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There is need to find better ways and solutions to mitigate future agricultural challenges toward increasing productivity across the crops and equip them with the desirable genes for resistance to biotic and abiotic stresses and to mitigate the impact of climate change and also to make them nutritionally superior. Here comes “Plant Genomics”—a newly evolved discipline of plant sciences—targeting to decode, characterize, and study the genetic composition, structures, organizations, functions, and interactions/networks of all plant genes in a genome-wide scale. Being evolved from plant molecular genetics, biology, and biotechnology, plant genomics represents the key sub- divisions of structural, functional, comparative, evolutionary, physiological, and genetical genomics. Its development and advances, however, are tightly interconnected with plant science sub-disciplines, such as proteomics, metabolomics, epigenomics, phenomics, metagenomics, transgenomics, breeding-assisted genomics, bioinformatics and system biology as well as modern instrumentation and robotics sciences.

Plant genomics is a recent convergence of many sciences. Simply stated “Genomics” is the new science that deals with the discovery and noting of all the sequences in the entire genome of a particular organism. The genome can be defined as the complete set of genes inside a cell. Genomics, is, therefore, the study of the genetic make-up of organisms. Determining the genomic sequence, however, is only the beginning of genomics. Once this is done, the genomic sequence is used to study the function of the numerous genes (functional genomics), to compare the genes in one organism with those of another (comparative genomics), or to generate the 3-D structure of one or more proteins from each protein family, thus offering clues to their function (structural genomics). In crop agriculture, the main purpose of the application of genomics is to gain a better understanding of the whole genome of plants. Agronomically important genes may be identified and targeted to produce more nutritious and safe food while at the same time preserving the environment. Genomics is an entry point for looking at the other ‘omics’ sciences. The information in the genes of an organism, its genotype, is largely responsible for the final physical makeup of the organism, referred to as the “phenotype”. However, the environment also has some influence on the phenotype. DNA in the genome is only one aspect of the complex mechanism that keeps an organism running – so decoding the DNA is one step towards understanding the process. However, by itself, it does not specify everything that happens within the organism. The basic flow of genetic information in a cell is as follows. The DNA is transcribed or copied into a form known as “RNA”. The complete set of RNA (also known as its transcriptome) is subject to some editing (cutting and pasting) to become messenger-RNA, which carries information to the ribosome, the protein factory of the cell, which then translates the message into protein.

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.

When conditions in the plant growing environment are less than the optimum, the plants experience stress which is broadly termed as abiotic stress. Major abiotic stresses impacting crop yield significantly are as follows (Grover et al., 2004; Acquaah, 2007):

Drought: This is the environmental condition caused by lack of adequate rainfall. This is also termed as water stress or desiccation stress. Effects of drought on crop plants are complex and variable and are greatly accentuated by a number of interacting factors. The onset of drought in general has been observed to reduce germination, emergence, hypocotyl length, water uptake and the mobilization of dry matter reserves even at the early growth stages. Drought stress causes a marked reduction in leaf area. Soil moisture availability at the seed germination, anthesis and at post-anthesis growth stages determines as to what extent production potential of crops would be expected in drought-prone situations.

The yield losses in field crops may be attributed to inadequate water availability at the critical growth stages. Crops therefore differ in their susceptibility of growth stages to water stress. Stress exposed plants immediately lower down relative water content (RWC) of their leaves, leaf water potential, osmotic potential. Turgor pressure may also be decreased unless plants have finally adapted to drought by opening of stomata again and improving the water potential. It has been reported that low leaf expansion rate at the early stage and accelerated leaf senescence accompanied by mortality of older leaves at later stage decreases total leaf green area.

This chapter starts quoting first para of the book entitled Disease Resistance in Plants by Van Der Plank (1968). “In 1958 the American Phytopathological Society met to celebrate its Golden Jubilee and review the problems and progress in plant pathology during the 50 years, 1908 to 1958. J. C. Walker was elected to review the problems and progress in controlling plant diseases by host resistance, a fitting tribute to one who perhaps more than any other had contributed during those 50 years both to understanding of nature of resistance and to the practical application of resistance to problems in horticulture and agriculture. In his summary Walker wrote “By and large the development of resistant varieties must be looked upon as a continuing program. The potential variability of most pathogens (including viruses) will not permit any currently successful variety to remain so for an indefinite period”. This opening para tells the importance of breeding for resistance to diseases in crop plants on a continuous basis as the fight between host and the pathogen will go on and on.

Mangelsdorf (1951) has opined that hybrid corn has been the most far-reaching development in applied biology. Hybrid cultivars have contributed enormously to world’s food and feed resources. Although dramatically successful at first in corn, hybrids have spread to several other crops both in cross-pollinated and self-pollinated species. Their use is likely to spread more in time to come. Hybrid varieties are those in which F1 populations are used to produce commercial crop. Parents of F1 may be inbred lines, clones, varieties, or other populations. Hybrid breeding is historically rooted in development of hybrids in corn and therefore most of the issues covered in this section relate to hybrid breeding in maize.

A variety produced by crossing inter se a number of genotypes selected for good general combining ability in all hybrid combinations with subsequent maintenance of the variety by open-pollination. According to Hayes and Garber (1919), the synthetic production of an improved variety by inbreeding and cross-breeding seems a reasonable plan. Synthetic cultivar is a commercial entity and a combination of number of inbred lines, sibbed lines, clones or other populations of cross-pollinated crops. The features of the components are as follows:

1. They will have been tested for their combining ability.
2. They will be preserved for future syntheses of the synthetic variety.
3. The component lines will be combined in a manner so as to allow random mating.

Synthetic varieties are normally used in cross-pollinated crops in those situations where hybrid development and organized seed production are in the preliminary stages. Inbred lines are common components of synthetics because they are easy to maintain and can be used again and again as per requirement of reconstituting the synthetics. When selfing is not possible, sibbing may be used. In case of perennials, clones are used as components. Combining ability of the component lines is determined in different ways. General combining ability is desired more than the specific combining ability because there are several components to a synthetic variety and each is required to combine well with the rest other lines. Random crossing of components of a synthetic variety is assumed and each line should contribute the same amount of seed to the next generation. Because a synthetic variety is a mixture of many genotypes, it might change under selection pressure during multiplication.

The concept of recurrent selection grew out of need to increase the number of superior genotypes that could be obtained from breeding stock of corn. This could have been possible by increasing the frequency of superior genes in the gene pool and by increasing the chances for genetic recombination to occur. Both can be achieved by recurrent selection which is defined as “a method of breeding designed to concentrate favourable genes scattered among a number of individuals by selecting in each generation among the progeny produced by mating inter se of the selected individuals (or their selfed progeny) of the previous generation.” The original idea behind recurrent selection was proposed first by Hayes and Gerber in 1919 and independently by East and Jones in 1920. Jenkins (1940) was the first to describe the method in detail and Hull (1945) proposed the name ‘recurrent selection’. Each cycle of recurrent selection requires (i) evaluation and selfing of selections and (ii) crossing of the progenies of superior selfed plants in all combinations and bulking of equal amount of seed from each cross. The selection of plants before selfing is possible for maturity, plant height, ear/head characters, kernel characteristics and resistance to diseases and insects. In general, these are the characters which have high heritability. It is clear that the selection of plants before selfing is more for morphological traits and these evaluations do not include yield. Yield evaluations are done on the top cross progenies (crossing of selected plants to a tester). Such top crosses will be grown in the second year of the cycle during which time the selfed seed is held over until the evaluations for yield are over. Or the selfed seed may be grown out as S₁ lines which in turn are selfed. After yield evaluation is over, the selfed seed of superior plants is grown out for crossing. Progenies of selfed plants are crossed in all possible combinations. This is done manually or by growing progenies together in an isolated block. In isolation planting, random mating should be ensured. After manual crossing or random mating in isolation, equal amounts of seed of each are bulked and this bulk seed is used to start the second cycle of selection, selfing and crossing.

Mass selection is the simplest, oldest and least expensive method of plant breeding as applicable to cross-pollinated crops. The method involves planting balanced bulk seed of the population to be improved, in isolation, inferior plants rogued out before pollination wherever possible and selecting and bulking superior genotypes that already exist in the population. A balanced bulk of selected ears, for example, in corn is made for planting the next cycle. Selection units are individual plants. Selection is surely on phenotypic performance. This method exploits additive gene effects plus additive x additive interactions. The efficiency of this method depends largely on the heritability of the trait under selection. Selection results using mass selection have been quite effective for less complex traits. Mass selection could be very effective for those traits that can be identified or selected prior to flowering, for example, curd/head shape, size, colour in cauliflower and cabbage, root shape, size, colour and quality traits in radish and carrot and bulb shape, size, colour and weight in onion. A few examples of such traits in maize could be flowering, leaf angle, prolificacy, resistance to thrips, fall armyworm, reduced plant and ear height, reduced anthesis-silking interval and barrenness and tolerance to pre-flowering diseases.

Lack of pollination control is major limitation of this method as both desirable and undesirable pollen will be involved in pollination of the selected plants. Further, if selection intensity is very high (small plant population size advanced), the possibility of inbreeding depression is increased. This selection is not very effective if the heritability of the trait under selection is low (less than 10% on individual plant basis). Mass selection is likely to be more effective for individual or a combination of few traits rather than a whole series of characters. Despite some limitations, mass selection can be very useful and relevant procedure in breeding of cross-pollinated crops in many situations characterized by resource limitations, non-availability of trained scientific manpower and additional test sites, lack of seed storage facilities even for short term and lack of continuity of technical personnel. Lack of control on soil variability also makes this method less effective.

Initially, exploitation of heteosis was confined to corn and a few other open- pollinated crops but presently heterosis is being exploited practically in all species cutting across mode of reproduction. More and more evidences are emerging that heterotic expression in a cross is a function of genetic backgrounds and genes. Heterotic grouping would remain a key strategy in management of diverse genetic backgrounds and genes for full exploitation of heterosis. The commonly used methods in developing hybrids in self- pollinated crops are listed and explained as follows:

Manual emasculation and Pollination Method

In this method, female parent flower buds are emasculated manually and the emasculated buds are pollinated by the pollen grain collected from protected flowers of the male parent. This method is effective and successful where the crossed fruits produce plenty of seeds and the seed requirement for planting the commercial hybrid seed is much less. Consequently, this method is being used in a routine manner on a commercial scale in vegetable crops mostly by private sector seed companies in India and south-east Asian countries. The crops covered under this method of hybrid seed production are as follows:

Tomato, hot-pepper, sweet pepper, eggplant, okra, bottle gourd, bitter gourd, ridge gourd, smooth gourd, cucumber, pumpkin, water melon and muskmelon. Cucurbits are included here as although they are cross-pollinated but behave like self-pollinated crops in terms of almost no inbreeding depression.

The application of back-cross breeding first proposed by H. V. Harlan and M. N. Pope in 1922 provides a precise way of improving varieties that excel in a large number of attributes but are deficient in a few key characteristics. F. N. Briggs too started an extensive back-crossing programme to develop bunt resistant varieties of wheat in 1922. As the name implies, the back-cross method of breeding makes use of a series of back-crosses to the variety to be improved during which the character or characters in which improvement is sought is maintained by selection. At the end of back-crossing, the gene (or genes) being transferred will be heterozygous. Selfing at the end of last back- cross produces homozygosity for this gene pair and coupled with selection will result in a variety similar to the well adapted and recurrent parent but superior for the particular characteristic for which improvement programme was initiated.

In back-cross method of breeding, the adapted and highly desirable parent is called the recurrent parent and the source of desirable character being transferred is called as donor parent. It is most effective and easy to apply when the missing trait is qualitatively inherited, dominant and produces a phenotype that is readily observed in a hybrid plant. The procedure for transferring a recessive trait is similar to that for dominant trait but involves an additional step of selfing. Back-crossing is also used to transfer entire sets of chromosomes in a foreign cytoplasm to create a cytoplasmic male sterile (CMS) genotype as has been practiced in maize, onion and wheat, etc. This is done by crossing the donor (of chromosomes) as male until all donor chromosome are recovered in the cytoplasm of the recurrent parent. Back-cross breeding has also been used to develop isogenic lines (lines that differ only in alleles at a specific locus) for traits like disease resistance and plant height, etc.

Bulk population breeding developed by the Swede H. Nilsson Ehle in 1908 and later on supported and practiced by H. V. Harlan in barley breeding in 1940s is a breeding strategy in crop improvement in which natural selection is allowed to play its full role where the F2 generation is planted in a plot large enough to accommodate several hundreds of plants. Planting density and cultural practices are usually the normal ones followed for commercial crop planting. At maturity, the plot is harvested in bulk and the seeds are used to plant a similar plot in the next season. This process is repeated till at least F5 where the plants are space planted to allow individual plant evaluation for effective selection. During period of bulk propagation natural selection plays a key role in shifting gene frequencies in the bulk population. This role is of crucial importance as bulk handling is continued over a number of generations. Bulk population handling can be aided by artificial selection at any time during the period of bulk propagation. Aggressive and highly competitive but undesirable plants may be physically rogued out of the population to avoid increasing the frequency of undesirable genes. For example, determinate bush types of beans do not compete well against indeterminate, vine types. And if the breeder is interested only in determinate types, artificial selection against the indeterminate types is certainly called for. There is also good reason to apply artificial selection against seed colour, pubescence, awns or other characters that are undesirable in the variety to be developed but may be more or less neutral in survival. Bulk population handling often provides opportunities to make use of artificial aids to selection. For example, bulk harvesting when only part of plants are mature is an effective and inexpensive way to select for earliness. If particular sizes of seeds are required, screens or mechanical devices provide a rapid way of eliminating inferior types. Naturally occurring or artificially induced disease or insect infestation, of course, provide opportunities to rogue susceptible individuals from the bulk plot. In F6, the plants selected in F5 are progeny rowed and superior progenies are selected from where again few plants can be selected and seed bulked within a selected row. Depending upon seed requirement for yield trial in the following years, even the seed from selected entire row can be bulked. The follow up yield evaluation trials are as given in case of pedigree selection. This method is operationally best suited for seed crops such as small grains, beans and soybean and is almost totally unsuited for fruit crops and for most vegetable crops.

This method has been first described by H. H. Lowe in 1927. This is the most widely used method to handle segregating generations following crosses between two parents to develop new cultivars combining desirable traits from both the parents. In this method, superior types are selected in successive segregating generations and a record is maintained of all parent-progeny relationships. The records help the breeder to advance only progeny lines with plants that exhibit genes for the desired traits. Selection begins in F2 generation where individual plants are selected which in judgment of breeder will produce the best progeny in F5/F6 when the selection is finally concluded. In F3 and F4 generations, many loci will have become homozygous and family characteristics begin to appear. By F5/F6 generation, most families are expected to be homozygous and uniform and hence selection within such families is no longer effective. At this stage selection emphasis shifts to the selection among families rather than within families.

Selection of parents is of great significance for the success of this method. Normally, this method is used to replace already established variety. Therefore, one parent should be selected on the basis of proven performance in the particular area where the breeding is in progress. The second parent should be such that it complements the first parent for the character under improvement. Sometimes, three or four parents may also be used to supply the desired character by way of three-way or double crosses.

Alinehomozygousatallloci, ordinarilyobtainedbysuccessive self-fertilization in plant breeding is known as pure-line. W. L. Johannsen (1903), a Danish biologist provided a sound scientific basis for selection in self-pollinated crops when he defined ‘pure-lines’ and described the genetic mechanism by which they are established through a series of experiments for seed weight selection in bean, variety Princess. Pure-lines in principle are supposed to be 100% homozygous but that hardly happens in practical plant breeding programmes and usually the so called pure-lines are ‘near pure-lines. Pure-lines tend to be uniform in the traits of interest. Genetic mutations, admixtures and limited out-crossing are the main causes of variation within pure-lines. This is a rapid and most in-expensive method. Pure-line theory may be summarized as follows:

Polyploid is any organism with other than two basic sets of chromosomes, that is, monoploid, triploid, tetraploid, and various aneuploids. Species that have their chromosomes as multiples of a basic number (x) are polyploids. Many of the species which have been developed most recently are polyploids. Autoploidy is not known to have significantly impacted the evolution of species. Autoploids of commercial importance include banana, a triploid which is seedless (diploid bananas have hard seeds not desirable for consumption). Other important autoploids are tetraploid crops, namely, alfalfa, peanut, potato and coffee. Spontaneous autoploids are important in horticultural crops where gigas feature has produced superior varieties of flowering ornamentals of narcissus, tulip, hyacinth, gladiolus, and dahlia among others. Triticale is the most common example of man-made cereal through allopolyploidy. A number of economically important crops are natural alloploids. These include wheat, oat, tobacco, cotton, sugarcane, strawberry and blueberry, wild mustard, black mustard, rutabaga/rape, etc.

The discovery of mutagenic effects of X-rays on the fruit fly (Drosophila) by H. Muller in 1927 and by L. J. Stadler in barley and maize in 1928 paved the way for researchers to experiment with its effects on various organisms. In 1928, H. Stubbe showed the use of mutagenesis in producing mutants in crop plants like tomato, soybean and others. The first commercial mutant was produced in tobacco in 1934. Reports by B. Sigurbjornsson and A. Micke mentioned 77 cultivars that were developed through mutagenesis prior to 1995. In 1995, this number was 484. This number has since been significantly increased covering a large number of crops, namely, corn, wheat, pea, chrysanthemum, poinsettia, dahlia, citrus, apple, peach and the modified traits include plant maturity, winter hardiness, lodging resistance, protein and lysine content and numerous ornamental mutants. By the end of 20th century, the number of mutant varieties rose to 2252 covering a range of crops like cereals, oilseeds, pulses, vegetables, fruits, fibres, and ornamentals. Majority of these mutants were released as direct mutants and the rest as a result of cross breeding with the mutants. Most of the mutant varieties have come as a result of using physical mutagens (X-rays, gamma rays, thermal and fast neutrons) with gamma rays alone accounting for more than 60% of the mutant varieties. By 2017, nearly 3250 mutant varieties belonging to 175 plant species have been developed and released where China, Japan, India, Russia, the Netherlands, Germany and USA are the leading countries. India with 345 commercialized mutants stands third after China (810 mutants) and Japan (481 mutants). Thus mutation breeding is a significant contributor to the development and release of commercial cultivars in several crops and for several traits.

Phenotype is the product of genotype and environment. In presence of genotype x environment interaction (differential performance of genotypes over the environments), phenotype is the product of genotype, environment and genotype x environment interaction. A stable genotype is one which interacts less with the environment or shows a minimum of g x e interaction. When g x e interaction is significant, one must investigate the specific types of g x e interactions such as genotype x location, genotype x year and genotype x location x year interactions by growing selected genotypes over multiple locations and years. Normally, the genotypes are evaluated for three years. A typical analysis of variance for g x e interaction is given in Table 7.1 (Allard, 1960).

In a large random-mating population both gene frequencies and genotype frequencies remain constant from generation to generation in absence of migration, mutation and selection and the genotype frequencies are determined by the gene frequencies. These properties of a random mating population were first explained by G. H. Hardy and W. Weinberg independently in the year 1908 and are generally known as Hardy-Weinberg law. The operational understanding of this law involves three steps as follows:

1. From parents to the gametes they produce.
2. From union of the gametes to the genotypes in zygotes produced.
3. From genotypes of the zygotes to the gene frequencies in the progeny generation.

The gene and genotype frequencies in the original parent generation are assumed as follows:

Any phenotype is the result of interaction of genotype and the environment. Any genotype cannot express itself unless proper environment for its expression is made available. Likewise, environment cannot create any phenotype unless a genotype is there to be acted upon by the environment. However, the effect of genotype and the environment is not fixed, its keeps on changing depending upon the relative role of the genotype. Heritability therefore specifies the proportion of the total phenotypic variability that is due to genetic causes. In other words, heritability is defined as the ratio of genetic variance to the total phenotypic variance. Heritability is the degree to which the characteristics of a plant are repeated and expressed in the progeny. This can be expressed quantitatively as follows:

Heritability (h²) = Genotypic variance/Phenotypic variance

Heterosis or hybrid vigour is the condition where an F1 hybrid falls outside the range of the parents with respect to some character or characters. It is also defined as a manifestation of heterozygosity, expressed as increased vigour, size, fruitfulness and resistance to diseases, insects or climate extremes. It has been observed in nearly every crop including both self and cross-pollinated crops. It is converse of inbreeding depression. However, even the species that show little or no inbreeding depression, often benefit from crossing and resultant hybrids. Therefore, heterosis has been more emphasized than the inbreeding depression. It is defined in two basic ways:

Plant genetic resources (PGR) are the genetic material of plants which are of value for present and future generations of humankind. Often used as a synonym to plant germplasm, it can be defined as a seed, a plant or plant part including cell cultures, genes and DNA sequences that are held in a repository or collected from wild as the case may be and that are useful in crop breeding, research or conservation because of genetic attributes. The term is used to describe a collection of genetic resources for an organism or genetic material which forms the physical basis of inherited qualities. In brief, germplasm is the sum total of the hereditary materials in a species. Germplasm is the foundation and lifeblood of plant breeding without which plant breeding activities cannot be conducted. Germplasm is the genetic material that can be used to perpetuate a species or a population. The base germplasm can be improved for better performance of the crop. In the initial stage of a breeding programme, breeder evaluates the available germplasm lines and makes a selection from them for further test and final release to the farmers. Later on, the germplasm serves as a source of the parental lines which are used to initiate another phase of the breeding programme. Besides, using the base germplasm, breeders generate new variability using a variety of breeding methods such as crossing parental lines and developing new lines, induced mutations and more recently gene transfer. This new variability is again subjected to appropriate selection methods leading to identification and further evaluation of new and promising genotypes for release as cultivars. Generally, germplasm includes following types:

Self-Incompatibility

This is lack of self-fruitfulness and is a condition where the pollen from a flower is not receptive on the stigma of the same flower resulting into no seed setting. This happens despite the fact that pollen and ovule development both are normal and viable. This is caused by genetically controlled physiological hindrance to self-fertilization. This occurs widely among diverse families of flowering plants including the Leguminosae, Onagraceae, Rosaceae, Scrophulariaceae, Solanaceae, Compositae, Cruciferae, Papaveraceae and the Gramineae (now called as Poaceae). The incompatibility reaction is genetically governed by a single locus designated as S with multiple alleles whose number can go more than 100 in some species such as Trifolium pretense. East has estimated that this occurs in more than 3000 plant species distributed over 20 families. Lewis classified incompatibility systems into two main groups, namely, heteromorphic and homomorphic and homomorphic system has further been divided into gametophytic and sporophytic types as illustrated below:

Definition

Based on various standard sources, plant breeding has been defined in various ways. A few important and standard definitions are:

The art and science of changing plants genetically.

Plant breeding is the genetic adjustment of plants to the service of man.

Improvement of crop plants as the result of process of evolution directed by man for his own ends. The basic principles of plant breeding are thus the principles of evolution. Directed evolution as imposed in plant breeding differs from natural evolution chiefly in a greatly reduced time-scale, and in a more precise control over the factors which govern hybridization and selection.

The science and art of manipulating the heredity of plants for a specific purpose.

Plant breeding is a deliberate effort by human to nudge nature, with respect to the heredity of plants, to an advantage. The changes made in plants are permanent and heritable and the professionals who carry out this task are called plant breeders. This effort at adjusting the status quo is instigated by a desire of humans to improve certain aspects of plants to perform new roles or enhance existing ones. As a result, the term “plant breeding” is often used synonymously with “plant improvement” in recent years. Normally the term plant breeding connotes the involvement of sexual process in effecting a desired change; however, it is also true that modern plant breeding also includes the manipulation of asexually reproducing plants (plants that do not reproduce through the sexual process). Breeding is therefore about manipulating plant attributes, structure, and composition, to make them more useful to humans.

Gepts and Hanock (2006) have defined plant breeding as an applied, multidisciplinary science. It is the application of genetic principles and practices associated with the development of cultivars more suited to the needs of human than the ability to survive in the wild; it uses knowledge from agronomy, botany, genetics, physiology, pathology, entomology, biochemistry and statistics. Of particular importance is the ability to transfer, in addition to major genes, large suites of genes conditioning quantitative traits such as productivity and other traits of interest to humans. The ultimate outcome of plant breeding is mainly improved cultivars. Therefore, plant breeding is primarily an organismal science even though it is eminently suited to translate information at molecular level (DNA sequences, protein products) into economically important phenotypes. The traditional definition of plant breeding includes only those scientists who develop new cultivars and improved germplasm, however, many feel this definition should be expanded to include scientists who contribute to crop improvement through breeding research.

Objectives

• Better understand the phenomenon of probability.

Introduction

The concept of probability is basis to many principles of classical genetics (segregation, independent assortment etc.) The principals of population genetics are based on the considerations of laws of probability. Probability is the likelihood of occurrence of an event.

Trial

A trial refers to an opportunity provided for an event to occur, e.g. tossing of a coin once constitute one trial as it provides an opportunity for head or tail to occur. A new borne can be either a boy or a girl.

Objectives

• Better understand the various types of gene interaction.

Introduction

Gene interaction is the phenomenon of two or more genes that affect each other’s expression in different ways in the development of a single character of an organism. It is the modification of normal phenotypic expression of gene due to interaction between alleles or non-alleles. In such situation, two or more than two genes may interact to give rise to a particular phenotype

Objectives

• Better understand the phenomenon of multiple alleles.

Introduction

The word allele is a general term to denote the alternative forms of a gene or contrasting gene pair that denote the alternative form of a gene is called allele. These alleles were previously considered by Bateson as hypothetical partner in Mendelian segregation. Mendel and his followers used the term ‘allele’ or ‘alleleomorph’ to denote the alternative form of the normal gene. It means the genes for tall and dwarf characters of pea plant are alleles. The former is normal or wild allele and the later is mutant allele. A gene can mutate several times producing several alternative expressions. When three or more alleles are found for any particular gene, these are called ‘multiple alleles’. These occupy the same locus in homologous chromosomes.

Multiple alleles are defined as genes that are members of the same gene pair and are located on the same locus. All of them control the same character but each of the allele affects that character somewhat differently than the others. In any diploid organism, a particular gene pair is represented by two alleles of the series, one allele on each of the two chromosomes of a homologous pair. This is because an organism has just two chromosomes of each type. These form a homologous pair. However, in the individuals of a population or species, many alternative forms of the same gene may be present. The grouping of all the possible alleles of a gene pair is defined as a system of multiple alleles and their mode of inheritance is called multiple allelism. The multiple allele system can be represented as A1, A2, A3, A4 etc.

Objectives

• Study of gene mapping.

Introduction

All the genes that are linked together form a linkage group. Genes of a linkage group may be presented on a single straight line in the same order in which they are normally present on the concerned chromosome. The number of different linkage groups in a species is, as a rule, equals to its gametic chromosome number (n). The distance between two neighbouring genes is proportional to the frequency of recombination (%) between them depicted on a line drawing. Such a line drawing depicting the linked genes the recombination frequencies between them is known as Linkage map, Genetic map or Chromosome map. Linkage maps provide information on the genes that are linked together and the frequencies of recombination that may be expected between them. The frequency of recombination between two linked genes cannot exceed 50% which is the frequency in case of independent segregation.

Objectives

• Detection of linkage using Chi-square test for goodness of fit.

Introduction

The tendency of two or more genes to stay together during inheritance is known as linkage and it is the consequence of the concerned genes being located in the same chromosome. Linked genes do not show independent segregation, as a result the ratios obtained in F₂ and test cross generation are significantly different from the expected ratios of 9:3:3:1 and 1:1:1:1, respectively.

Detection of linkage χ² using test

In genetic experiments, when the material under study is segregating simultaneously for two characters, it may be of interest to know whether the two characters are inherited independently or they are linked. The χ² test can be used for this purpose. χ² test is used in detecting linkage in back crosses and inter crosses.

First the χ² is computed based on the theoretical segregating ratios. If χ² is not significant it may be concluded that the loci segregate independently. If χ² is significant we may suspect linkage between the loci. The χ² is then partitioned into components assignable to different factors.

Objectives

• Chi-square test for goodness of fit of genetic ratios.

Introduction

Karl Pearson developed the chi square test of statistical significance which is commonly used in Mendelian and population genetics. Chi square (χ²) test is a test of statistical significance which is used to test the significance difference between observed and expected frequencies or ratios. The purpose of χ² test is to decide if a set of observed data is according to an expected ratio or if it agrees well with an expected or theoretical distribution.

The chi square test of independence allow us to evaluate whether the segregation of alleles at one locus is independent of the segregation of alleles at another locus. To distinguish between inheritance patterns that obey Mendel’s laws versus those that do not, a conventional strategy is to make crosses and then quantitatively analyze the offspring’s. Based on the observed outcome, an experimenter may make a tentative hypothesis. For example, it may seem that the data are obeying Mendel’s laws. Hypothesis testing provides an objective, statistical method to evaluate whether the observed data really agree with the hypothesis.

The underlying principles behind a statistical approach is to evaluate the goodness of fit between the observed data and the data that are predicted from a hypothesis. This is sometimes called a null hypothesis because it assumes there is no real difference between the observed and expected values. A high deviation would be found between the observed and expected values. If this occurs, the hypothesis is rejected. Hopefully, the experimenter can subsequently propose an alternative hypothesis that has a better fit with the data.

The null hypothesis is a particular claim concerning how the data is distributed. More will be said about the construction of the null hypothesis later. The null and alternative hypotheses for each chi square test can be stated as

Objectives

• Better understand the law of independent assortment.

History

The law was proposed by Gregor Johann Mendel with the other laws together called as ‘Mendelian laws of inheritance’, in 1866. He used pea plant as a model organism, and studied 7 characters.

Principle

The Law of Independent Assortment, also known as “Inheritance Law”, states that alleles of different genes assort independently of one another during gamete formation. Independent assortment for two genes can be explained by assuming that the two genes are located in two different chromosomes. The two alleles of a gene will be located in the two homologues of the concerned chromosome. Independent separation of these two pairs of chromosomes at anaphase I of meiosis will lead to the independent segregation of the genes located in them. Thus any allele of one gene is equally likely to combine with any allele of the other gene and pass into the same gamete. Independent segregation of two genes produces four different types of gametes in equal proportion. A random union among these gametes gives rise to sixteen possible zygotes. These zygotes yield a 9:3:3:1 phenotypic ratio, which is known as the typical dihybrid ratio. When two pairs of independent alleles enter into F₁ combination, both of them have their independent dominant effect. These alleles segregate when gametes are formed but the assortment occurs independently at random and quite freely.

Objectives

• Better understand the dihybrid cross.
• Calculation of dihybrid phenotypic, genotypic and testcross ratios.

Principle

A cross is made between two true-breeding parents differing in two pairs of genes, producing an F₁ generation. These plants are inter-crossed to produce an F₂ generation. Mendel second law i.e., Law of independent assortment can be explained by studying the inheritance of two characters at a time, simultaneously. When two phenotypically distinct parents differing with respect to two characters governed by two pair of genes are crossed together. Each pair of genes assorts independently into all possible combination forming four kinds of progeny, two of these are parental type and two are recombinant types.

Objectives

• Better understand the monohybrid cross.
• Calculation of monohybrid phenotypic, genotypic and testcross ratios.

Principle

Monohybrid cross deals with the study of inheritance of one pair of contrasting characters. The alleles of contrasting character selected in the monohybrid cross will show exact dominance and recessive relationship. It is also defined as a cross is made between two true-breeding parents differing for a single trait, producing an F₁ generation. These plants are intercrossed to produce an F₂ generation. Monohybrid crosses study led to the Mendel’s law of segregation. Monohybrid cross was first produced in pea by Mendel to explain the “law of segregation”. When parents with distinct phenotypes are crossed, in F₁ generation, only one type of plants appears phenotypically. However, segregation can be observed in F₂ progeny and the population can be divided into two phenotypes classes. After counting the individuals. It is observed that 75% of them express the dominant phenotype and 25% of them express recessive phenotype.

Objectives

• Find out the number and types of gametes and gametic recombination in monohybrid, dihybrid and trihybrid crosses.

Principle

Gametes are reproductive cells that join together to form a new cell called a zygote during sexual reproduction. Pollen in seed-bearing plants, is the gametophyte producing male gamete. Female gametes (ovules) are included in the ovary of plant. At maturity a sexually reproducing individuals forms the gametes. Homozygote generate only one form of gamete. Homozygous referring to a diploid cell or organism possessing two identical alleles of a specific gene (e.g. AA or aa). Heterozygote generate different types of gametes. Heterozygous referring to a diploid cell or organism possessing two different alleles of a specific gene (e.g. Aa).

Objectives

• Better understand the process and different stages of meiosis.
• Prepare your own specimens of onion root in which you can visualize all of the stages of meiosis.

Principle

Meiosis is a type of cell division in which the number of chromosomes is halved (from diploid to haploid) in the daughter cells, i.e., the gametes. It occurs in cell that produce gametes in sexually reproducing organisms. The division is completed in two phases, meiosis I and meiosis II. Meiosis I is a reductional division in which the chromosomes of homologous pairs separate from each other. Meiosis II maintain same number of chromosomes, hence, is called as equational division. Stages of meiosis can be observed in a cytological preparation of the pollen mother cells of the anthers of f lower buds.

Objectives

• Better understand the process and different stages of mitosis.
• Prepare your own specimens of onion root in which you can visualize all of the stages of mitosis.

Principle

The genetic information of plants, animals and other eukaryotic organisms resides in several (or many) individual DNA molecules, or chromosomes. For example, each human cell possesses 46 chromosomes, while each cell of an onion possesses 8 chromosomes. All cells must replicate their DNA when dividing.

DNA replication in eukaryotes is followed by the process called mitosis which assures that each daughter cell receives one copy of each of the replicated chromosomes. During the process of mitosis, the chromosomes pass through several stages known as prophase, metaphase, anaphase and telophase. The actual division of the cytoplasm is called cytokinesis and occurs during telophase. During each of the preceding stages, particular events occur that contribute to the orderly distribution of the replicated chromosomes prior to cytokinesis.

An onion root tip is a rapidly growing part of the onion and thus many cells will be in different stages of mitosis. The onion root tips can be prepared and squashed in a way that allows them to be flattened on a microscopic slide, so that the chromosomes of individual cells can be observed easily. The super coiled chromosomes during different stages of mitosis present in the onion root tip cells can be visualized by treating with DNA specific stains, like Feulgen stain and Acetocarmine stain.

Objectives

• Differentiate between fixatives and stains.
• Describe methods of staining.
• List the commonly used fixatives and stains and their composition.
• Describe the uses of above mentioned solutions and stains.

Introduction

Every time a part of an organism is removed, the action of bacteria will soon disintegrate, dry or putrefy it. They must be kept as close to normal as possible or in other words preserved and fixed in order to study these. Chemicals are required in many practical of Biology. Some of these chemicals preserve and specifically colour certain cell parts while others are used as solutions. You will learn about certain fixatives (preservatives) and stains in this chapter.

Objectives

• To study working principles of compound microscope
• Study different parts of compound microscope

Introduction

A compound microscope is an optical instrument consisting of two short focal-length convex lenses that are used to observe the highly magnified images of small objects by naked eyes. The compound microscope is capable of magnifying up to 1000 the image of a small object by complex system of lens arrangement. The working distance varies from 0.14 to 4 mm. Compound microscopes generally require the sample to be seen to be sufficiently thin, or translucent, to allow the light to pass. Such microscopes provide high magnification, but the view is two-dimensional.

Objectives

• To study working principles of simple microscope
• Study different parts of simple microscope

Introduction

This is the first ever microscope. It was founded by Leeuwenhoek in 17^th century. He combined a convex lens with a specimen holder, for seeing the magnified images of small objects. It looks like a magnifying glass because it has the capacity to magnify between 200 and 300 times. A simple microscope is a small focal lens used to view the magnified images of small objects. It is just like a hand lens and glass with relatively lower magnification power.

Model organisms are widely used in biological researches to describe basic biological processes. When selecting living organisms as models to work with, a wide range of characteristics are used which include: 1) rapid development with short life cycles, 2) small adult size, 3) ready availability and 4) tractability. Being small, growing rapidly and being readily available are crucial in terms of housing them, given the budget and space limitations of research and teaching laboratories. Tractability relates to the ease with which they can be manipulated. Many model organisms have been used including fruit fly, Drosophila melanogaster, the most obvious organism used for teaching Mendelian genetics and developmental biology; Escherichia coli, a favoured organism for molecular biological studies involving recombinant DNA technology. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model organism.

C. elegans is a popular research organism as it possesses all the characteristics mentioned, yet shares many essential biological properties with humans. For instance, researchers who study apoptosis (programmed cell death) use C. elegans as an experimental organism in the hope of finding treatments for certain types of human cancers, such as leukaemia.

C. elegans is easy and inexpensive to maintain in laboratory conditions with a diet of E. coli. Embryogenesis occurs in about 12 hours, development to the adult stage occurs in 2.5 days and the life span is 2-3 weeks. The short, hermaphroditic life cycle (~3 days) and large number (300+) of offspring of C. elegans allows large-scale production of animals within a short period of time. Since C. elegans has a small body size, in vivo assays can be conducted in a 96 well microplate. Laboratory stocks of C. elegans can even be stored in liquid nitrogen for 25 years without losing their viability. The transparent body allows clear observation of all cells in mature and developing animals. Furthermore, the intensively studied genome, complete cell lineage map, knockout (KO) mutant libraries and established genetic methodologies including mutagenesis, transgenesis and RNA interference (RNAi) provide a variety of options to manipulate and study C. elegans at the molecular level and for a more detailed presentation of genetic and genomic resources.

Nematode associated with insects are referred as entomophilic, entomogenous and entomophagous nematodes. Generally they belong to the superfamilies Tylenchoidea, Rhadbitoidea, Oxyuroidea and Mermithoidea of the phylum Nematoda.

Nature of parasitism

Christie (1914) divided the nematodes associated with invertebrates into three groups.

• Those nematodes which live in the alimentary tract of he invertebrates.
• Those nematodes which are more or less closely related to free living species and often have a combination of saprophagous and parasitic habits.
• Those nematodes which parasitizes the body cavity or tissue of their host.

Entomophilic nematodes are group of parasites that cause debilitation, sterility or death of insects. Entomophilic nematodes vary greatly in size and shape having the insects as intermediate or as definite hosts. Many group of insects are parasitised by nematodes.

Nematode Control

Plant parasitic nematodes can be controlled by several methods. The nematode control aims to improve growth, quality and yield by keeping the nematode population below the economical threshold level. The control measures to be adopted should be profitable and cost effective. It is essential to calculate the cost benefit ratio before adopting control measures.

The nematode control methods are

1. Regulatory (Legal) control
2. Physical control
3. Cultural control
4. Biological control
5. Chemical control

Black Pepper

Black pepper (Piper nigrum) is indigenous to the tropical forests of Western Ghats of South India. The crop is grown in Kerala, Karnataka, Tamil Nadu, Andra Pradesh and Assam.

The root-knot nematode, Meloidogyne incognita and the burrowing nematode, Radopholus similis are important pests of this crop. The root-knot nematode infested vines show yellowing of lower leaves and the leaves loose natural luster. The yellowing of leaves gradually progresses upwards. The affected vine leaves become flaccid and wither. The infested plant root show root galls of varying sizes.

The burrowing nematode also causes serious damage to the vine. Var der Vecht (1950) first reported slow wilt in this crop due to R.similis infestation in Indonesia. The nematode in association with Fusarium and Rhizoctonia causes serious damage to the crop.

Crossandra

Crossandra (Crossandra undulaefolia) is one of the important commercially grown flower crop in Tamil Nadu. In recent years there is a marked decline in the cultivation of this crop in Madurai, Dindigul, Coimbatore, Salem, Thiruvannamalai and Tiruchirappalli districts. The common problem with the crop is death of plants in patches during the second and third year. This is due to the nematode-fungal complex disease in the crop.

Investigations revealed the association of root-knot nematode, Meloidogyne spp. and the root-lesion nematode, Pratylenchus delattrei with the crop along with fungal patheogen, Fusarium solani.

Root-knot nematode

Both M. incognita and M. javanica are reported to cause damage and yield loss to the crop. The affected plants exhibit stunted growth, yellowing of leaves and also have chlorotic symptoms. The nematode in association with R. solani causes serious damage to the crop. The infested plants show root galls.

Potato

Potato is one of the most important vegetable crop grown in India. It thrives best in cool climate. Therefore it is a summer crop in the hills and a winter crop in plains.

Twenty seven species of nematodes have been reported on potato among them the cyst nematodes (Globodera rostochiensis and G. pallida) and the root-knot nematodes (Meloidogyne incognita, M. javanica and M. hapla) are important in India.

Cyst nematodes (G.rostochiensis and G. pallida)

In India, the cyst nematode menace on potato was first reported by Dr. Jones during 1961 from Nilgiri Hills.

Geographical distribution

The potato cyst nematode is distributed in Central, South and North America, Europe, Iceland, Western USSR and South Africa.

In India it is distributed in Nilgiri and Kodai Hills and in New Delhi.

Citrus (Citrus spp.)

Citrus is an important fruit crop and ranks third in area which is followed by mango and banana. They are grown in 105,396 hectares in India. Among the oranges, mandarin oranges, limes and sweet oranges are very popular while lemons, grape fruits, pummelos, sour and bitter oranges are of minor importance. The Citrus spp. are grown in larger extent in the states of Maharashtra, Karnataka, Kerala, Tamil Nadu, Andhra Pradesh, Punjab, Haryana, Rajasthan, Assam, Orissa and Bihar.

Nematode menace in citrus gardens are very much realised. In 1912 the citrus nematode, Tylenchulus semipenetrans was reported from California and found to cause ‘slow decline’ disease. More than 30 genera of plant parasitic nematodes are associated with the Citrus spp. Among them, Tylenchulus semipenetrans, Radopholus citrophilus, Meloidogyne spp. Pratylenchus spp. Xiphinema spp. and Hoplolaimus spp. are often associated with the crop.

Rice

Plant parasitic nematodes cause serious damage to rice crop. Thirty two species belonging to 13 genera were observed in association with the crop. Among them few are considered to be important. They are the rice white - tip nematode (Aphelenchoides besseyi), rice stem nematode (Ditylenchus angustus), rice root nematode (Hirschmanniella oryzae), root-knot nematode (Meloidogyne graminicola) and the cyst nematode (Heterodera oryzicola).

The white-tip nematode (Aphelenchoides besseyi)

The yield loss due to the white-tip nematode is estimated to be as much as 17.4 to 54.1 per cent. The nematode is distributed in India, Bangladesh, Sri Lanka, Japan, Indonesia, Taiwan, Former USSR, Italy, Cuba and Madagascar.

Plant parasitic nematodes favour the establishment of secondary pathogens viz., fungi, bacteria, virus etc. The nematodes alter the host in such a way that the host tissue becomes suitable for colonization by the secondary pathogens. Even though the nematodes themselves are capable of causing considerable damage to the crops, their association with other organisms aggravate the disease. The nematodes cause mechanical wound which favours the entry of microorganisms. In some cases, the association of nematode and pathogen breaks the disease resistance in resistant cultivators of crop plants.

Nematode - Fungus Interaction

Nematode - fungus interaction was first observed by Atkinson (1892) in cotton. Fusarium wilt was more severe in the presence of Meloidogyne spp. Since then the nematode - fungus interations had received considerable attention on important crops like banana, cotton, cowpea, brinjal, tobacco and tomato. Some examples of nematode - fungus interaction are given in the following table.

The nematode feeding on plant can be divided into above ground feeders and below ground feeders.

I. Above ground feeders

a) Feeding on flower buds, leaves and bulbs

Seed gall nematode : Anguina tritici

Leaf and bud nematode : Aphelenchoides

Stem and buld nematode : Ditylenchus

Sampling for nematode population estimation

Sampling for nematode communities has been the basis for the development of appropriate control strategy. The major purposes of sampling for nematodes include population estimation for general detection, advisory or predictive programme, disease diagnosis and also for research purposes.

Plant parasitic nematodes are usually confined to top 20-25 cm soil and may vary depending upon the soil type, moisture content, host plant and climatic condition. Surface soil do not harbour any nematode. The roots and rhizosphere of severely infested plants do not harbour numerous nematodes as the nematodes tend to move to adjacent healthy plants. Hence soil and root samples need to be collected from plants showing partial symptoms. Samples should not be collected from dead or wilted plants.

Plant parasitic nematodes cause serious problems in sustained crop production. For a successful management of nematodes, their morphology, biology and host - parasitic relationship should be thoroughly studied. A thorough study is achieved only when its taxonomical position is known. Thus, in a simple way taxonomy can be defined as the theroretical study of classification of an organism.

The systematic arrangement of organisms into groups on the basis of their relationship is termed as classification.

Nematodes are placed in the group invertebrate, Kingdom Animalia.

Hyman (1951) revised the phylum Aschelminthes and included six classes viz., Rotifera, Gastotricha, Echinodera, Priapulida, Nematoda and Nematomorpha.