eChapters

Abstract

Bioinformatics is a field of science which studies biology, computer science, and information technology. The ultimate goal is to obtain useful information by data acquisition, analysis and interpretation of sequences data. In the current decade, a huge volume of sequence data is stored in the data bank due to global genome initiatives of many organisms. Management and understanding of the genome data cannot be possible without the bioinformatics tools. A large number of tools and softwares packages are available either commercial or freely online for the bioinformatics applications. The use of bioinformatics tools enhances the research capability for crop improvement through genome sequencing, database management, assembly, alignment, primer designing, markers development, genes prediction and annotation, gene expression, phylogenetics, protein structure identification, metabolic pathways analysis and many other applications.

Abstract

Bioinformatics, an integrated science of biology and informatics is a repository of new emerging dimensions like proteome, genome, drug discovery etc, whose concepts have varied applications in various sciences/areas including agricultural/horticultural sciences. Bioinformatics tools are employed to investigate interactions between different biological systems i.e. gene-gene, protein-protein, gene-protein interactions and this information has tremenduous application in agricultural/horticultural sciences. It is the computer aided  data handling approach to understand the life process precisely. Biological problem require innovative database prospective for gene sequencing (management and alignment), recognition of genes and regulatory elements, protein structure prediction, evolution and phylogenetic studies, etc.

ABSTRACT

Bioinformatics is a critical tool in designing the molecular biology experiments. The xeroxing of specific part of genome needs correct primer designing. Primer designing has central role in molecular biology right from cloning, sequencing, gene expression profiling by real time PCR, genotyping by RFLP, SNP analysis by real time PCR and auto sequencer. In this chapter we are describing how to proceed for experimental designing right from data mining from GENEBANK to designing of primers for various common molecular genetic analysis work. The write up also describes in silico evaluation of primers, various off line commercial and non-commercial software, on line free software and trouble shootings in primer designing, The different strategy described in context of primer designing would be of immense use of researchers.

Introduction
Bioinformatics software plays an important role in the identification of plant varieties through employing genetic and genomic data to distinguish various kinds from each other. The software uses such approaches to DNA sequencing, molecular markers, and computational algorithms to increase precision in crop identification. Techniques such as SNP genotyping, DNA barcoding, and machine learning models are helpful in easily classifying and validating crop varieties. Farmers and breeders, for instance, will benefit from bioinformatics because it ensures genetic purity, improves genetic selection in crops, and provides more yields. It also incorporates bioinformatics tools that are revolutionizing plant breeding and conservation and allow the accurate identification of diverse highquality crop varieties for sustainable agriculture and food security (Derreper et al., 2011; Heo et al., 2024).
Crop variety identification has prime importance as per agriculture, food security, and conservation of biodiversity it maintains genetic purity for crops resulting in more yields with disease resistance and adaptability to climate. Correct identification will help farmer’s select superior seeds and maximize resources for increased productivity; further crop variety identification would participate in breeding programs ensuring superior crops varieties with desirable characteristics like drought tolerance, pest resistance, and better nutritional content. Accurate crop variety identification, in terms of food security, creates a steady supply of food through supporting continuous cultures of high-yielding and hardy varieties for the farm. Welfare in crop variety identification would help prevent fraud and misrepresentation in the food because they would be able to ensure that what customers receive is the type of crop they were looking for both in planned nutrition and costs. Facilitate seed certification schemes for protection of farmers from counterfeit seeds that would result in low yields.
Maintenance of genetic resources through proper identification of crop varieties ensures conservation of biodiversity. Crop variety identification and registration is a huge stroke towards conservation of wild and traditional crop species, which are very important for breeding and climate resilience. Such an event becomes important in climate change where genetic diversity ensures the abilities of crops to adapt to changing environmental conditions (Kim et al., 2021; Nguyen et al., 2025; Pavan et al., 2020).

The microbial community is a gold mine for gene(s) and pathway(s) that encode novel biocatalysts for biosynthetic or biodegradation processes, including degradation of pollutants, synthesis of biofuels and production of novel drugs. Sequencing of the microbial genome will also provide insights into the ecology of  microorganisms that are beneficial to, or threaten, crop production, and that ensure the quality and provision of ecosystem services. These unique genetic and biosynthetic capabilities of microorganisms have made them likely  candidates for solving particular difficult problems in the agriculture. For many years microbiologist and microbial  ecologists have tended to differentiate microorganisms as beneficial and harmful according to their function and how they affect soil quality, plant growth, and yield and plant health.

Fruits with their delightful colours, flavours and tastes are nature’s wonderful gift to mankind. Apart from being the most nutritious food in the form of easily digestible simple sugars, vitamins, minerals and many phyto-nutrients (Plant derived micronutrients), they provide unique health benefits due to their antioxidant properties and valuable fibre. Antioxidants help protect the human body from oxidant stress, diseases, and cancers, and also boost the immunity of the body thus developing the capacity to fight against various types of diseases. The insoluble dietary fiber in fruits is known to provide protection from conditions like chronic constipation, hemorrhoids, colon cancer, irritable bowel syndrome, and rectal fissures etc. Due to their unique nutrition-profile the importance of fruits in our diet cannot be over emphasised.

Insects are a major limiting factor in fruit production. The infestation of insects pests on fruit trees in orchards adversely affects the quality and yield of fruits. The size, shape, taste, attractiveness and palatability of fruit deteroriates, due to which the market price is reduced and the growers incur losses. Fruit growers resort to use of chemical pesticides under such conditions. However many reports suggest that although the global production and use of pesticides in agriculture is increasing every year, but the damage due to insects has not decreased rather it has also increased, indicating that the use of pesticides is not the panacea remedy for all insect related problems. Many scientists are of the opinion that over-reliance on the use of synthetic pesticides in crop protection programs around the world has resulted in disturbances to the environment, pest resurgence, pest resistance to pesticides, and lethal and sub-lethal effects on non target organisms especially beneficial flora and fauna, including humans. Farmers spend thousands of rupees on pesticides. The residues of pesticides in food and fruits is yet another cause of concern. Fruits which are considered to be wonderful for health are often laden with unacceptable levels of pesticide residues nulling their beneficial properties. Pesticides have been linked to many diseases especially cancer. All these issues related with use of pesticides has triggered rethinking on the methods of control.The recent examples of the results of indiscriminate pesticides use , consequent crop failures and suicide by farmers now calls for introspection in this matter.

Introduction

Agricultural pests cause considerable yield losses throughout the world. In ancient times, farmers had to manage pest problem to safeguard their basic needs, and as a response, the farmers use to practice and develop cultural and mechanical pest control strategies based on their field experience. Over a period of time, these practices have become a part of their production management system. Pest management practices began to change in later stages of the 18^th century. Introduction of pesticides in agricultural ecosystems 1950’s contributed substantially in raising agricultural productivity and they become an integral component of intensive agricultural ecosystems. At the same time, environmentalists raised their concerns on deleterious effects of pesticides on environment, human health and non-target organisms. Excessive use and abuse of pesticides leads to the problems like resistance, resurgence and residues (Beaument, 1993). One of the deleterious effects of over use of pesticides is the death of effective predator and parasitoids. This ultimately leads to the imbalance in the agroecosystem. Concerns about the negative effects of pesticides led to research and promotion of alternative pest control practices – Integrated Pest Control or simply IPC. This new concept called Integrated Pest Control (IPC) and later Integrated Pest Management (IPM) was stimulated by symposia organized by the Food and Agriculture Organization (FAO) of the United Nations in 1966 and the International Organization for Biological Control (IOBC) in 1967. IPM made a paradigm shift in the philosophy of pest control, from pest eradication to pest management. Instead of single tactic control, emphasis was placed on the use of a combination of available tactics in a compatible manner keep the pest below economic injury levels. Consequently, a more integrated approach of pest control was advocated considering the natural mortality factors. IPM is a complex system approach that comprises judicious use of cultural, physical, mechanical, biological, host plant resistance, regulatory and chemical methods.

Introduction

Banana (Musa sp; family: Musaceae) is the second most important fruit crop in India next to mango. Its year round availability, affordability, varietal range, taste, nutritive and medicinal value makes it the favorite fruit among all classes of people. It has also good export potential. Banana evolved in the humid tropical regions of South East Asia with India as one of its center of origin. Modern edible varieties have evolved from the two species – Musa acuminata and Musa balbisiana and their natural hybrids, originally found in the rain forests of S.E. Asia. During the seventh century AD its cultivation spread to Egypt and Africa. Banana and plantains are grown in about 120 countries. Total annual world production is estimated at 86 million tonnes of fruits. India leads the world in banana production with an annual output of about 14.2 million tonnes. Other leading producers are Brazil, Eucador, China, Phillipines, Indonesia, Costarica, Mexico, Thailand and Colombia. In India banana ranks first in production and third in area among fruit crops. It accounts for 13% of the total area and 33% of the production of fruits. Production is highest in Maharashtra (3924.1 thousand tones) followed by Tamil Nadu (3543.8 thousand tonnes). Within India, Maharashtra has the highest productivity of 65.70 metric tones /ha. against national average of 30.5 tonnes/ha. The other major banana producing states are Karnataka, Gujarat, Andhra Pradesh and Assam.

Introduction

Brinjal is an important vegetable crop grown extensively throughout India. In India, brinjal is cultivated in around 730.4 ha with a production of 17.5 million tonnes in the year 2017-18. It is also called as poor man’s vegetable. It is consumed in variety of ways depending upon the eating habits of the different parts of the country. It is grown extensively in Bihar, Orissa, Karnataka, Tamil Nadu, Andhra Pradesh, Maharashtra, West Bengal, Uttar Pradesh and states with matching climatic conditions in the tropics and subtropics.

Brinjal is an important vegetable crop, but insect pests are making more losses in brinjal cultivation. In brinjal, more than 36 pests have been reported from the time of planting to harvest (Regupathy et al., 1997). Among all insect pests shoot and fruit borer (Leucinodes orbanalis), hadda beetle (Epilachna vigintioctopunctata), jassid (Cestius phycitis), Ash weevil (Myllocerus subfasciatus), white fly (Bemisia tabaci), lace wing bug (Urentius hystricellus) are important (Barker and Pritchrad, 1960).

Despite serious nature of the pest, its management tactics by and large is limited to frequent sprays of chemical insecticide without much impact on the yield. Such practice of pesticide usage is detrimental to environment, also increases the cost of production and chances of insecticide residues in the fruit. About 47 per cent insecticides are used for management of fruit and shoot borer out of the total pesticide consumed in vegetables. In this background major emphasis, now-a-days, is being given on Biointensive integrated pest management as alternate to the insecticides for management of any pest. More than a dozen parasitoids and three pathogens have been recorded as natural enemies of insect pest. But the extent of parasitisation/predation under field condition is very low. In this context, inundative release of bio-agents, particularly egg parasitoids in pest management may be more advantageous.

Introduction

Chilli (Capsicum annuum var.annuum L.) is one of the most important economical and popular vegetable crops grown for its green fruits as vegetable and red one as a spice¹. It is a native of southern Texas and Maxico and was introduced in India by the Portuguese in 19^th century². Chilli is mainly used in culinary adding flavor, color, pungency and rich source of vitamins like A, C, E, P and having medicinal properties³. Chilli is one of the important cash crops grown in almost all parts of the country and is widely grown in the tropics and subtropics as also under glass houses in temperate regions⁴. The plants are very sensitive to excessive rainfall, water lodging and frost^2,5. The ideal condition for its cultivation are well drained loam soil rich in organic matter but can also be grown in many type of soils⁶. India is a major producer, exporter and consumer of chilli⁷. Chilli is presently grown extensively throughout the country, both under rainfed and irrigated conditions, in almost all the states covering an area of 792.1 thousand Ha with annual production of 1223.4 thousand metric tonnes⁸. Andhra Pradesh is the largest producer of chilli in India. It contributes about 30% to the total area under chilli, followed by Karnataka (20%), Maharashtra (15%), Orissa (9%), Tamil Nadu (8%) and other states contributing 18% to the total area under chilli⁸.

Introduction

A symposium organized by the Food and Agricultural Organization (FAO) in 1966 and International Organization of Biological Control (IOBC) in 1967, felt the need for the development of a new concept called “Integrated control” which was later replaced by “Integrated Pest Management”. The origin of IPM was necessary after the serious failure of the chemical age which started in the 1940’s. The pesticides were used as the only tactic to completely annihilate the pests from the crop ecosystem, which did miraculously decreased the pests and increased the production of the crop extensively, but they failed to realize the balance of life, by nature and by virtue of the selection pressure pests started developing resistance against all kind of pesticides being dumped on them.While the pests were getting resistant, the dumped pesticides were accumulating in the environment and biomagnifying inside the bodies of animal (WHO, 1990; Alewu & Nosiri, 2011; Eskenazi et al., 1999). The indiscriminate use of pesticides led to the significant health hazard to the humans (WHO, 1990; Alewu & Nosiri, 2011; Sanborn et al., 2007; Mnifet al; 2011; Semchuk et al., 1992; Goad et al., 2004; McKinlay et al., 2008; Gasnier et al., 2009; Lin et al., 2015; Waddell et al., 2001), reproductive malfunction in male (Jamal et al., 2015), nervous system (Jaga and Dharmani, 2003; Rosenstock et al., 1991; Wesseling et al., 2002; Eskenazi et al., 2006), cardiovascular system (Hung et al., 2015) and ultimately death (WHO, 1990; Gunnell et al., 2007). From the lessons acquired of the hazards, the concept of IPM proposed the concept of “pest eradication” was replaced with “pest management”. There are more than 64 definitions of IPM but the most accepted one came from FAO (1967) which defined IPM as “a system in context with associated environment and the population dynamics of pest species, utilizes all suitable techniques and methods in as compatible manner as possible and maintains the pest populations at level below those causing economic injury”. IPM decreased the pest pressure of the crop and increased the productivity of the crop and income of the farmers. IPM is a complex approach that advocates the integration of several components such as physical, mechanical, biological, legal, ecological and chemical tactics, in a compatible manner in a complete ecological set up, so that natural mortality has a role in checking the pest population building up above economic injury level (EIL).

Introduction

Biointensive integrated pest management (BIPM) is essentially a component of integrated pest management which helps to reduce the dependence on chemical pesticides thereby preventing ecological deterioration. The major elements of this approach includes many factors viz. host plant resistance, use of beneficial organism, agronomic practices, bio pesticides, parasitoids, predators, plant exudates etc. It also includes all other conventional non-chemical methods of pest control like use of botanical insecticides preferably plant based insecticides like Azadirachtin from Neem (Azadirachta indica), Rotenone from Derris chinensis and Derris elliptica, Nicotine from Tobacco (Nicotiana tabacum), Juvocimene 1 or 2 and Ocimin from Ocimum sanctum, Atropine from Datura stramonium, Annonine and Squamocin from Annona squamosa etc.

Introduction

Cucurbits belong to the family cucurbitaceae; constitute the largest group of summer vegetables grown all over the world which includes about 118 genera and 825 species. Cucumbers, muskmelons, watermelons, squashes, gourds, luffagourd, tissel-gourd and pumpkins are commonly grown cucurbits are mostly important one. These crops are attacked by a variety of insect pest and diseases throughout its growth period; generate wounds that help to transmit of viral particles, bacteria and invasion of fungal pathogens. Major insect pests include cucumber beetles, red pumpkin beetles, fruit flies, epilachna beetles, squash bugs, aphids, white flies, squash vine borers, two-spotted spider mites, and nematodes affects significant damages from seeding stage upto harvest. Insect pest infestations in cucurbits bring about heavy losses through reduction in yield, lowered quality of produce, defoliation of leaves, damage roots or flowers, contribute to poor crop standard increased cost of production and harvesting besides expenditure incurred on materials and equipments to apply control measures.

Introduction

The guava fruit is a good source of vitamin C, pectin, calcium and phosphorus. The fruit is used for the preparation of processed products like jams, jellies and beverages. Guava jelly puree is very popular for its attractive purplish-red colour, pleasant taste and aroma. The puree can be used in juice, cakes, puddings, sauces, ice-cream, jam and jelly. Fruits can be preserved by canning as halves or quarters, with or without seed core (shells). Good quality salad can be prepared from the shell of ripe fruits. Their cultivation in India about 1.32 lakh ha area with production is 17.12 lakh tonnes. Biointensive pest management is use to major emphasis on conservation and enhancement of natural enemies and utilization of all compatible methods for achieving effective economical and safe pest control. These methods are the most appropriate in horticulture and in protected cultivation. The major aim of Biointensive pest management is to provide guidelines and options for the effecting management of pests and beneficial organisms in an ecological context. It will help to reduce the dependence on chemical pesticides and ecological deterioration. Biointensive pest management includes bio-pesticides derived from microbes, parasitoides, predators, botanicals and all conventional non-chemical methods or use of need based. Large number of insect pests has been reported to occur on guava at various growth stages. More than 80 species of insects and mites have recorded on affecting the growth and production. About three species of fruit flies, Bactrocera dorsalis, B. Cucurbitae and B. Zonata found to attack guava fruits, B. Dorsalis being the dominant. Maximum activity of fruit flies is observed during August to December reaching its peak during September. Two species of bark eating caterpillars, Indarbela quadrinota and I. Tetraonis are commonly found in the region. Sucking pests included Mealy scale, Chloropulvinaria psidii, Mealy bugs Ferrisia virgata, Plannococcus citri, Tea mosquito bugs, Helopeltis antonii, aphid, jassids etc (Azad Thakur et al., 2009). The major pests of guava that are economically damage on this crop given below:

Introduction

Litchi (Litchi chinensis Sonn), like most fruit tree crops, is usually attacked by two or three key pests, several secondary pests and a large number of occasional pests in localized areas where it is grown. Litchi is an important subtropical evergreen fruit crop belongs to family Sapindaceae. It is known as queen of the fruit due to its attractive deep pink/red colours and flavoured juicy aril (Singh et al., 2012).

Insect pest attacks on litchi, in China there are 193 species of litchi pests in two classes, 11 orders, and 57 families. In India, nearly 42 insects and mite species reported to attacking on trees and fruits of litchi at different stages of growth (Singh et al., 2012). The majority belong to the Lepidoptera and Coleoptera, followed by the Homoptera and Hemiptera. However, only about three or four key pests including fruit and flower borers, sucking bugs, stem borers and erinose mites which require regular control, and the species involved vary between orchards. Secondary pests viz., fruit-piercing moths, defoliators etc generally occur at sub-economic levels, but can become serious pests as a result of changes in cultural practices and litchi cultivars or because of indiscriminate use of insecticides against a key pest. Recently, litchi fruit borer and litchi leaf roller have acquired the status of major pests and now, litchi looper, litchi bug and bag worm are emerging pests of litchi (Choudhary et al., 2013; Singh et al., 2014). Occasional or incidental pests also can cause economic damage only in localized areas at certain times; the great majority of pests reported here fall within this last category.

Introduction

Okra (Abelmoschus esculentus L. Moench) also known as lady’s finger or bhendi, belongs to family Malvaceae. Tender fruits are used as vegetables and thickening of gravies and soups, because of its high mucilage content. The roots and stems of okra are used for cleaning cane juice (Chauhan, 1972). In okra several pest may damage the tender fruit that leads to reduction in yield which can be controlled by holistic approach to develop sustainable agriculture. There are several ways among this the Biointensive integrated pest management (BIPM) is one of the best way to discourage the development of pest populations and keep pesticides free so that it makes economically justified to farmers, reduce risks to human health and the environment. Biointensive integrated pest management (BIPM) is essentially a component of integrated pest management which helps to reduce the dependence on chemical pesticides thereby preventing ecological deterioration. The major elements of this approach includes many factors viz., host plant resistance, use of beneficial organism, agronomic practices, biopesticides, parasitoids, predators, plant exudates etc.

Introduction

Papaya is a tropical tree fruit crop that cannot tolerate freezing temperatures. It has commercial importance because of its high nutritive and medicinal value. Papaya cultivation had its origin in South Mexico and Costa Rica. Total annual world production is estimated at 6 million tonnes of fruits. India leads the world in papaya production with an annual output of about 3 million tonnes. Other leading producers are Brazil, Mexico, Nigeria, Indonesia, China, Peru, Thailand and Philippines. Papaya fruit are borne on peduncles attached to the main trunk of the papaya tree and are clustered, starting a few feet above the ground and extending up to a foot below the top of the plant adequate water is essential to the uninterrupted growth and production of papaya fruit. There is number of factors which affect quality and quantity of papaya production. Out of insect pest is one of the important factors to reduction of papaya fruit production. List of insect pests of papaya given as below:

Pomegranate (Punica granatum L.) also known Anar in Hindi it is belonging to the Punicaceae family, it is grown in tropical and sub-tropical regions. Originated in Indo-Burma region Iran and is extensively cultivated in the Mediterranean region since ages (Sheikh and Manjula, 2009). Pomegranate is used as table purpose, making juice, jam, jelly and paste. The fruit peel, tree stem and leaves and root bark are good source of secondary metabolites such as tannins, dyes and alkaloids (Mirdehghan and Rahemi, 2007). The edible part of the fruit is the seeds having a fleshy covering and called arils.

India is major pomegranate producing country in the world. In India main pomegranate producing states are Maharashtra, Karnataka, Gujrat, Andhra Pradesh, Madhya Pradesh, Tamil Nadu and Rajasthan. Maharashtra is leading state of pomegranate production in India. The prominent pockets where pomegranate cultivated area are concentrated are Solapur, Nashik, Sangli, Satara and ahemednagar districts of Western region of Maharashtra.

Indian total pomegranate crop covers 0.24 Mha and production is 2.87 MT in India (Anonymous 2017). The export of pomegranate from India is only 0.04 MT it is very low. Pomegranate is majorly exported to UAE (43%), Bangladesh (16%) and European Countries (14%) A few tons also go to Saudi Arabia, Russia, Thailand, Nepal, Kuwait etc.

Introduction

Potato (Solanum tuberosum) is the most important food crop of the world. Potato is a temperate crop grown under subtropical conditions in India. The potato is a crop which has always been the ‘poor man’s friend’. Potato is being cultivated in the country for the last more than 300 years. For vegetable purposes it has become one of the most popular crops in this country. Potatoes are an economical food; they provide a source of low cost energy to the human diet. Potatoes are a rich source of starch, vitamins especially C and B1 and minerals. They contain 20.6 per cent carbohydrates, 2.1 per cent protein, 0.3 per cent fat, 1.1 per cent crude fibre and 0.9 per cent ash. They also contain a good amount of essential amino acids like leucine, tryptophane and isoleucine etc.

Potatoes are used for several industrial purposes such as for the production of starch and alcohol. Potato starch (farina) is used in laundries and for sizing yarn in textile mills. Potatoes are also used for the production of dextrin and glucose. As a food product itself, potatoes are converted into dried products such as ‘potato chips’, ‘sliced’ or ‘shredded potatoes’.

Potato is grown almost in all states of India. However, the major potato rowing states are Himachal Pradesh, Punjab, Uttar Pradesh, Madhya Pradesh, Gujarat, Maharashtra, Karnataka, West Bengal, Bihar and Assam.

The main constraint to potato farming in India are: It is vulnerable to control the pests hence implying a high risk of failure, growing potatoes requires substantial capital and the crop needs intensive care and attention. However, a proper Biointensive insect pest management programme will minimize losses to potato crop.

Introduction

Biotic stresses, particularly insect pests adversely affect the economical yield potential and the quality of the widely cultivated spice crops. These pests attack the crops at various developmental stages of the crops. For instance, Pollu beetle alone in black pepper is the most destructive pest and causing 30 to 40% yield loss in humid, tropical evergreen forests of India (Devasahayam, et al., 1988). Considering the cost of cultivation and profitability, it is very important to develop and recommend low cost, economic easily adoptable technologies. Food production process in India during the green revolution period has been based on the use of more chemical fertilizers and pesticides which are detrimental to the environment. The challenge before the crop protection scientists is to boost the yield from the available land without harming the environment. To manage the problem of insect pests in spice crops, farmers are over using synthetic chemical pesticides indiscriminately and this result in environmental degradation and high pesticide residue levels in the produces are are mainly hindering the export. Now the focus is on organic spice production, therefore a search for safer measures of pest and disease management is gaining importance. Integration of various approaches like use of resistant/tolerant varieties, disease or pest free planting materials and exploitation of biological means such as bio- control agents, bio-pesticides, entomo-pathogens, parasitoids and predators at the right time paved the way to achieve this goal (Dhanya et al., 2019; Prakash et al., 2016). Incorporating ecological and economic factors into decision making and addressing the public concerns about environmental quality and food safety is the need of the hour. There is now wide array of techniques available to replace the use of conventional chemical insecticides in IPM programmes. These issues can be sorted out by adopting eco-friendly Biointensive Integrated Pest Management strategy.