eChapters

Moisture plays by far the most important role in soils as regards vegetation. It is through the medium of water that the plants obtain their quota of mineral food vital for their growth. If water is gradually withheld from the soil, at a certain stage, the plant will begin to wilt and soon dry up. The soil may still contain some moisture but the plant is unable to make use of it. The minimum moisture in the soil below which wilting will take place is called the Wilting Coefficient and at one time great importance was attached to it. The determination of this Coefficient, however, is tedius. One must grow a number of plants and slowly watch them wilt and determine the moisture content at that point. Moisture content of the soil is determined by heating a weighed quantity of the sample in an oven kept at 100-110 ^oC. The moisture is expressed as percentage on the oven-dry soil.

Clouds play very important role on weather and climate. The formation of clouds takes place when water condenses in the sky. Clouds are visible accumulation of tiny water droplets and ice crystals in the Earth’s atmosphere. The moisture is always present in the atmosphere though it may not be visible. Clouds form when air becomes cooler until the water vapour present in it condenses to liquid form. The condensation over oceans occurs around solid particles like salt, dust, smoke etc. suspended in the atmosphere. The type of clouds depends upon temperature and wind. The clouds are classified based on physical appearance and the height at which clouds are formed (Fig. 7.1).

Term moisture stress is generally applied to the stomata opening and transpiration increases with time until they close due to high temperature.

5.1. Causes of moisture stress in plants

Main reason is extent of transpiration which is affected by leaf size and composition, size and distribution of stomata on leaf, atmospheric humidity, temperature, wind velocity and day length.

High atmospheric temperature due to intense sun and increased transpiration causes closure of stomata and wilting of leaves even, if soil moisture content is not limiting.

This deficit is made up during night due to decreased transpiration.

In plants, moisture content decreases either due to increased transpiration or reduction in absorption or both.

Abstract

Anantapur is the driest district of Andhra Pradesh and hence, agriculture conditions are very often precarious. Groundnut grows where other crops fail and thus it is the predominant crop of Anantapur district. Groundnut is grown in about 7.5 lakh ha in Anantapur district; however the average yields are low at 500 kg ha^-1. Among various available vegetation indices, normalised difference vegetation index (NDVI) is widely used for all reasons, which is a single numerical indicator of presence and condition of green vegetation. NDVI mapping at a regional scale helps to assess the spatial changes in the vigour of green vegetation and thus occurrence of any moisture stress. Climate tools have a great role in understanding the crop performance and estimating the yields. This study was taken up by using freely available MODIS data to understand NDVI in terms of abiotic stresses over Anantapur district and linking with the actual rainfall conditions, groundnut crop acreage and production. Results indicate that low groundnut yields in general could be related to NDVI-based stress measurements and rainfall quantum and distribution in the area however, with a few exceptions. It is hoped that by combining improved practices through IWM with climate-adapted crop varieties, rainfed farmers of Anantapur district can sustain their crop production under present climate variability and become resilient to future climate change.

Keywords: Climate, MODIS, NDVI, Anantapur, Groundnut, Integrated Watershed Management

Extraction of DNA from Tissue
(Using HiPurATM Multi-sample DNA Purification Kit)
Kit contents
Re-suspension buffer, Lysis solution, Prewash solution concentrate, Wash solution concentrate, Elution buffer, Proteinase K, HiElute Miniprep Spin Column (Capped), Collection tubes (uncapped), Collection tubes Dilute the prewash, wash solution and Proteinase K according to the kit.
Protocol
Prepare tissue
Weigh 25 mg of tissue, add approximately 3 ml of 0.8 per cent of normal saline. Homogenize the tissue with homogenizer or with mortar and pestle. Transfer the homogenized tissue with saline to a microcentrifuge tube. Centrifuge at 14000 rpm for 10 minutes. Discard the supernatant and use the pelleted tissue for further lysis.
Digest tissue
Add 180 μl of resuspension buffer and 20 μl of Proteinase K solution to the pelleted tissue in microcentrifuge tube. Mix by vortexing. Incubate the sample at 55oC until the tissue is completely digested (2-4 hours) in a shaking water bath. Vortex briefly after complete digestion.

MOLECULAR BREEDING

Molecular breeding is the application of molecular biology tools, often in plant breeding.

Genetic markers

Genetic marker is defined as a gene whose phenotypic expression is usually easily discerned, used to identify an individual or a cell that carries it, or as a probe to mark a nucleus, chromosomes or locus (King and Stansfield, 1990). Three broad classes of genetic markers are morphological markers, biochemical markers and DNA or molecular markers.
 
(1) Morphological markers

Morphological markers are based on the visually assessable traits viz., morphological and agronomic traits. However, they are limited in number.

MOLECULAR BREEDING

Molecular breeding is the application of molecular biology tools, often in plant breeding.

Genetic markers

Genetic marker is defined as a gene whose phenotypic expression is usually easily discerned, used to identify an individual or a cell that carries it, or as a probe to mark a nucleus, chromosomes or locus (King and Stansfield, 1990). Three broad classes of genetic markers are morphological markers, biochemical markers and DNA or molecular markers.

(1) Morphological markers

Morphological markers are based on the visually assessable traits viz., morphological and agronomic traits. However, they are limited in number.

Features of morphological markers

i.They are easy to identify, there is no need of any complex analysis. Trait of interest can be identified visually.

ii.Morphological markers are inherited qualitatively or quantitatively.

iii.Frequency of availability of morphological markers is less in number i.e., morphological markers may not be available for all the traits of interest.

iv.They are influenced by environment.

v.Since they are influenced by environment, they are unstable in inheritance.

vi.They are stage specific i.e., a particular marker will be useful to identify in a particular stage of plant and not any stage of the plant.

vii.They are influenced by genotype and developmental stages of the plant.

Besides drawbacks, the morphological markers are useful to the plant breeders for the selection purpose in certain situation.

Introduction
The most extensive diversity is found in the realms of plants and insects, encompassing over 1 million arthropod taxa, primarily comprising insects, which have been comprehensively described, along with more than 350,000 plant taxa. Notably, a substantial portion of the described insect species serve as either pollinators or herbivores. Over millions of years, insects and plants have coevolved, constantly adjusting and adapting to each other’s characteristics. Plants have developed numerous morphological and biochemical features to withstand damage from insects, while in response, insects have evolved a range of defensive and adaptive mechanisms. These mechanisms include behavioural, morphological, physiological, biochemical, and genetic traits, enabling them to either tolerate or adapt to the defensive traits of plants (Schmelz et al., 2006; Wu et al., 2007; Howe & Jander, 2008; War et al., 2018). Plant defenses against insect pests can be broadly categorized into two main types: antibiosis and antixenosis resistance. Antibiosis involves the direct impact of plant defensive traits on insect growth, development, and survival. In contrast, antixenosis defense relies on morphological or chemical factors that alter insect behaviour, deterring them from feeding and laying eggs on the plant. The trichomes, spines, cuticles, thorns, and lignified cell walls, are the morphological traits of defense that directly protect plants from insect pests. The biochemical defense mechanisms are typically activated in response to insect attacks and are characterized by their dynamic nature (War et al., 2018). Plant volatiles serve a significant function in the indirect defense of plants against insect herbivores. They accomplish this by either deterring the insect pests or by luring the pests’ natural adversaries. Among the various attributes associated with plant defense, chemical barriers, whether they are induced by stress or present constitutively, along with the nutritional composition of the plant, are regarded as particularly crucial for impeding insect growth and development (Peters & Constabel, 2002; War et al., 2019).
Chemical resistance entails the production of secondary metabolites, whether inherently present (constitutive) or induced as a response to a threat, to fortify the plant’s defense mechanisms (Figure 1). Constitutive defense metabolites, initially stored in an inactive state, referred to as phytoanticipins, become activated when herbivores attack. This activation is facilitated by the enzyme ß-glucosidase, which subsequently triggers the release of various aglycone metabolites possessing biocidal properties (Morant et al., 2008). Metabolites that are induced in response to herbivore activity are referred to as phytoalexins. These compounds encompass a variety of substances such as isoflavonoids, terpenoids, alkaloids, and more. They are recognized for their capacity to influence the growth and viability of herbivorous organisms (Walling, 2000). Furthermore, a notable role in imparting host-plant

Introduction

Livestock contribute directly to the livelihoods of nearly one billion of the world’s population. Livestock provide protein and minerals for human consumption, manure for crop production, and fibre and leather for industrial uses. Animals are also a source of draught power. Beyond their role of providing food and inputs for agriculture and industry, livestock provide security to farmers in developing countries, especially in emergencies such as crop failure. To many of the resource-poor, both smallholder farmers and landless livestock keepers, animals are a living bank, facilitating both income distribution and savings. In addition, by consuming crop residues and by-products, in addition to well-managed grazing, livestock production contributes positively to the environment, particularly in mixed crop-livestock production systems. Thus, livestock are an important source of income and employment that contribute to poverty alleviation and enhance the household food security of farmers.

INTRODUCTION

Molecular tools generally refer to molecular genetic tools. Although the first use of these tools began more than four decades ago, whenLewontin & Hubby (1966) used allozymes to find out the amount of genetic variation present in wild populations of Drosophila, the lack of expertise and high cost of these tools have prevented their widespread use among ecologists in general and behavioural ecologists in particular. But recently the accessibility and costs of these techniques have come down a lot and with the right kind of collaboration, lack of expertise is no longer an issue.

As was mentioned above, the Lewontin & Hubby’s (1966) investigation was done using allozymes. Although still an option, user-friendly neutral nucleotide markers are more preferred by investigators nowadays. The discovery of the polymerase chain reaction (PCR) in 1983 by Kary Mullis was the single landmark in this field, if one has to mention one. The use of molecular markers has totally revolutionized the field of ecology. It has provided ecologists the tool to ask questions, which were hitherto impossible to tackle and also to answer questions with much more precision and accuracy than was possible till now. It has toppled long held beliefs, sometimes, romantic ones, by ecologists.

Introduction
Infectious diseases in aquaculture are becoming increasingly important to address to support the growth and sustainability of the industry. This is especially true as many view farmed seafood production as a key solution for feeding the world’s growing population and reducing poverty in numerous countries (FAO, 2016). It is essential to establish biosecurity programs that effectively prevent, manage, and eliminate diseases within aquaculture operations. Biosecurity plays a critical role in safeguarding agriculture and aquaculture operations from the devastating effects of disease outbreaks. These programs are critical to safeguarding the health of aquatic species, protecting ecosystems, and ensuring the sustainability of the industry. At first, implementing biosecurity measures in aquaculture may seem like a simple concept. The well-known saying “prevention is better than cure” is especially relevant to aquaculture diseases, given the significant economic consequences of disease outbreaks. Effective biosecurity practices can help prevent these costly issues from arising. Biosecurity is a comprehensive and coordinated strategy that includes policies and regulations designed to assess and manage risks across various sectors, such as food safety, animal health, and plant health, while also addressing related environmental risks. Biosecurity measures focus on preventive practices such as quarantine, hygiene protocols, and environmental management.

Abstract

Nitrogen is the most essential nutrient for all plants and is also the major limiting factor in plant productivity. High yielding varieties of all crops are responsive to nitrogen but its ever-increasing use has shown detrimental impact on the environment along with extremely low use efficiency. Nitrogen use efficiency (NUE) in crop plants depends on various internal and external factors, which are dealt in detail. There has been a significant interest in genetic engineering of the crops to improve NUE. The use of biotechnological interventions by manipulating genes of the nitrogen utilization pathway to improve NUE has not been very successful. But transgenics/mutants with modified capacities for nitrate uptake, assimilation and remobilization have enhanced our understanding of the genetic control of NUE. In both cellular, and at whole plant level the mechanisms involved in N remobilization from the senescing organs towards the grain have recently gained importance but their understanding is still preliminary. Recent evidences have shown that grain filling during later stages of crop growth is supported by N recycling.

Although thousands of plant species exist on the earth, only those that were found to be useful for humans as food, feed, fiber, timber and other utility materials have been selected for domestication. When these plant species were affected by various biotic and abiotic causes, the necessity arose to determine the ways and means of protecting the valuable plants species and to understand the host plant defense mechanisms and pathogenic potential of the microbial pathogens causing enormous losses to the cultivators. All plant species have built-in resistance to most microbial plant pathogens existing in the environment. Susceptibility of plants to some of them is an exception, since they are endowed with genes which effectively nullify the possible adverse conditions created by the microorganism. Likewise, microbial pathogens possess genes for survival and pathogenicity to survive in the absence of susceptible plant species and to successfully establish infection in suitable plant species. The microbial pathogens have evolved highly specialized tactics to overcome the defense responses and to rapidly multiply in plants for their survival and perpetuation in a geographic location / ecosystem

Introduction
• Arrival of the nerve stimulus at the motor end plate result in reversal of the polarization of the sarcolemmal surfaces and the muscle gets activated
• This causes momentarily loss of potassium and sodium ions impermeability by the sarcolemma and Ca++ ions combined with calsequestrin in the sarcotubular system gets dissociated bringing Ca++ ion equilibrium with the sarcoplasm
• The junctional foot protein (JFP) and the L-type calcium channel (LTC) are the two big protein complexes responsible for the calcium release mechanism (Fig. 10.1)
• This leads to increase in level of Ca++ ion from nearly 0.10 mM to 10 mM
• Thus, troponin C, the calcium-binding site of the troponin complex becomes saturated bringing a structural modification resulting in interaction of actin with the MgATP2- on the H-meromyosin heads of the myosin molecule as the troponin I, the inhibitory protein, no more inhibits this interaction
• The interaction of actin with the MgATP2- intensely activate contractile ATP-ase near the bonding leading to break down of MgATP2- to MgADP– at a greater rate and liberating energy for inward (towards the sarcomere center) pulling of the actin filament
• This leads to breaking of bond between actin and myosin and thus, the myofibrillar part involved in above mentioned activity gets contracted

• General considerations

 • Polyacrylamide gel electrophoresis (PAGE)

 • SDS-polyacrylamide gel electrophoresis (SDS PAGE)

• Nucleic acid hybridization

 • Radio labelled probes

 • Biotin labelled probes

 • DNA finger printing

 • Polymerase chain reaction (PCR)

 • Reverse transcriptase polymerase chain reaction (RT PCR)

The shift from vegetative to reproductive phase in plants is the result of multiple gene cascades in response to photoperiodic and temperature dependent pathways, gibberellic acid pathway, vernalization pathway and autonomous pathway. The environmental cues are initially detected in the leaves and the mRNA of the flowering signal integrator FT gene, moving to the shoot apical meristem, acts as a long-distance signal for floral meristem identity. At SAM, FT-FD protein complex, based on signals from above said pathways in association with the signals from age-dependent and miRNA pathways, leads to the activation of master regulator gene of flowering AP1. The activation of genes involved in ABCDE model of floral organ differentiation, based on the directions of various cadastral genes lead to the development of floral organs. Thus, the sequential action of floral meristem identity genes, floral organ developmental genes, floral meristem size and organ number genes, floral organ pattern genes and cadastral genes leads to the flower development. This chapter sums up the gene interactions happening in leaf and SAM, leading to the development of a complete flower.

Introduction

Biochemical techniques are fundamental tools that allow scientists to investigate the molecular intricacies of biological systems, including DNA, RNA, and proteins. These techniques are essential for understanding cellular processes, genetic functions, and disease mechanisms. By employing biochemical methods, researchers can dissect complex biological systems at the molecular, cellular, and genomic levels, paving the way for advances in basic biology and therapeutic interventions.

Introduction to Molecular Biology Techniques Molecular biology is the domain of biology concerned with DNA replication, RNA synthesis (transcription), translation, and the role of proteins in cellular function, while molecular biology techniques are the keystones of modern biology, facilitating scientists to decode these molecular foundations of life. These molecular techniques aim to analyze and understand the structure, function, and interactions of biomolecules such as DNA, RNA, and proteins. These techniques facilitate an understanding of complex life processes such as gene expression, genetic variations, and cellular mechanisms. Researchers have used these molecular tools to unravel complex biological processes from genetic inheritance to cellular signaling pathways. The knowledge gained has been applied to solve challenges in various domains of biological science such as medicine, agriculture, and environmental science. During 1960’s methods to identify, isolate and manipulate molecular components were developed by molecular biologists. The field of molecular biology emerged in mid 20th century, driven by groundbreaking discoveries such as the deduction of the double-helix of DNA

Introduction

Nucleic acids, primarily DNA and RNA, are essential for the storage and expression of genetic information. Under physiological conditions, the amino and oxo tautomers of purines and pyrimidines predominate. Adenine a., guanine (G), cytosine c., thymine (T), and uracil (U) are the main building blocks of nucleic acids. Other building blocks include 5-methylcytosine, 5-hydroxymethylcytosine, pseudouridine, and N-methylated heterocycles. A -glycosidic bond connects D-ribose or 2-deoxy-D-ribose to the N-1 of a pyrimidine or the N-9 of a purine, with the syn conformers being the most common.

Nucleotides are the monomeric units of nucleic acids that contain a phosphate group attached to the sugar’s 3’ or 5’ hydroxyl. Extra phosphate groups form nucleoside diphosphates and triphosphates. These have high group transfer potential and help make covalent bonds. Cyclic phosphodiesters cAMP and cGMP act as second messengers. 3′ 5′ phosphodiester bonds link nucleotides to form polynucleotides, which have a directional 5′ and 3′ end. Four bases—A, G, C, and T—compose DNA, and hydrogen bonds (A to T, G to C) hold them together to form a double helix. Human DNA consists of approximately 3 billion base pairs organized into 23 chromosomes, encoding around 25,000 protein-coding genes and various non-coding RNAs (ncRNAs).

Introduction

Improvement of wheat grain quality depends on the knowledge of quality requirements of different end-use products and the genetic components controlling different quality traits. In previous chapters we have dealt in-depth with quality requirements of different end-use products and their genetic components. Depending upon the goal of quality improvement, different strategies are adopted to improve wheat quality. It depends upon the number of genes controlling the traits as well as the availability of the simple methods for phenotyping the traits especially during early segregating generations. In addition stability analysis of the traits across the environments is essential before we go for breeding. Constraints in time, cost, and sample availability usually necessitate the use of predictive tests during early generations, followed by milling and baking tests on advanced lines that have met a number of agronomic, disease and predictive quality criteria. Knowledge of germplasm lines having specific quality traits is needed to initiate breeding for the improvement of wheat grain quality for different end-use products. The quality requirements of different major end-use products are provided in the following table (Table 1).

Introduction

Food supply is a major concern in the near future as the human population touches 9 billion in 2050 and therefore, more food has to be produced. This has to be achieved in the face of climate change amounting to constant pressure of biotic and abiotic stresses. However, Swaminathan (2007) opined that science and technology can play a very important role in stimulating and sustaining an evergreen revolution leading to long-term increases in productivity without associated ecological harm. Rice is considered as global grain since it is consumed by more than half of the world population. In India rice supplies calorie requirement to more than 70 per cent of its population. This is evident from the fact that rice is cultivated in all the 30 states and 5 union territories of the Indian subcontinent of diverse ecologies ranging from below sea level to mountainous regions. Though India tops in rice acreage (43.61 mha) its productivity of 3.19 t/ha (rough rice) is far below world average of 4.12 t/ha and that of Asia’s average of 4.19 t/ha (Shobharani et al., 2010). This low productivity is mainly due to unfavourable ecologies of the varied ecosystems which, rice encounters during critical stages of its growth. Salinity and submergence are major abiotic stresses, next to drought, limiting rice production in South East Asia including India.

In India nearly 8 mha are salt affected of which 2 mha are coastal saline and 3.4 mha are sodic (Singh, 1994). Rice is predominant crop in these areas especially in vast stretches of eastern and western coasts of India. The presence of salts, in excess to plant growth, in the soil solution makes the soil detrimental to crop growth. The source of the excess salt may be from soil or irrigation water. The content and composition of salts (ions) in tandem with types of soil and weather conditions prevailing during the crop period decides the severity of salt stress. Similarly, f lash floods or short-term submergence regularly affect rice growing areas in South and Southeast Asia. Even more favorable irrigated areas experience flooding problems during the monsoon season. It is also prevalent in rainfed lowlands where most of the present day rice varieties do not survive complete submergence for more than a week. In India 30% of the rice growing area is prone to such menace resulting in severe yield losses (Neeraja et al., 2007).

Introduction

Over decades, improvement of domestic animal species has been done by selecting superior animals, mainly based on individual performance and their subsequent breeding to get progenies with higher production potential. Within the 20th century, understanding of inheritance of economic traits, factors influencing genetic potential and their interactions provided better criteria for selection and this has resulted into faster genetic gains. Several selection criteria which were composite ones based on the individuals as well as its relative performances were being used.

Introduction
Aquaculture has emerged as the fastest-growing sector in global agriculture. The total fish production worldwide includes both wild catches and aquaculture outputs. In recent years, fish production has consistently risen, reaching around 130.9 million tons, which accounts for 52% of the fish available for human consumption (FAO, 2024). Molecular breeding in fisheries and aquaculture utilizes cutting-edge genetic technologies to enhance favourable traits in aquatic species. This approach encompasses the application of molecular markers, genome-wide association studies (GWAS), and gene editing techniques to improve attributes such as growth rates, disease resistance, and resilience to environmental stressors. For example, marker-assisted selection (MAS) facilitates the identification and selection of superior broodstock by leveraging genetic markers associated with advantageous traits.

Introduction

Genetic programs in livestock have been extensively used to improve their productivity over the last 50 years. The traditional approach of breeding, based on quantitative genetics principle, has been very successful (Schaeffer, 2006), without knowledge of genes increasing or decreasing in herds. Effective progeny testing program and use of genetically proven bulls have made drastic genetic improvement in livestock populations. Further advances in computation for genetic merit have further added to improvement process. Livestock producers presently are focusing on overall development of livestock with improved health, production, reproduction and longevity and therefore, the traits are becoming the part of selection program (Decker et al., 2009). Advancement in molecular biology along with high-throughput genotyping has led to discovery of a number of single nucleotide polymorphisms (SNPs) in livestock (Van Tassell et al., 2008). SNP arrays covering the entire genome may explain most of the genetic variation in important traits of livestock (Meuwissen et al., 2001). These SNPs may act as molecular markers and be used as a substitute for phenotypic selection. This process, in a broad sense is known as molecular or marker-assisted breeding and describes selection strategies including marker-assisted selection (MAS) and genome wide selection (GWS) or genomic selection (GS).

Spectacular productivity gains have been achieved in wheat and rice in south and south-east Asia and also several other developing countries in Latin America and central Asia due to introduction of dwarfing genes in these two crops purely through conventional plant breeding approaches and these developments were christened as “Green Revolution” (Reynolds and Borlaug, 2006). The wheat breeding progrmme was being spearheaded by Norman Borlaug at CIMMYT (International Maize and Wheat Improvement Centre, Mexico) supported by Sanjay Rajaram and the rice breeding programme was under leadership of Gurdev Singh Khush at IRRI (International Rice Research Institute, Manila, Philippines) coinciding with these exciting developments during mid-sixties to mid-seventies. In recognition of these quantum jumps in yield of wheat and rice, Borlaug was awarded Nobel Peace Prize for Peace in 1970. Later on World Food Prize was instituted by joint efforts of Borlaug and his colleagues to honour Agricultural Scientists and others on pattern of Nobel Prize who had made significant contributions to sustainable food production and food and nutritional security globally. M. S. Swaminathan happened to be Director General, Indian Council of Agricultural Research when Green Revolution was taking roots in India and because of his enormous contributions to provide effective leadership to ensure that Green Revolution happened in India, M. S. Swaminathan is credited as “Father of Green Revolution in India” and he was the first recipient of World Food Prize in 1987 for spearheading the introduction of high-yielding wheat and rice varieties in India. G. S. Khush along with Henry Beachell received 1996 World Food Prize for achievements in enlarging and improving the global supply of rice during a time of exponential population growth and Sanjay Rajram was the 1914 World Food Prize recipient for his scientific research that led to huge increase in world wheat production.

ABSTRACT

Black pepper (Piper nigrum L.), known as the ‘King of Spices’ is an important export- oriented spice crop, valued for its medicinal and condimental properties. A perfect protocol for the rapid in vitro multiplication of this plant is available. However, systemic bacterial contamination is the single major constraint in the large scale in vitro production of plantlets. Based on morphological and biochemical characters, this bacterium was identified as Beijerinckia indica It grows profusely on nitrogen-free Jensen’s agar and solubilizes CaCO in the medium by acid production. It is resistant to a range of antibiotics and produces indole acetic acid. The bacterium is slow growing and has pH optima of 5.5 and temperature optima of 27oC. It has both endophytic as well as epiphytic association with the plant, the colonization being more in the stem and petiole. A single plasmid of 4.0 kb size was isolated from the bacterium and characterized. Competent cells of E. coli DH5a, transformed with this plasmid survived on Jensen’s nitrogen free agar, indicating its ability to fix atmospheric nitrogen. We stipulate that the nif genes are located on the plasmid of the bacterium. Since endophytic bacteria are known to stimulate plant growth through antagonistic activity against pathogens, production of growth promoting substances and inducing systemic resistance in several other agricultural crop species, the symbiotic association between Bejerinckia indica and black pepper could be further exploited through integrated nutrient management for improved growth and yield of this spice crop.

ABSTRACT

An effort was made to characterize twelve ber genotypes using RAPD markers. Of the twenty random decamer primers tested, 17 generated polymorphic bands, while rest of the primers showed monomorphic bands. The primers that amplified all the 12 genotypes were OPC-20, OPD-1, OPD-3 and OPD-4. The size of amplified DNA fragments varied from 0.56-4.26 kilobase pair. In total, 109 bands were obtained, of which 85 bands were polymorphic, while 24 bands were monomorphic. For the cultivars tested between 2-9 bands were obtained for each primer with an average of 5.45 bands per primer. The highest number of bands (9) were generated by OPA-4 and OPD-3. With un-weighted group method using arithmetic mean (UPGMA) cluster analysis, the twelve ber genotypes fell into four major clusters. The pair wise dissimilarities of ber genotypes showed that genotypes G-9 and G-8 were close to each other. Maximum dissimilarity was observed between the genotypes G-8 and G-12.

Molecular characterization involves the use of techniques that are available to analyze variation in plants and animals at the DNA level. Differences in gene sequences can be directly observed and described with a precision previously impossible to achieve. Many of the techniques that have been developed have already been used in evolutionary and taxonomic studies. They have immense value in studies of accessions identity and for the detection of novel useful variation in the plant germplasm. Molecular markers provide genetic information of direct value in key areas of conservation both ex situ and in situ. For ex situ conservation the key issues are:

ABSTRACT

The study was conducted to fingerprint and to analyze genetic diversity among 20 genotypes. of Psidium guajava and two species P. friedrichsthalianum and P. cattleianum using random amplified polymorphic DNA. Genomic DNA was isolated using modified CTAB method and polymerase chain reaction was carried out using standard protocols. In all 41 primers were used, 39 of which amplified 376 alleles with 347 polymorphic alleles. All the primers discriminated between two and more genotypes. Primers produced 2-16 alleles. The size of amplified DNA alleles ranged from 0.12-2.2 kilobase pairs. Polymorphic index content value was found to be maximum for primer OPB-12 (0.916). In the dendrogram all the 22 genotypes were grouped into two major clusters. Cluster 1 comprised of Spear Acid, Apple Colour and P. friedrichsthalianum, while Cluster 2 constituted rest of the 19 genotypes. Thus, RAPD markers detected a high level of polymorphism and can be used for breeding of improved guava varieties.

ABSTRACT

Piper colubrinum is a wild relative of the cultivated species of black pepper, Piper nigrum. The enzyme hydroxy methyl glutaryl Co A reductase which catalyses mevalonate synthesis, is the key enzyme in isoprenoid biosynthesis.This is the rate limiting step in the pathway which leads to the formation of sesquiterpene phytoalecins, a group of plant defense metabolites. Piper colubrinum is known to be tolerant to the dreaded disease called foot rot, incited by Phytophthora capsici. The hmgr gene is reported to confer resistance to fungal pathogens. Hence we made an attempt to isolate gene encoding this enzyme. cDNA was synthesised by reverse transcription from total RNA of P.colubrinum using oligo dt primers. Specific degenerate primers designed based on the conserved boxes among various plant species were used for amplifying hmgr gene from the cDNA. The 700 bp amplicon was cloned in pGEMT vector and sequenced with T7 primer. Multiple sequence alignment using clustal W 1.8 revealed homology of the cDNA fragment with hmgr genes in several other plant species. Maximum similarity was observed among P. colubrinum, Solanum xanthocarpum and Nicotiana tabacum. The cDNA library of P. colubrinum constructed in lTriplEx2 when screened with radiolabelled hmgr amplicon, yielded positive signals. Attempts are being made to isolate full length gene from these clones, which could be later used for imparting biotic stress tolerance to cultivated crop species.

Constituents of meat
i. Water- 75%
ii. Protein- 19%
iii. Soluble and non-protein substances- 3.5%
iv. Fat- 2.5%
• The muscle fibre is important unit of muscular tissue consisting of
a) Myofibrils- formed protein structures embedded in sarcoplasmic fluid
b) Sarcoplasmic reticulum- a fine system of tubules
c) Sarcolemma- a very thin membrane surrounding the myofibrils and around the exterior side of this membrane, the connective tissue is found
• 19% of protein in the muscle is muscle fibre (Table 11.1)
• α-alanine, glycine, glutamic acid and histidine are the major free amino acids present in the fresh muscle

INTRODUCTION

All plant species grown on this universe are attacked by insect-pests and diseases, resulting huge yield losses in agriculturally important species. Among diseases, extensive yield losses occurred due to soil borne fungal plant pathogens. Soil borne fungal pathogens infect roots or stem bases, their dispersal and survival stages are primarily confined to the soil. Although many soil pathogens may also produce air or water dispersed spores which results in long distance dispersal. Soil borne fungal diseases are specifically those diseases where the soil borne fungi has the capacity to survive in soil for long periods in the absence of their hosts, or survive in the soil outside of seed or host residues, but infection and symptom expression are confined to the subterranean organs of the plant. Soil borne fungi may be divided into two classes: i) The  soil inhabiting fungus which is characterized by its ability to survive indefinitely as saprophyte (e.g. Rhizoctonia, Sclerotium) and ii) The soil invading or root inhabiting fungus which is characterized by an expanding parasitic phase and a declining saprophytic phase after  the hosts death.

Abstract

The conventional methods of pathogen identification have often depended on identification of disease symptoms, isolation and culturing of the organisms, and identification by morphology and biochemical tests. The major limitations of these culture based morphological approaches, however, are the reliance on the ability of the organism to be cultured, the time consuming nature and requirement of extensive taxonomic expertise. Furthermore, diagnosis of plant diseases can be even more difficult with asymptomatically infected propagative materials such as tree grafting stocks or potato tubers. The use of molecular methods can circumvent many of these shortcomings. Accordingly, there have been significant developments in the area of molecular detection of plant pathogens in the last three decades. The polymerase chain reaction (PCR) which revolutionised molecular diagnostics and biological sciences. In the last decade the range of targets that can be diagnosed using diagnostic PCR have grown tremendously. The very flexibility and application specific variations in the basic theme of the system have allowed the development of many PCR variants adapted to wide range of applications. Furthermore, diagnostic PCR has been greatly improved by the introduction of the second generation PCR, known as the Real time PCR where closed-tube fluorescence detection and quantification during PCR amplification (in real time) is possible eliminating the need for laborious post-PCR sample processing steps which greatly reduces the risk of carryover contamination. Using Real Time PCR, it is possible not only to detect the presence or absence ofthe target pathogen, but it is also possible to quantify the amount present in the sample allowing the quantitative assessment of the number of the pathogen in the sample. Enumerating the pathogen upon detection is crucial to estimate the potential risks with respect to disease development and provides a useful basis for diseases management decisions. Crops can be attacked by many pathogens which, in addition, often occur in complexes. Therefore, many disease diagnostic applications require simultaneous detection and quantification of several targets. Methodological limitations, however, are in many cases the reason for developing simplex or assays designed for only few targets. The DNA Microarray technology, originally designed to study gene expression and generate single nucleotide polymorphism (SNP) profiles, is currently a new and emerging pathogen diagnostic technology, which in theory, offers a platform for unlimited multiplexing capability. It is viewed as a technology that fundamentally alters molecular diagnostics. The fast growing databases generated by genomics and biosystematics research provides unique opportunity for the design of more versatile, high-throughput, sensitive and specific molecular assays which will address the major limitations of the current technologies and benefit plant pathology.

ABSTRACT

Central Plantation Crops Research Institute at Kasaragod maintains largest collection of coconut germplasm accessions representing different geographical regions. So far, morphological and isozyme markers were employed for germplasm characterization. To overcome the difficulties associated with the morphological markers, DNA based molecular markers are presently employed for germplasm characterization. In the present study, Inter Simple Sequence Repeat (ISSR) markers are utilized to estimate the genetic diversity among South East Asian germplasm accessions. Nineteen ISSR primers were used to amplify 8 germplasm accessions (4 palms per accession referred as population). The PCR products were electrophoresed in 1.80 % agarose gels. Binary data were analyzed using the software POPGENE ver. 1.32. Dendrogram was constructed based on Nei’s unbiased measure of genetic distance. Nineteen ISSR primers detected a total of 85 polymorphic markers across 32 individuals belonging to eight populations. The average genetic distance among the eight populations ranged from 0.7908 to 0.9327 with a mean of 0.8540. Of the 28 pair wise comparisons the accessions Laguna Tall and Kongthienyong Tall (KTYT) showed the highest genetic identity (0.9327). The lowest identity (0.7908) was between San Roman Tall (SNRT) and Philippines Dalig Tall (PDLT). The Shannon’s index ranged from 0.1615 to 0.299. Diversity parameters viz. number of effective alleles, gene diversity, number of polymorphic markers were calculated for each population. The dendrogram constructed based on the genetic distance revealed clustering of Kongthienyong Tall (KTYT) and Laguna Tall (LAGT) while Philippines Dalig Tall (PDLT) was positioned separately. In the genetic improvement programmes the diverse accessions can be used in hybridization for increased heterosis.

ABSTRACT

Purine Nucleoside Phosphorylase (PNP) is an enzyme that functions in the purine salvage pathway by catalyzing the phosphorolysis of purine nucleoside thereby releasing the purine bases and phosphorylated sugar. Interest in PNP as a drug target arises from its role in T-cell proliferation and T-cell mediated autoimmune diseases. Recently, we have isolated the compound, coixol, from the plant Scoparia dulcis L. and its three-dimensional structure has been elucidated. As the structure of the coixol mimics the structure of PNP inhibitors, we have undertaken the molecular modeling studies of this compound with Human PNP, as a screening test for further in vivo studies. Generally PNP inhibitors have been synthesized with a ribose sugar moiety attached to them. As the plant Scoparia dulcis L. contains glucose and rhamnose (six membered ring), these sugar moieties are also included along with ribose in the presen study. In order to understand the binding mode and interactions of the isolated compound attached with different sugar groups, we have carried out the docking studies with Human PNP. The interactions between the ligand molecules and active site residues of Human PNP are similar to those of solved complexes and the energy values are also comparable, which clearly indicate that these ligands may act as inhibitors.

Summary

Molecular evolution is the process of evolution at the scale of DNA, RNA, and Protein. Molecular evolution emerged as a scientific field in the 1960s as researchers from molecular biology, evolutionary biology, and population genetics sought to understand recent discoveries on the structure and function of nucleic acids and protein. It covers two broad areas of study : the evolution of macromolecules, and reconstruction of the evolutionary history of genes and organisms. The evolution of macromolecules refer to the characterization of the changes in the genetic material (DNA or RNA sequences) and its products (Proteins of RNA molecules) during evolutionary process, and to the rates and patterns with which such changes occur, and also the mechanism responsible for such changes. The second area also known as “molecular phylogenetics”, deals with the evolutionary history of organisms and macromolecules as inferred from molecular data and the methodology of tree reconstruction.

Summary

Molecular farming is the large scale production of pharmaceutically important and commercially valuable proteins in plants and animals. Molecular farming in plants has the potential to provide an inexpensive and convenient system in the production of unlimited quantities of recombinant proteins for use as therapeutics, diagnostics, vaccines, antibodies, plasma proteins, cytokines and growth factors. Plants are also being used for the production of oils, starches, plastics, enzymes for food processing and other uses and spider silk etc. However, quality and safety of the final product and wider effects of molecular farming on health and environment need to be addressed. The benefits of molecular farming should not be outweighed by risks to human health and environment.

4.1 Introduction

Many important traits such as yield, quality and some forms of disease resistance are controlled by many genes and are known as quantitative traits or characters (also called ‘metric’,‘polygenic,’ ‘multifactorial’ or ‘complex’ traits). The regions within genomes that contain genes associated with a particular quantitative trait are known as quantitative trait loci (QTLs). The identification of QTLs based only on conventional phenotypic evaluation is not possible. A major breakthrough in the characterization of quantitative traits that created opportunities to select for QTLs was initiated by the development of DNA (also called molecular) markers in the 1980s.

One of the main uses of DNA markers in agri-horticultural research has been in the construction of linkage maps for diverse crop species. Linkage maps have been utilised for identifying chromosomal regions that contain genes controlling simple traits (controlled by a single gene) and quantitative traits using QTL analysis. The process of constructing linkage maps and conducting QTL analysis–to identify genomic regions associated with traits–is known as QTL mapping (also called ‘genetic,’ ‘gene’ or ‘genome’ mapping). DNA markers that are tightly linked to agronomically important genes (called gene ‘tagging’) may be used as molecular tools for marker-assisted selection (MAS) in plant breeding. MAS involves using the presence/absence of a marker as a substitute for or to assist in phenotypic selection, in a way which may make it more efficient, effective, reliable and cost-effective compared to the more conventional plant breeding methods. The use of DNA markers in plant (and animal) breeding has opened a new realm in agriculture and horticulture called ‘molecular breeding’.

5.1 Introduction

The development of quantitative trait loci (QTL) mapping methods to identify genes or QTLs controlling quantitative traits was a landmark achievement in plant genetics research in the late 1980s. Since then literally thousands of research papers have reported the identification of genes or QTLs for important traits across a diverse range of plant species. This wealth of genetic information was built on the foundation of decades of research in crop molecular genetics and genomics.

The selection and enrichment of QTLs within breeding material was the inevitable next step from QTL discovery to application, and there have been numerous reports of successful tracking of genes and QTLs within breeding programmes. DNA (or molecular) markers have enabled selection of major genes or QTLs for critical or important traits in a process called marker-assisted selection (MAS), which has revolutionized plant breeding. DNA markers are used as tools by breeders to improve the accuracy or efficiency of selection as well cost and time efficiency. Apart from MAS, DNA markers have numerous applications including DNA fingerprinting, genetic diversity analysis and parental characterization.

Recent developments in genotyping platforms and systems to implement molecular breeding schemes offer new tools for modern plant breeders. Single nucleotide polymorphism (SNP) markers are biallelic, co-dominant markers which are abundant in the genome. Insertion-deletion (Indel) markers are also prevalent and can be screened using high-throughput genotyping platforms. These platforms are cost-efficient, can handle large sample sizes and provide fast data turn-around time. The availability of genome sequences and genomic resources continues to provide a wealth of SNP and Indel markers which will undoubtedly be the marker type of choice for decades to come.

The availability of high-throughput SNP platforms in conjunction with advances in computational methods has also led to the molecular dissection of traits using genome-wide association studies (GWASs) across diversity panels and the development of genomics-based molecular breeding strategies. Association mapping (AM) has now emerged as a standard method for gene and QTL discovery for major crops.

Rice (Oryza sativa L.) is the most popular crop and source of food for more than one-third of the world’s population. About 90 % of the world’s rice is grown in Asia and more than 3 billion Asians rely on rice for 30–75 % of their total calories (Braun and Bos 2004). It has been cultivated in four different ecosystems viz., irrigated, rainfed low land, upland and flood-prone (Halwart and Gupta, 2004). Since rice planting has been started around 8,000 to 9,000 years ago, the level of diversity would be more than it expected. The genetic diversity plays a major role in survival and adaptability of a species, as changes happen in environment. Organism needs to make changes in the phenotype that enables it to adapt and survive in unfavorable conditions. The inadequate knowledge on diversity of a species reduces the chance of widening the genetic base of that species. The venture of green revolution in Indian agriculture has narrowed down the genetic base of any popular crops. Therefore, collection, conservation and utilization of germplasm are very much needed in the present scenario for improving the varieties against biotic and abiotic stress.

Morphological and biochemical trait based diversity studies being largely influenced by environment as phenotype and/or enzymes are altered by the environmental and developmental changes. Therefore, adapting DNA based molecular markers for genetic diversity studies would be more reliable to overcome the environmental influence. Being molecular markers as a versatile tool, it establishes its strong holds in several fields of life science. Molecular marker based technique does not require DNA sequencing but it is generally based on nucleic acid hybridization or polymerase chain reaction (PCR). The PCR based tests has several advantages over hybridization technique as it is cheaper, speedy and sensitivity. Therefore, PCR based markers have been used extensively in genetic diversity study for assessing genetic variation within the species. The recent advent of molecular and computational tools now enables the estimation of genetic diversity and allele frequency between the genotypes easy.

DNA is the master molecule which carries the genetic information from one generation to the other. Study of Molecular Genetics accelerated since April 25th, 1953 when James Watson and Francis Crick proposed the structure of DNA which was published in Journal called ‘Nature’. Molecular Genetics deals with the flow of genetic information and its regulation. In simple terms it can be defined as the field of biology which studies the structure and function of genes at molecular level.
Scope of Molecular Genetics
Development of techniques like nucleic acid hybridisation, cloning, sequencing etc. brought a revolutionary change in Molecular Genetics. It is of major interest to the students of biology and medicine. Though it has a lot of significance in many fields, we’ll confine ourselves to the applications of molecular genetics to the mankind. They are as follows:
i) Diagnosis of infectious diseases: Normally microorganisms are detected in the laboratory using biochemical methods. In case of molecular techniques, microorganisms are detected by using probes (short DNA or RNA sequence) which are complementary to a part of genome of the microbe. The advantage of using molecular methods is:
• Identification of pathogen is done within a short time;
• No need to cultivate the microbes;
• Latent infections can also be identified when no antibody is formed; and
• The technique can be used even when the microorganism cannot be cultured.
ii) Diagnosis of genetic diseases : Before the advent of the above techniques, counselors used to give risk estimate like one fourth risk of getting the disease, if the parents are heterozygous for an autosomal trait. But now by directly testing for the mutation, they are able to confirm the presence or absence of mutation in the fetus. It is of immense help in prenatal diagnosis.

Molecular markers or DNA markers are considered to be one of the most successfully applied component of molecular biology techniques that have relevance in almost every sphere of biology, from paleobotany to transgenic technology. In true sense, a marker is a characteristic of an individual that differentiates the individual from others. Morphological descriptions like cotyledon colour of Pea, eye colour of Drosophila, shape and size of fruits in summer squash etc. are examples of typical morphological markers. However, a single morphological marker is not sufficient for describing the uniqueness of an individual, for many pea plants will have green cotyledon or many Drosophila may have red eye. To define the uniqueness of an individual, we have to find a number of marker traits characteristic of that individual. Unfortunately, morphological variations are not sufficient to differentiate between a large number of individuals, or between groups or sub groups within a species, simply because the level of polymorphism is low. Besides, morphological characters or phenotypic expressions are affected by environmental changes, so stability of expression is low and sometimes uncertain.

Introduction

Plant genetic resources management essentially consists of two phases; its conservation and utilization. Germplasm conservation includes acquisition, in which germplasm is safeguarded in situ (by establishing reserves) or ex situ (by assembling collections through exchange or exploration). It also involves maintenance, protecting germplasm in situ in reserves or storing it ex situ under controlled conditions, propagating it while preserving its original genetic profile with maximum fidelity, monitoring its viability and health in storage or in situ and maintaining associated passport information and other data. Germplasm conservation also involves characterization, assessing highly heritable morphological and molecular traits for taxonomic, genetic, quality assurance and other management purposes. The second phase of germplasm management, encouraging utilization, includes evaluation, assessing agronomically or horticulturally important traits with relatively low heritability and high components of environmental variance e.g. yield adaptation and host-plant resistance to certain abiotic/biotic stress. It also includes genetic enhancement, making particular genes more accessible and usable to breeders by adopting exotic germplasm to local environments without losing its essential exotic genetic profile and/or introgressing high value traits from exotic germplasm into adapted varieties. Genetic enhancement can be subdivided into introgression i.e. backcrossing a few genes controlling desired characters into adapted stocks and incorporation i.e. the large scale development of locally adapted populations good enough to enter the adapted genetic bases of the crops concerned.

Plant breeding is considered as current phase of crop evolution. It is a combination of art and science, which involves designers activity, conventionally, economically important traits dispersed in different parental lines are combined together to develop a new variety or cultivar and to change the genetic constitution of a plant to make it more suitable for human need with available scientific knowledge. Although plant breeding has been existing since time immemorial, modern plant breeding methods are based on scientific principles begins only with the rediscovery of Mendel’s laws of inheritance in 1900 and chromosomal theory of inheritance in 1902. Significant achievements have been made in crop improvement through phenotypic selections for agronomically important traits, considerable difficulties are often encountered during this process, primarily due to genotype-environment interactions.

Molecular markers may be a short DNA sequence that flanks base pairs like SNP, a Single Nucleotude Polymorphism, small fragment or SSR Single Sequence Repeat or an extended site as in the case of microsatellites. Schematic representation of the SSR assay is shown in Fig. 1. Genetic markers have to be easily identified, linked to a specific locus and polymorphic. Molecular markers are subdivided into codominant monolocus and polyallelic markers and the second group contains dominant, polyallelic and biallelic markers. 

ABSTRACT

Genetic improvement of crop plants through conventional plant breeding has made tremendous contributions to the breakthrough in the global agricultural production. Recently, an array tools and techniques in the field of molecular biology has become available for supplementing the conventional genetic approaches. Consequently, new integrated approaches are being designed. One of the approaches employs molecular markers for genome mapping, gene tagging and marker assisted selection (MAS). With the complete sequencing of whole plant-genomes and a large number of random cDNAs in many different crop species, newer opportunities are emerging. This presentation is an attempt to briefly describe the current applications of molecular markers and to highlight their future prospects.

Molecular markers

Molecular markers are heritable differences in nucleotide sequences of DNA at corresponding position on homologous chromosomes of two different individuals, which follow a simple Mendelian pattern of inheritance. These differences are detected employing two basic techniques: (a) Southern blot hybridization and (b) Polymerase chain reaction (PCR). Restriction Fragment Length Polymorphism (RFLP) is the first molecular marker system to be conceived and developed. It is based on the southern blot technique. Markers such as random amplified polymorphic DNA (RAPD), sequence tagged site (STS) and amplified fragment length polymorphism (AFLP) are generated by enzymatic amplification of DNA by extension of oligo nucleotide primers and therefore, are based on PCR. Single/simple nucleotide polymorphism (SNP) markers are based on DNA sequence differences as revealed by sequencing and assayed by various techniques.

Abstract

Molecular markers play key role in crop improvement. There are severalmarkers such as RAPD, SSR, AFLP, SNP, DArT and many more are available for their practical uses. From the past markers like RAPD, AFLP, and SSR have been used extensively in the crop breeding. Recently new markers such as SNP and DArT have become popular among the researchers of molecular biology for use in genomics-assisted crop breeding. These markers have been applied for study of genetic diversity, germplasm management, cultivar identification, genetic mapping, gene tagging and genomics etc. Though the conventional method of breeding willcontinue to play a primary role in the crop improvement, molecular marker technology is becoming one of its integral components. Agarose-based DNA markers like ISSR, CAPS, RAPD, SCAR and AS (allele specific) have the potential for faster and accurate breeding for target traits through MAS.

Introduction

Genetic markers are genes or DNA sequences associated with a specific gene or trait, often arising from mutations or alterations in genomic loci (Samarai and Kazaz, 2015). Recently, there has been a growing interest in molecular markers, which reveal polymorphisms at the DNA level. These markers play a crucial role in animal genetics studies, as they help identify genetic resources and differences between domesticated and wild animals. Cytological markers, which use chromosome karyotypes, bandings, repeats, translocations, deletions, and inversions, are widely used for elucidating species origin and classification (Becak et al., 1971; Jonker et al., 1982).

Abstract

People dealing with forest tree seeds are very much concern with the collection and supply of pure and quality seed. Assessing genetic purity of tree seed is always a challenge. Besides, studying tree diversity and tree improvement are also the key components of forestry. With the discovery of DNA based molecular markers these tasks have been made easier and authentic. So, the basic concepts behind different molecular markers were the principal concerns of this chapter. It has been focused here about the pros and cons of the markers along with their applicability. The application may be expanded towards hybrid seed testing and even to clonal forestry.