%), India (73%), and Ethiopia (79%). However, current consumer interest in nutrition and human health may help restore barley’s status in the human diet. Nutritional qualities of barley have been known since ancient times. For example, Ajgaonkar 1972 described how ancient Indian physicians effectively stabilized type II diabetics some 2400 years ago. Treatment was remarkable simple and not really different from recommendations that are given to diabetic patients today, i.e., lose weight, change diet, and increase exercise.

Introduction

Rice is grown in more than 100 countries in the world and is an important crop for nutritional security of large part of the population. World rice production in 2007 was approximately 645 million tones. Around 50 countries have an annual production of more than 1 million tones. Ninety percent of the total rice is produced in Asian countries, with two countries, China and India, growing more than half the total crop. Top ten rice producing countries are China, India, Indonesia, Bangladesh, Vietnam, Thailand, Myanmar, Japan, Philippines, and Brazil. In Bangladesh, Cambodia, Indonesia, Lao PDR, Myanmar, Thailand, and Vietnam, rice provides 50-80% of the total calories consumed. Major part of the rice is consumed locally where produced and only 6-7% of world rice production is traded internationally.

Introduction

Maize (Zea mays, or corn as it is known in some countries) is the principal cereal crop in tropical and subtropical regions throughout the world. The increasing use of maize as a staple food reflected the much higher yields per hectare, compared with wheat, rye and barley. Because maize was cheap, it became the dominant food and main source of dietary energy and protein for poor people, particularly those in rural and underprivileged segments of society. Maize is considered to be a native of the Americans. There are different views about the introduction of maize in India. One view is that maize was introduced into India by the Portuguese during the seventh century. Other view is that maize was introduced in Pre-Colombian era through the Atlantic Arabian trade route. This is supported by the more recent variability that has been observed in the maize collections made from the north eastern Himalayan region. However, the historic records regarding the cultivation of maize in India date back only to the Maratha Empire.

Definition, Significance and Importance

Landscape design and gardening is the technique of design application to beautify our surroundings, our homes, office buildings and everywhere in open space with plants and garden features to give the soothing effect on the body, mind and soul. Rapid urbanization, industrialization with population explosion has been constantly depleting our natural resources through deforestation, ripping of hills and exposing them to erosion, pollution of rivers, streams and lakes with little understanding of the natural environment which supports human life. It is the application of the art and techniques of Landscape Gardening that can spell magic to our surroundings enhancing aesthetic beauty besides, improving and conserving environment. Besides, landscape beautification and ecological balance provision, other beneficial influence of gardens in human life have been researched and studied. Psychologists have found that access to plants and green spaces provides a sense of rest and allows workers to be more productive. Flowers convey our inner feelings sympathy, romance or celebration (pride and joy) or contrition in the most beautiful and delicate manner. Flowers are also used to express religious feelings. Interaction with gardens and natural spaces offers a variety of mental, physical and social beneficial influence for humans, ranging from stress reduction, quicker healing and mitigation of Attention Deficit Disorder in children to decreasing crime and air pollution. Studies throughout the world have proven the power of green spaces to improve human health. Recent studies in the Netherlands and Japan show that people with easy access to green space showed better health and lower mortality rates.

Gardens have been considered important, sacred from ancient time and the styles developed being inspired form its surroundings. Thus the influences of climate, general landform, religion, spiritual vision, culture, nation, prevailing political conditions, social factors, architectural styles, etc have influenced in developing specific garden style in a particular region. These styles developed slowly over hundreds of years and remained insulated and remained intact till the travelling approach between different countries got well established. Later as the mobility between different countries became widespread, these style forms became intermingled and refined even to new forms. This resulted into the development of Japanese garden style or the arts of ‘bonsai’ making which had its origin in China, or the creation of west coast American garden that originated from the Bauhaus and modern movement that stated life in Germany, the mughal garden style in India based on Persian style from Iran etc.

Basically, the different garden styles can be classified into formal, informal, intermediate and wild garden styles. Aristotle, the father of mathematics and Pythagorus, the father of geometry and disciple of Aristotle, strongly influenced the geometry, mathematics and calculative features of formal garden style. While informal garden style have evolved from the eastern vision of thoughts, originated with Laotsu and Confucious contemplation (preaching) that manifested gardens to express peaceful and compassionate atmosphere influencing meditation, silence and internal harmony.

Modern garden designs are classified on the basis of utility, need, location and materials used. Nowadays, garden types are focused on issues contributing towards ecological balance, biodiversity, environmental moderation and sustainability as well as personal preference and taste. This has given new perspectives to roof gardening, rock gardening, home gardening, kitchen gardening, green belt development, traffic islands, avenue plantation etc. Further there is incorporation of alternative energy sources like solar systems, water harvesting, etc. A garden could be for entertainment or a place to relax for some people and for others, a productive kitchen or herbal garden is more important. Some common garden types are given below, where in it is also possible to combine elements of two or three different types to create something entirely different.

Garden should serve the feelings of comfort and pleasure along with soothing effect on mind and soul of the owner and the visitors. This should be the basic aim of the landscape designer along the budget. Landscape artist should never imitate another garden which has secured popularity but should develop one’s own design. Every plot or site may not be even and ideal for designing a garden. The principles of landscape design work together to create the overall look of the garden. Natural undulations of a barren landform should be utilized with its advantages and also to break the monotony of leveled plain. The principles of garden designing interact with the elements of color, texture, line, form and scale to develop a unified landscape design that blends the beauty of nature with the splendor of modern architecture.

Landform, water and plants form the three basic elements of garden designing. Each of these basic element is described and discussed in detail.

I Landform

“Landform” refers to three-dimensional relief of earth’s surface. Thus, in simple words it is the lay of land, synonymous with, “topography”. Land is defined as the surface of the earth and all its natural resources. Landform is thus 3-D view of earth’s surface including all the visible feature of an area of land and landscape refers to the picture representing a view of natural inland scenery. Landform is the common module in exterior environments, a base, an axis, a thread, which ties all the physical elements, space together along the horizon or the water edge. Landforms can be classified as macro-landforms, micro-landforms and mini-landforms. Macro-landforms refers to valleys, mountains, rolling hills, prairies, desert, seashore and plains. Micro-landforms refers to mounds, slopes, level areas or elevation changes using steps and ramps. Mini-landforms refers to subtle, undulations or ripples of a sand dunes or the textural variation of stones and rocks.

Different techniques are used for explaining and representing the type of landform. These include (i) Contour lines, (ii) Models, (iii) Ratio method, (iv) Value and colour, (v) Spot elevation, (vi) Computer graphics, (vi) Hatches (disconnected lines are used) and (viii) Percentage method. These techniques are used for proper study of the landform, to identify loopholes and need to modification in order to establish proper drainage or to modify the site in order to accommodate of various elements or to create an aesthetically pleasing ground plan.

Definition and Significance

Garden Components are the garden features that form the expressions of garden, adding charm to the basic garden landscape and constitute its style, contributing strongly to its texture and structure. Thus, garden features are important as they provide face lift to the garden skeleton, giving it a filling effect with charismatic appeal. Garden features include garden wall, fencing, arches, pergolas, hedge-edge, topiary, etc. Creating sudden and unexpected change of scenery sometimes reveal good contrasts. Thoughtful planning of garden features make an invaluable contribution to garden design. It is possible to design a garden with a large number of man-made artistic items. However, indiscriminate and haphazard use of these items results in clutter. Further, new and strange features in the garden always attract visitors and give unbounded pleasure. During ancient time, because of the traditional style of architecture and high craftsmanship, garden features and adornments have played a big role in many famous gardens of the world. Selection of features and positioning of ornaments in a garden are the visible evidence of the owner’s taste of nature and aesthetic sense. Whatever features are chosen, they must add charm, create an atmosphere of naturalistic design and improve the quality of landscape design. Garden features and ornaments are many, but they must be utilized in the design with restraints. Some important garden features are described below.

INTRODUCTION
Over the past two decades climate change has evolved from a debate about whether the planet is really warming to an increased focus on how to mitigate and adapt to its impacts. After an extensive review of the available literature on evidence of climate change, the Working Group I to the Fourth Assessment Report of the IPCC, 2007 concluded that “the warming of the climate system is unequivocal, as is now evident from observations of increases in global average air and ocean temperatures, widespread melting of snow and ice, and rising global average temperature”. “The scientific evidence is now overwhelming; climate change presents very serious global risks, and it demands an urgent global response” (Stern 2007).

INTRODUCTION

The North-Eastern Himalayas comprise of eastern-Nepal, entire Bhutan, parts of North Bengal and the eight states of North-East India viz. Arunachal Pradesh, Assam, Meghalaya, Mizoram, Nagaland, Manipur, Sikkim and Tripura. The region is characterised by diverse agro-climatic and geographical situations. This has a predominantly humid sub-tropical climate with hot, humid summers, severe monsoons and mild winters. The total forest covering this part of India is 17.50 m ha (which includes 8 NE states and hills of West Bengal) which is about 65.94 per cent of the total geographical area (FSI 2013), and the rest either under crops or non-agricultural uses or un-cultivated land. The low area under agricultural crops is due to natural corollary of the physiographic features of the region, as major chunk of the land has more than 15 per cent slope, undulating topography, highly eroded and degraded soils, and inaccessible terrain. Continuous depletion of the forest cover in the region due to shifting cultivation, firewood, and timber collection is posing the most crucial problem resulting in poor soil health and the resultant environmental degradation. In order to overcome these problems the farmers of the Eastern Himalaya have evolved various types of crop rotations in consonance with the varied environmental conditions and agronomic requirements with tradition by practising different approaches since ages. These practices so developed through major and minor adjustments in land use strategies are mostly sustainable from ecological point of view (Dash and Mishra 2001). 
The practises of agroforestry in this region exhibit a great deal of variation in crop diversity which is influenced by the crop composition and crop rotation. Along an altitudinal gradient, diversity in agroforestry practices is influenced by variation in ecological factors and difference in agricultural practices. Agroforestry has the potential to improve livelihood as it offers multiple alternatives and opportunities to farmers to improve farm production and income and also provides productive and protective (biological diversity, healthy ecosystems, protection of soil and water resources, terrestrial carbon storage) forest functions to the ecosystems. It is accepted as the sustainable management system that encompasses the variety and variability of animals, plants and micro-organisms which can be combined together to derive key functions of the agro-ecosystem, its structure and processes for, and in support of food production and food security. It is promoted widely as a sustainability-enhancing practice that combines the best attributes of forestry and agriculture. This practice is now recognized widely as an applied science and is instrumental in assuring food security, reducing poverty and enhancing ecosystem resilience at the scale of thousands of smallholder farmers in the tropics (Sharma et al. 2007). Therefore, strengthening linkages between knowledge systems using “Community” participatory management approaches is now seen as critical for sustainable forestry and agroforestry systems (Adhikari et al. 2007; Dhakal et al. 2007; Ramakrishnan 2007). 
The mountain communities of eastern Himalayan regions have also adopted diverse agroforestry systems as their land use. Environmental, biological, socio-cultural and economic variation existing in the eastern Himalayas have led to the evolution of diverse and unique traditional agro-ecosystems, crop species and livestock, which facilitate the traditional mountain farming societies to sustain themselves. Appropriate agroforestry systems have the potential to check soil erosion, maintain soil organic matter and physical characteristics, augment nitrogen build-up through nitrogen fixing trees and promote efficient nutrient cycling (Patiram et al. 2003).These systems have today become an established approach of integrated land management system not only for renewable resource production but also for ecological consideration (Saha et al. 2012).

INTRODUCTION

Agroforestry has long tradition since dawn of the civilization. Farmers and/or land owners integrate different woody perennials in their cropping system along with the animal unit depending upon the physiographic and climatic conditions. It is well proven fact that such adopted systems/practices are location specific and information on such systems is very limited. Therefore, the benefits accrued from such systems are underexploited in comparison to its potential. With depletion of agricultural lands due to shift in rainfall pattern, landslide, run off, regular leaching of nutrients, drying up of natural springs and lack of irrigation facilities have resulted into uneconomical agriculture in the mountain regions of India in general and particular in Jammu & Kashmir. Most of the villages in mountains witness migration on a large scale and lands turning up barren and un-productive. The agroforestry system can provide a viable solution for such problems.

INTRODUCTION

Rajasthan is the largest state of the country with a geographical area of 342,239 Km₂ which constituents 10.41% area of the country. The state can be divided into four major regions; the Western desert with barren hills, level rocky and sandy plains; the Aravalli hills running south west to north-east; eastern plains with rich alluvial soils; and south-eastern plateau. The state has varied climate from semi -arid to arid. The average rainfall in the state ranges from 480 mm to 750 mm, being as low as 150 mm in arid region and 1000 mm in south-eastern plateau (FSI 2009). The recorded forest area is 32,639 Km2 which is 9.54 % of the state’s geographical area. The maximum forests are found in the Districts of Alwar, Banswara, Baran,, Bundi, Chittorgarh, Dhaulpur, Dungarpur, Jhalawar, Kota, Rajasamand, Swaimadhopur, Sirohi and Udaipur. The hot arid and semi-arid regions in the country accounts for 20 % of the country’s geographical area spread over seven states namely Rajasthan, Gujarat, Andhra Pradesh, Punjab, Haryana, Karnataka and Maharashtra. It comes nearly 31.63 m ha out of which 19.61 m ha alone is in the states of Rajasthan (62.00 % of total arid region). This area is characterized by low erratic rainfall, high temperature and wind velocity, coarse textured soils with low organic carbon and soil fertility status and poor water holding capacity. The underground irrigation water is limited and highly saline in most of the cases (Chandra 2005). Mono-cropping is a gamble in arid tract of Rajasthan due to low and erratic rainfall and frequent occurrence of drought during crop growth period leading to complete crop failure. To avoid complete crop failure the farmers are adopting mixed cropping system from very ancient time. But the system is not perfect during the adverse climatic situation due to low yield, long duration of traditional varieties and unmatched crop combinations. Therefore, in mixed or multi cropping system, the choice of drought hardy, short duration varieties of crops are necessary to ensure the production of crops even under adverse situations. It has been seen that drought occurrence during month of July and August leads to 67-100 percent decrease in production of pearlmillet and short duration pulses which are the main crops of the region grown under rainfed condition.
The people in arid regions of India, since time immemorial has developed location specific agroforestry systems. The scattered trees /shrubs in the agricultural fields are common features of the landscape. Since the beginning of cultivation the farmers deliberately allowed the trees/shrubs to grow with crops. These trees provided them insurance during drought years and provided fodder, fruits, vegetables, timber, fuel, fiber etc. during lean period.

INTRODUCTION

India is endowed with a rich and vast diversity of natural resources. However, increasing demographic pressure, unscientific use of soil and water, rapid industrialization and urbanization are leading to over exploitation of the resources. Prime agriculture lands are being diverted for non-agriculture use. The per capita availability of cultivated land has declined over the years from 0.53 ha in 1950 to 0.32 ha in 2001 and is expected to further reduce to 0.23 ha by 2025 and to 0.09 ha by 2050 (GOI 2011). Owing to population pressure the consumption of fuel-wood and fodder in the country is much higher than what can be sustainably removed from forests. In India, nearly 86 million tonnes of fuelwood is being removed from the forests and plantations every year in excess of what they are capable of producing on sustained basis (Planning Commission 2001). Our rich and bountiful biological diversity is also showing signs of erosion which is affecting the livelihoods of millions of people who are directly or indirectly dependent on it. Further, water is mostly treated as a free commodity in the country which is leading to its unsustainable exploitation. Erosion due to wind and water is also leading to depletion of natural resources. About 5334 m tones of soil is lost (16 t ha-1) due to wind and water erosion annually which is highest in black soils (24-112 t ha-1) followed by Shiwaliks (80 t ha-1) and shifting cultivation (27-40 t ha-1) (Mandal et al. 2008). It is now widely accepted that future of food, livelihood and environmental security depends upon the attention paid to conservation, sustainable development and management of natural resources. Corrective measures are immediately required to check the damage caused to the resource base and environment. 
Traditionally, trees and crops were grown in association with each other on farm lands. The reason was to get multiple outputs from same piece of land, though such systems were exclusively meant for sustenance with little or no commercial intent. As the population increased there was a need to produce more food and hence slowly the tree component vanished from the farmlands and monocropping became dominant. Over a period of time, due to monocropping, soil degradation had been observed. The need of the hour is to accept the trees as an integral part of the farming system to revert soil degradation and erosion and also to reduce the dependence of external inputs in form of fertilizers, pesticides etc. in the production system.
Of late, incorporating trees on the farm lands has been given impetus to get multiple products (fodder, fuel, timber, fiber and fruits) on one hand and resource conservation (soil, water and environment) on the other. Different agencies (institutes, universities and NGO’s) are working on developing region specific agroforestry models to derive maximum advantage of production and conservation from every unit of land. Agroforestry is capable of yielding both wood and food besides conserving and rehabilitating ecosystems. Agroforestry generates high income and minimises risks through efficient utilization of available resources and is thus considered   a potential technology for commercial and protective farming.
The extent of the area under agroforestry is not very clear. Trees outside forests in India is estimated between 14,224 million (Ravindranath and Hall 1995) and 24,602 million (Prasad et al. 2000) which is spread over an equivalent area of 17 million ha (GOI 1999) supplying 49% of the 201 million tonnes of fuelwood and 48% of the 64 million m3 of timber consumed annually by the country (Rai and Chakrabarti 2001). Dhyani et al. (2006) reported 7.45 million ha under agroforestry.  As per one of the estimates, about 27.52 million ha is under various types of tree plantations, which include agroforestry, social forestry, farm forestry and others (Table 1). The task force on Greening India (Planning Commission 2001) has identified a potential of 10 millions ha in irrigated lands and another 18 million ha in rainfed areas that could be developed through agroforestry on watershed basis. 
The present chapter focuses on the advantage of integrating trees on the farm lands in form of agroforestry for natural resource management.

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.