eChapters

1.     Chromatography
    
2.     Identification of Sugar in Fruit Juice by Thin Layer Chromatography
    
3.     SDS-PAGE
    
4.     Composition for Native PAGE
    
5.     Silver Staining of Protein Gels

1.     Isolation of Plant DNA
    
2.     RAPD Analysis of Genomic DNA
    
3.    Agro Bacterium based Transformation in Plants
    
4.     Assay for Gus Operon
    
5.     Confirmation of Transformation using Polymerized Chain Reaction (PCR)
    
6.     Primer Designing
    
7.     Isolation, Purification and Identification of Plant Secondary Metabolites
    
8.     Evaluation of Antioxidant Activity of Plant Extract
    
9.     Estimation of Total Phenolic Content in A Plant Extract
    
10.     Estimation of Total Flavanoid Content

ALL LIVING ORGANISMS ARE MADE UP OF UNITS CALLED CELLS

All living creatures are made from 1 or more cells

All cells are produced from previously existing cells (no spontaneous generation)

All cells appear to be descended from the first cell which existed about 4 billion years ago

For a species to exist its reproductive cells must be potentially immortal (no aging)

Our bodies start from a single cell and contain about 100,000,000,000,000 (10^14) cells at maturity

MOST OF THE ENERGY FOR LIFE COMES FROM SUNLIGHT

Total rate of energy delivery from sun to earth (at the top of the atmosphere) = 175,000 terrawatts

Terrawatt = 10^12 watts

Rate of energy capture by plants from the sun = net primary productivity (NPP) = 100 terrawatts

Only ~ 0.06% of sunlight is captured

Captured in chemical bonds, especially in sugar

Small amounts of energy are available to specialized microorganisms from chemical reactions not linked to sunlight

It is estimated that 99% of the energy used by living cells comes from the sun

Incorporation of sunlight into chemical bonds occurs through the process of photosynthesis

“Invented” by cyanobacteria about 2 billion years ago

Some traits are carried on the sex chromosomes, X and Y. Most traits carried are present on only the X-chromosome. The Y-chromosome is smaller, and so, very few genes are located on this chromosome. Sex traits can be categorized into three types of inheritance:
Sex limited,
Sex-linked, and
Sex-influenced.
Sex-limited traits are traits that are visible only within one sex. For instance, barred colouring in chickens normally is visible only in the roosters. Sex-linked traits would be considered traits like sickle cell anemia and colour blindness. They are said to be linked because more males (XY) develop these traits than females (XX). This is because the females have a second X gene to counteract the recessive trait. Thus, the trait is more likely to be visible in the male.
Sex Influenced Inheritance
The condition in which the same gene acts as dominant in one sex and recessive in other sex is called as sex influenced dominance. That is, the sex influences the gene either to be dominant or recessive. The sex influenced genes are present in autosomes. This differential behaviour of the gene is due to female and male sex hormones. For example, in human being baldness is due to sex influenced gene. This trait is dominant in men and recessive in women. A man is bald in homozygous recessive as well on heterozygous condition for baldness. Whereas women exhibit baldness only in homozygous recessive condition for baldness and heterozygous condition for baldness in female sex produce normal phenotype. HN, HN -Normal female and normal male

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.

To understand how population genetics came into being, and to appreciate its intellectual significance, a brief excursion into the history of biology is necessary. Darwin’s Origin of Species, published in 1859, propounded two main theses: firstly, that modern species were descended from common ancestors, and secondly that the process of natural selection was the major mechanism of evolutionary change. The first thesis quickly won acceptance in the scientific community, but the second did not. Many people found it difficult to accept that natural selection could play the explanatory role required of it by Darwin’s theory. This situation— accepting that evolution had happened but doubting Darwin’s account of what had caused it to happen—persisted well into the twentieth century (Bowler 1988).
Opposition to natural selection was understandable, for Darwin’s theory, though compelling, contained a major lacuna: an account of the mechanism of inheritance. For evolution by natural selection to occur, it is necessary that parents should tend to resemble their offspring; otherwise, fitness-enhancing traits will have no tendency to spread through a population. In the Origin, Darwin rested his argument on the observed fact that offspring do tend to resemble their parents—‘the strong principle of inheritance’—while admitting that he did not know why this was. Darwin did later attempt an explicit theory of inheritance, based on hypothetical entities called ‘gemmules’, but it turned out to have no basis in fact.
Darwin was troubled by not having a proper understanding of the inheritance mechanism, for it left him unable to rebut a powerful objection to his theory. For a population to evolve by natural selection, the members of the population must vary—if all organisms are identical, no selection can occur. So for selection to gradually modify a population over a long period of time, in the manner suggested by Darwin, a continual supply of variation is needed. Fleeming Jenkin argued that the available variation would be used up too fast (Jenkin 1867). His reasoning assumed a ‘blending’ theory of inheritance, i.e., that an offspring’s phenotypic traits are a ‘blend’ of those of its parents. (So, for example, if a short and a tall organism mate, the height of the offspring will be intermediate between the two.) Jenkin argued that given blending inheritance, a sexually reproducing population will become phenotypically homogenous in just a few generations, far shorter than the number of generations needed for natural selection to produce complex adaptations.

A population, in the genetic sense, is not just a group of individuals, but a breeding group and the genetics of a population is concerned not only with the genetic constitution of the individuals but also with the transmission of the genes from one generation to the next. In the transmission the genotypes of the parents are broken-down and a newest of genotypes is constituted in the progeny, from the genes transmitted in the gametes. The genes carried by the population thus have continuity from generation to generation, but the genotypes in which they appear do not. The genetic constitution of a population, referring to the genes it carries, is described by the array of gene frequencies, that is, by specification of the alleles present at every locus and the numbers of proportions of the different alleles at each locus. If for example, A1 is an allele at the A locus, then the frequency of A1, is the proportion or percentage of all genes at this locus that are the A1 allele. The frequencies of all the allele at any one locus must add up to unity, or 100 percent.
The gene frequencies at a particular locus among a group of individuals can be determined from knowledge of the genotype frequencies. To take a hypothetical suppose there are two alleles A1 and A2, let the frequencies of genes and of genotypes be as follows:

I. Definitions

Transpiration - evaporation of water from a plant surface

Evapotranspiration - evaporation of water from a plant surface and the soil (and abiotic surroundings.

Take-home-lesson: Plants loose a lot of water by transpiration. See text for some specific examples.

1. Individual or mass selection
The terms individual selection and mass selection are often used interchangeably, and they refer to selection solely based on the individual´s phenotype. This is a well-known and widely used method of selection in animal breeding. It can be used on characteristics that can be measured in the candidate animal itself, as weight gain is most efficient in characteristics of high heritability. Individual selection is usually the simplest method to operate and, in many circumstances, it yields the most rapid response. It does not require individual identification or the maintenance of pedigree records, hence, it may be considered the least costly method. In principle, it can produce rapid improvement if the heritability of the trait(s) under selection is high. It can be suitable for growth rate and morphological traits (easily assessed, expressed in both sexes). By contrast, individual selection is not suitable for situations in which the estimation of breeding values requires the slaughter of the animals (carcass and flesh quality traits). When applying individual selection, the evaluated animals must be under equal environmental conditions; therefore, the environmental conditions must be controlled. In this case, the influence of external conditions should be minimal and kept the same for all individuals to be compared at any life cycle stage. In this manner, the probability of correct ranking of the individuals based on thus genetic merit is maximized. Differences between individuals or groups of individuals for environmental factors may reduce the accuracy of the selection substantially, and in that way, can also reduce the possibility for genetic improvement. it is important to form contemporary groups and select within them. To obtain as equal environmental conditions as possible all individuals to be compared should be reared under identical environmental conditions. Therefore, it is important to form groups of animals with similar ages, grown in the same production systems, with similar control of environment, handling, and feeding. However, mass selection may be unsuitable if there is large uncontrolled systematic environmental variation (for example age differences). Additionally, there is no control of inbreeding with mass selection.

Thus the average value of progeny genotypes in response to selection of parental phenotypes depends largely on Cov (G, g), the genetic covariance of parent and offspring which is half the additive genetic variance of the parents.
We know that on an average, half of genes of a parent are passed to the offspring and with them a random half of his additive merit. One-fourth of his additive x additive gene combinations are also transmitted and lesser fractions of higher additive combinations. No dominance combinations are transmitted, since only one member of each allelic gene pair reaches the offspring. Similarly all epistatic gene combinations involving allelic gene pairs are broken up at gamete formation. If dominance and epistatic gene combinations involving allelic gene pairs are important in determining genetic superiority for the trait, then direct selection of superior parents will not produce genetically superior offspring. Some form of mating system which will recreate these combinations in the offspring, together with the formation of lines or groups within the population is needed in these circumstances.
Thus, the aim of selection is to identify and select as parents individuals with high additive genetic merit. By selecting the parent on additive merit, we also ensure that a fraction of any parallel merit for additive type epistasis is also passed on. In considering response to selection, little is lost by treating the response as if it were wholly determined by the additive effects of genes

Livestock is an important source of income for the rural poor and marginal farmers which enables earn income and food security using common resources.It is a best option to utilize such waste resources in proper way to earn income. About 65-69% of Indian population consisting of small and marginal farmers and land less laborers reared animal as supplementary occupation by feeding their animals agriculture by products. Indian agriculture is very difficult to sustain without dairy animals. Per capita availability of milk comes out to 281gm per day, which is below than the average of 300gm recommended by Nutrition Council of ICMR. Thus, there is a further need to increase the milk production of the country in view of minimizing difference between per capita availability and requirement. Milk production in India has increased from a modest 22 million tons during 1970-1971 to about 122 million tons in 2011—2012 (Deptt. of Animal Husbandry and Dairying).

Dairy buffalo production has been a tradition in Asian region and some other parts of the world where fresh  buffalo milk, dahi (cultured sour milk), ghee (butter oil) and yoghurt are very popular. In Italy, the dairy buffalo industry is flourishing; thanks to the popularity of buffalo mozzarella cheese. Because of the market for Mozzarella, buffalo farming is a profitable enterprise and is carried out in an organized manner with modern equipment.

Introduction

In India 70 to 75 per cent of the indigenous cattle and buffaloes are designated as non-descript that is they do not come under any well defined breed. Among the animals of defined breed also, less than 5-10 per cent of the population can be considered as elite and used for the production of breeding stock. Average productivity of cross-bred and desi cows is 2141 kg/lactation & 634 kg /lactation, respectively, which is still very low. The average productivity of buffaloes is 1355 kg/lactation only.

Introduction

Agricultural biodiversity must be an integrated part of climate change adaptation and mitigation efforts. Climate change adaptation, biodiversity conservation and poverty alleviation should complement each other (FAO, 2007, 2008). Climate affects vectors, pathogens, hosts and host-pathogen interactions from the level of cellular defence to that of the habitat. Hoberg et al. (2008) provide an overview of predicted responses of complex host-pathogen systems to climate change. Climate change may affect the spatial distribution of disease outbreaks, and their timing and intensity (Epstein 2001). Outbreaks of African horse sickness, peste des petits ruminants, Rift Valley fever, bluetongue virus, facial eczema and anthrax are triggered by specific weather conditions and changes in seasonal rainfall profiles.

Maintaining the required type of information in the form of records is primary for any type of animal breeding analysis and this chapter explains the importance of records and ways to maintain them in the form of registers or computer databases. The formats for different types of registers to be maintained are also given as a template in appendix. Any breeding plan is formulated to improve the economic traits depending on the utility of species reared and the chapter lists important economic traits of livestock and poultry with definitions and formulae, where ever required.

Basic record maintenance is a must for any animal breeding program. Every farm or breeding program is expected to maintain records in the form of registers or computerized databases. The goal of animal breeding is to select mates with the objective to improve economically important traits. In this chapter, the most common economic traits in different species of livestock are described. Even though the list is not exhaustive the basic economic traits that have been worked for improvement are explained. Breeders also explore new composite traits which are a combination of these base traits.

Reproduction is the backbone of animal production and productivity is the key to development. Reproductive inefficiency is one of the most important causes of economic losses in animal industries and it is realized throughout the world. Despite the remarkable advancement that has been made in the field of reproductive physiology in recent years, infertility due to low conception rate and high embryonic mortality rate remains a major problem. To meet future needs and to be able to sustain agricultural production, agricultural research and its applications need to use all emerging technologies one of which is modern reproductive biotechnologies.5 Thus, various assisted-reproductive techniques have been developed and refined to obtain a large number of offspring from genetically superior animals or obtain offspring from infertile (or sub-fertile) animals in addition to disease control. Reproductive biotechnologies intend to be used routinely to shorten generational intervals and to propagate genetic material among breeding animal populations. To achieve this goal, reproductive technologies have been developed in generations over the years, namely artificial insemination (AI), embryo transfer (ET), manipulation of fertilization in vitro (IVF), cloning and transgenesis. These, together with sperm separation techniques, including that of selection of spermatozoa for chromosomal sex (commonly named sex-sorting) all face today a strong wave of increasing commercialization.9 Hence, this review paper highlighted the reproductive biotechnology options and their roles in the improvement of livestock production.
Roles of Reproductive Biotechnology in Animal Production
Biotechnology is defined as a technique that uses living organisms to make or modify and improve products. The emergence and development of reproductive technologies have been driven by the economic gain offered by the potential increase in the number of offspring from genetically superior animals or simply to safeguard the genetic pool of infertile or sub-fertile animals. In other words, reproductive technologies were developed to offer possibilities for wider use of superior germplasm.In recent times, there has been increasing challenges for

Traits such as growth, lactation test day yield, semen evaluation are longitudinal traits measured repeatedly on the animal and random regression models (RRM) have been found to be suitable for modeling these traits, The methodology used, data requirement, assumptions, validity, software available and application of RRM are explained in this chapter.

Growth, test-day milk yield, and semen traits are examples of longitudinal traits measured repeatedly on the animal and random regression models (RRM) have been found suitable for modeling such traits. RRM is based on a covariance function which could be defined as “a continuous function to give the variance and covariance of traits measured at different points on a trajectory” (van der Werf, 2001). Kirkpatrick et al. (1990) showed that variance components for longitudinal data can be modelled through covariance functions. Random regression models (RRM) and the resulting covariance function have been recognized as ideally suited for the analysis of longitudinal data (Hill, 1998; Meyer, 1998).

Meta-analyses has been used extensively to combine the results of existing studies and obtain powerful estimates of a parameter. In animal breeding, attempts have been made to obtain meta-analysis estimates for genetic parameters. This tool is more pertinent to animal breeding on account of heterogeneity in terms of location, sample size and other factors in the estimation of genetic parameters. This chapter explains the background, methodology, precautions and implications of meta-analysis with respect to genetic parameters.

A meta-analysis is a powerful tool of statistics that could combine several estimates from different studies for a parameter and the resulting weighted estimate could be used as a representative value for the particular parameter. However, not all the studies are similar with respect to location, sample size, and methodology used and thus various precautions are to be taken right from the selection of studies to incorporating of between-study heterogeneity in the models. In animal breeding, met-analysis is very much useful for obtaining meaningful estimates of genetic parameters and this chapter explains the methodology of meta-analysis in animal breeding.