eChapters

Variation in Chromosome Structure

Natural variation exists in chromosome structure

Changes in chromosome structure include deletions, duplications, inversions, and translocations

The loss of genetic material in a deletion tends to be detrimental to an organism

Duplications tend to be less harmful than deletions

Duplications provide additional material for gene evolution, sometimes leading to the formation of gene families

Copy number variation is relatively common among members of the same species

Comparative genomic hybridization is used to detect chromosome deletions and duplications

Inversions often occur without phenotypic consequences

Inversion heterozygotes may produce abnormal chromosomes due to crossing over

Translocations involve exchanges between different chromosomes

Individuals with reciprocal translocations may produce abnormal gametes due to the segregation of chromosomes

Introduction
Legumes that produce dry seed suitable for human consumption are known as pulses, and they are agronomically valuable plants in the field and in the food chain. In the past ten years, grain legumes—particularly pulses—have become more popular as a means of addressing global agricultural concerns. (Bohra et al. 2015, Varshney et al. 2015).The best plant-based sources of dietary protein, as well as other minerals including iron, zinc, magnesium, and dietary fiber, are pulses. (Bohra et al.2014, Kouris-Blazos and Belski 2016, Maphosa and Jideani 2017). According to Simpson and Campbell (2015), a plant-based agricultural diet high in fruit or legume fiber helps to improve microbial diversity and has a beneficial effect on short-chain fatty acid levels, both of which are critical for preserving gut health. Because of their unique ability to fix nitrogen symbiotically with Rhizobium spp. in their root nodules, legumes not only improve nutritional health but also increase soil fertility (Graham and Vance 2003, Stagnariet al. 2017). The Leguminosae, often known as the Fabaceae, are the third largest family of flowering plants, behind the orchid (Orchidaceae) and sunflower (Asteraceae) families (Walters 1960), with 750 genera and 20,000 species (Polhill 1981).With a productivity of 1016 kg ha-1, 93.23 million tons (m t) of pulses are harvested worldwide from 91.77 million (m ha) of land (http://faostat.fao.org/). With a cumulative average productivity of 1030 kg ha-1, the major pulse crops—dry bean (primarily common bean), chickpea, dry pea (pea), cowpea, pigeonpea, lentil, and faba bean—share 92.58% (84.05 million ha) of the world’s total pulse production, or 92.82 percent (86.53 m t) (http://faostat.fao.org/). According to their ability to adapt to tropical and temperate agroclimatic conditions, pulse crops can be broadly divided into two groups: 1) warm season crops, such as common bean, pigeonpea, and cowpea, and 2) cool season crops, such as pea, chickpea, lentil, and faba bean (Cannon et al. 2009, Young et al. 2003, Zhu et al. 2005). Chickpea, pea, and lentil are regarded as one of the founding grain crops and helped start modern agriculture because of its early domestication (around 11,000 years ago) (Zohary and Hopf 2000).Over the past 60 years, the global area under pulses has increased from 64 to 91.77 million hectares (http://faostat.fao.org/), and numerous high-yielding varieties have been developed and released as a result of extensive research on conventional breeding for pulse improvement due to their high agricultural value (Singh 2005, Saxena 2008, Pérez de la Vega et al. 2011, Torres et al. 2011, Gaur et al. 2012).Pulses are less productive than other crops, particularly cereals, due to factors such growing in risky settings, unpredictable rainfall, extended dry spells, and susceptibility to a range of pests and diseases (Borlaug 1973, Varshney et al. 2013a).

Varietal release and notification comes under the purview of the Seeds Act which is intended to provide for regulating the quality of certain notified seeds for sale and for marketing and for the matters connected therewith. Released and notified varieties are offered for seed certification by the seed certification agencies which ensure that the varieties under certification meet certain prescribed field and seed standards failing which they stand to be rejected during the process of seed certification.

Purpose of Release

The purpose of release of cultivars is to introduce the newly evolved varieties to the public for general cultivation in the region in which it is suitable. It enables the farmers to choose cultivars for cultivation in a region. In other words, release of a cultivar is in the nature of a recommendation to the farmers for its adoption. Therefore, notification of a variety is linked to the release of a variety, though the release process itself does not have statutory cover.

Crop breeders are continuously engaged in the improvement and development of crop varieties, in search of a genotype which will prove superior to the existence cultivars. A strain is duly released by appropriate duly empowered legal organization. Only when it is officially released, it is called variety, Before release, it is said to be strain or line. The release of new crop varieties consists of the following major steps:

1. Development of new strains

The new strains are developed by ICAR Crop Research Institutes and State Agricultural Universities for specific purposes. Various breeding methods are used for development of new strains. Some varieties are developed by selection without hybridization such as pure-line variety, mass selected variety and clonal variety. Development of some varieties involves hybridization and selection. This includes varieties that are developed by pedigree, bulk and backcross methods including multiline cultivars and population improvement methods.

2. Evaluation of performance

This trial is conducted at the research station, where new strains has breed. The object is to make sure that new strains are better in performance than the existence variety, so that it can be promoted to the trials where new strains has to be compete with other strains, developed by other scientists/researchers.

Breeding methods for vegetable crops are basically similar to those adopted in others like cereals, oilseeds or pulses. Certain aspects, peculiar to vegetables, however, require specific attention: (i) In many cases, the edible part of the plant is not the seed (as cauliflower, cabbage, carrot and onion) and hence while breeding for improved plant part that is used as vegetable, its seed production capacity needs due consideration, (ii) Vegetables like tomato, garden pea and onion are consumed in different forms (fresh or processed) and the end use of the product (like processing quality) has to be taken into account in breeding programmes, (iii) Consumer preferences (as for example in eggplant) size, colour and shape of the vegetable has to be given due emphasis, (iv) Being perishable in nature, keeping quality and suitability for long distance transportation are important attributes in vegetable crops unlike grain crops where bulk handling and haulage can be mechanised, (v) Another peculiarity with vegetable crops is that they vary widely in modes of reproduction necessitating appropriate choice of breeding methods. In addition to vegetatively propagated crops like potato, sweet potato, cassava (tapioca), garlic, pointed gourd or “Parwal (Trichosanthes dioica L.) and ivy gourd or ‘Kundru’ (Coccinia cordifolia L.), there are many seed propagated vegetable crops which are auto- or allogamous or intermediate (Table 1).

Within these broad groups, variations in the extent of cross- or self-pollination, namely, 15-20 per cent natural cross-pollination in chillies and 20-25 per cent natural self-pollination in muskmelon have been recorded.

A close relationship between the mode of reproduction of a cultivated plant and the methods to be employed for its improvement is now well accepted. Crop plants are broadly placed in two groups according to the mode of their reproduction: sexually reproduced and asexually propagated or reproduced plants. Asexual reproduction does not involve the union of gametes and/or reduction in chromosome numbers.

Plants may reproduce asexually in a variety of ways. In 1980, Mayo has identified the following methods of asexual reproduction on the basis of the classification made earlier by Stebbins in 1941 and Brown in 1972.

In this chapter, we will explore multiple comparison tests, with a particular emphasis on three significant tests: least significant difference (LSD), Bonferroni, and the techniques to visualize their outcomes. We aim to facilitate a comprehensive understanding of how to conduct and interpret the results of these comparison tests visualization using the R software.

Treatment Comparison

The “doebioresearch” package is commonly used for testing the significance of treatment groups in various experimental designs such as randomized block design (RBD), completely randomized design (CRD), and least significant difference (LSD). This package excels in conducting multiple comparison tests like LSD, Duncan’s multiple range test (DMRT), and Tukey’s honestly significant difference (HSD). It efficiently calculates all comparisons in the background, resulting in the generation of only group labels, as previously demonstrated in the output of the “doebioresearch” package. Additionally, the “agricolae” package is another useful tool that provides detailed values for multiple comparison tests. These three tests—LSD, DMRT, and HSD—are particularly popular in agricultural experiments and form the focus of our discussion.

I. Least significant difference (LSD) test

• To conduct the least significant difference test for comparing treatment means, the “agricolae” package is essential.

• To install the “agricolae” package, use the following code:

• install.packages (“agricolae”)

• After installation, activate the package with this command:

• library (“agricolae”)

• The data frame required for analysis in this context remains consistent with what is needed for randomized block design (RBD), completely randomized design (CRD), LSD, and variability analysis, among others. As an illustration, consider an example involving variability analysis.

Volumetric analysis, also known as titrimetric analysis, is an analytical method of estimating the concentration of a known solute (analyte) in a solution by measuring the volume of a second known solution of known concentration (standard solution), that reacts completely with the known solute of unknown concentration. The prerequisite of titration is that the two different analytes, present in solution form, must involve in a fast chemical reaction. The standard solution is more commonly known as ‘titrant’ and the solution whose concentration needs to be determined is frequently called ‘titrand’.

Introduction

A variety of glassware, plasticware, and other apparatus are used for experimental purposes in a laboratory. They need to be washed, cleaned, dried, and sometimes sterilized before they can be used in the next set of experiments. Glassware needs special care of handling during washing, drying, sterilization, etc. because even a minor mistake in handling of glassware may result in its cracking/breakage and it may become unserviceable. All of these may result in a delay in experimentation if spare piece of the glassware is not available or it may affect serviceability of the associated apparatus.

A large number of glassware such as beaker, flask, measuring cylinder, burette, test tube, etc. are regularly used in a laboratory, which requires careful handling during the different stages of experiment as well as after completion of the experiment while preparing them for another set of experimentation.

Glass being a complex silicate, its properties depends on the type of silicate anions in the structure and the cations formed. Thermal properties of glass changes by the addition of boron oxide (B2 O3 ); hence, borosilicate glass is extensively used in the laboratories. With this brief background information, let us discuss about the necessity, procedures, and precautions during washing, cleaning, drying and sterilization of laboratory-wares. Figure 3.1 shows various advantages of using borosilicate glass in a laboratory.

Good laboratory practices require clean glassware, because an experiment may give erroneous result if dirty glassware is used at any step of the experiment. Hence, the glassware must be physically and chemically clean; and in many cases, it must be microbiologically clean or sterile. The commonly used glassware in a laboratory include test tube, measuring cylinder, pipettes, beakers, flasks, microscopic slides, etc.

Water lily is an important aquatic ornamental flower crop valued for its attractive flowers, cultural significance and use in water gardens, ponds and decorative landscapes. Different flower colours and forms provide considerable ornamental diversity, while flowers also have importance in religious and ceremonial activities. The chapter introduces water lily through its botanical characteristics, origin, distribution, genetics and important varieties. It discusses the environmental conditions required for successful cultivation, including suitable water bodies, soil and temperature conditions. Propagation, planting, nutrient management, irrigation and routine cultural operations are described. The chapter also covers pest and disease management, flower harvesting, postharvest handling, yield and commercial possibilities associated with water-lily production.

Water, of its very nature, as it occurs automatically in the process of cosmic evolution, is fit, with a fitness no less marvelous and varied than that fitness of the organism which has been won by the process of adaptation in the course of organic evolution.

WATER IS ABSOLUTELY ESSENTIAL FOR ALL LIVING ORGANISMS

The evidence:

Most organisms are comprised of at least 70% or more water. Some plants, like a head of lettuce, are made up of nearly 95% water;

When organisms go dormant, they loose most of their water. For example, seeds and buds are typically less than 10% water, as are desiccated rotifers, nematodes and yeast cells;

Earth is the water planet (that’s why astronomers get so excited about finding water in space).

Water is the limiting resource for crop productivity in most agricultural systems.

WATER IS VERY SPECIAL IN BIOLOGY

Most abundant chemical of life

Special properties:

With Judicious Use of Herbicides

Herbicides are the chemicals used for killing or suppressing the growth of weed plants from field / horticulture / plantation crops as well as non-cropped areas/ water bodies etc. The herbicide is said to be an ideal herbicide when it is very safe to the crop on which it is applied and on the other hand, it must control all associated weeds effectively. Also, ideal herbicides should leave no residual effects on the succeeding crop(s). Herbicides are of two types i.e.

1. Selective herbicides and
2. Non-selective herbicides.

A selective herbicide is that which is very safe to crop plants but unsafe to weed plants e.g. atrazine in maize, clodinafop in wheat etc. On the other hand, non-selective herbicides are those which kill all green plants including crop and weed plants which come in their contact e.g. paraquat and glufosinate ammonium.

Introduction

In a research laboratory, we frequently need weigh chemicals and prepare different solutions of varying strength, as per the requirements. Accuracy in weighing and preparation of solution, with respect to weight/volume and strength, determines the success of experiment. In turn, the accuracy depends on weighing of solid chemical and/or measuring the volume of liquid chemical/making up the volume. In this Chapter, weighing of chemicals using appropriate weighing balance, preparation of solutions of different strength, their dilution, and precautions while preparing will be discuss in brief.

Weighing of Chemical

The primary method to determine the amount of chemicals to be used is weighing the chemical by using a balance.

In general, there are two types of balances to weigh chemicals in a laboratory:

1. Standard laboratory balance

2. Analytical balance

Standard Laboratory Balance

Generally, a standard laboratory balance is used for weighing a chemical when an error of ±0.02 g is acceptable. It is also used for pre-weighing, where approximate mass needs to be determined. Precise mass of the chemical is then determined using an analytical balance. Following are the steps in using a weighing balance in a laboratory.

Principle

Western blot analysis (also called protein immunoblot) is a useful tool for the detection of proteins in biological samples. It uses gel electrophoresis to separate native or denatured proteins by the length of the polypeptide (denaturing conditions) or by the 3-D structure of the protein (native/ non-denaturing conditions). The proteins are then transferred to a membrane (typically nitrocellulose), where they are probed (detected) using antibodies specific to the target protein.  It is a technique for analyzing and identifying protein antigens: the proteins are separated by electrophoresis in polyacrylamide gel, then transferred (“blotted”) onto a nitrocellulose membrane or treated paper, where they bind in the same pattern as they formed in the gel. The antigen is overlaid first with antibody, then with anti-immunoglobulin or protein A labeled with radioisotope, fluorescent dye, or enzyme. 

The method originated from the laboratory of George Stark at Stanford. The name “Western blot” was given to the technique by W. Neal Burnette and is a play on the name “Southern blot”, a technique for DNA detection developed earlier by Edwin Southern. Detection of RNA is termed northern blotting and the detection of posttranslational modification of protein is termed “Eastern blotting”.

Introduction

The western blot (alternatively, protein immunoblot) is an analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate native or denatured proteins by the length of the polypeptide (denaturing conditions) or by the 3-D structure of the protein (native/non-denaturing conditions). The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are probed (detected) using antibodies specific to the target protein.

There are now many reagent companies that specialize in providing antibodies (both monoclonal and polyclonal antibodies) against tens of thousands of different proteins. Commercial antibodies can be expensive, although the unbound antibody can be reused between experiments. This method is used in the fields of molecular biology, biochemistry, immunogenetics and other molecular biology disciplines.

Other related techniques include using antibodies to detect proteins in tissues and cells by immunostaining and enzyme-linked immunosorbent assay (ELISA).

The method originated from the laboratory of George Stark at Stanford. The name western blot was given to the technique by W. Neal Burnette and is a play on the name Southern blot, a technique for DNA detection developed earlier by Edwin Southern. Detection of RNA is termed northern blotting and the detection of post-translational modification of protein is termed Eastern blotting.