eChapters

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.

Introduction

Fresh and processed products derived from fruit crops provide vital contributions to human nutrition, health, and well-being, and collectively their production constitutes the economic backbone of many rural communities worldwide. Rapid development and distribution of new cultivars with improved characteristics which meet the industry, market (both domestic and export), and consumer preferences is the need of the day. Conventional methods of perennial fruit crop improvement have almost exclusively relied on traditional breeding techniques. These techniques are expensive, time consuming and space requiring, especially for tree species due to the need of a large population of seedlings from which only a few promising ones are selected. The juvenile period of tree crops may last three to five years before onset of fruits so that 20 years or more are common before the successful introduction of a gene of interest (Baird et al., 1996). Therefore in this context, molecular tools recently made available for breeders have become tools of choice because they permit to reduce cost by fastening the selection process of woody fruit plants. Further, traits of importance like fruit quality, resistance to diseases, high yield etc. are polygenic in nature for which classical breeding is generally not suitable for detection and selection of traits. A quantitative trait locus (QTL) analysis with help of markers and linkage maps may be more appropriate for detection of such traits of interest. Also, molecular markers are being used for maintenance of core collections, for the assessment of genetic diversity between genotypes and fingerprinting.