Preface I got an opportunity to be associated with the students of the College of Horticulture, Chiplima as Associate Dean for about one year. I realized two points: (i) absence of a suitable textbook for B.Sc. (Hons) Horticulture written as per the syllabus recommended by the 5th Deans’ Committee and (ii) most of the textbooks are not oriented towards horticultural crops. So, a textbook entitled “Horticultural Crop Breeding: Principles and Practices” was endeavoured to fulfill these two requirements. The course “Principles of Plant Breeding” is in the second semester of B.Sc. (Hons) Horticulture programme. The two important prerequisite courses of “Principles of Genetics and Cytogenetics”, and “Elementary Statistics and Computer Application” are taught in the first semester. With this academic background of the students the book is written. The whole of the book is spread over 29 chapters grouped into three sections. Section I deals with overview and biological foundations, Section II with breeding principles (also called ‘theory’) and Section III with breeding practices (also called ‘methods’, ‘techniques’, ‘practice’, ‘procedures’, ‘schemes’, ‘plans’ or ‘approaches’). Breeding practices may be conventional (also called ‘traditional’, ‘classical’ or ‘general’) or non-conventional (also called ‘unconventional’, ‘non-traditional’, ‘modern’ or ‘special’). Conventional breeding practices utilize variations present in nature or created by intra-specific (inter-varietal) hybridization for development of cultivars. On the other hand, non-conventional breeding practices utilize variations created by artificial mutagenesis, wide (distant) and somatic hybridization, polyploidy, somaclonal variation and genetic engineering (also called ‘recombinant DNA technology’ or ‘transgenic technology’). Besides, mission-oriented breeding practices such as breeding for biotic and abiotic stresses have been discussed. The author does not claim any originality of the book—it draws heavily from many text/reference books, review articles and some other references. Like others, this textbook is a history of the subject. It is an introductory level textbook – a first course in plant breeding. So, the size is limited so that it can be taught in one semester. A student in the class once asked me why she was reading the course “Principles of Plant Breeding”. The question was very pertinent. Hence, the textbook should be introductory as well as capable of inculcating in the mind of students the probable way of application in practical crop breeding programme. I acknowledge the assistance of Mr. Subrat Kumar Chhanda for computer-typing of the manuscript. I congratulate M/S New India Publishing Agency, New Delhi for their support and publishing in a short time. I cherish the encouragement and cooperation received from my wife Prasanti during the preparation of the manuscript. Though the book is primarily written for B.Sc. (Hons) Horticulture students, the counterparts of B.Sc. (Hons) Agriculture also may be benefitted. It may serve as a reference book for post-graduate students and horticultural plant breeders. Every effort has been made to render the book simple, lucid and correct in presentation. However, error if any is mine; I would highly appreciate if it is brought to my notice for rectification in next edition.

1.1 Introduction The word ‘horticulture’ was first used in 1600’s, and is derived from two Latin words, ‘hortus’(garden) and ‘cultûra’(cultivation), and it means ‘the culture (cultivation) of garden plants’. Relf (1992) defined “horticulture as an applied science and art of growing fruits, vegetables, herbs and spices, nuts, tubers, aromatic and medicinal plants, plantation crops, mushrooms and ornamental plants which include shrubs, flowering plants and turfs stimulating minds, spirits and emotions of individuals, enriching health and wellness of communities, and linking human beings to nature and its landscaped exteriors for wellness and wellbeing”. Fruits and vegetables are nourishing and protective foods. It has been recognized that fruits are a rich source of antioxidants which protect us from dreadful diseases. Vegetables and fruits contain vitamin E, K, and  carotene in addition to minerals like zinc, copper and manganese. To meet the ever-increasing demand of the country for fruits, vegetables, tubers, spices, flowers, ornamentals etc., we must strive hard to deliver better cultivars in as many aspects as possible to the society so that human beings will be in sound health physically as well as mentally. To achieve this goal plant breeding in general, and horticultural plant breeding in particular will come to our help.

2.1 Introduction Dear students, you shall be taught plant biotechnology during the third semester in the course ‘Elementary Plant Biotechnology’. But, for understanding of non-conventional breeding methods/techniques you should acquire some knowledge of basic plant biotechnology. Hence, in this chapter plant biotechnology is introduced to you in brief. 2.2 Definition The term ‘biotechnology’ stems from fusion of ‘biology’ and ‘technology’. It was coined by Karl Ereky, a Hungarian agricultural engineer, in the beginning of 20th century. According to him, all processes used to yield finished products from raw materials with the help of living organism come under biotechnology. It may be defined in number of ways. However, in simple terms, biotechnology may be defined as ‘the controlled use of biological agents, such as microorganisms, or cellular components, for beneficial use’ (U.S. National Science Foundation).

3.1 Introduction Genetics deals with genes and cytogenetics with chromosomes that harbour genes. On the other hand, plant breeding strives to upgrade the genotypes of crop plants. So, the plant breeding methods should be based on genetic principles. Dear students, you should have clear understanding of genetics in broad sense so that you can appreciate the applicability of breeding methods. As I have already pointed out that you have been taught the course ‘Principles of Genetics and Cytogenetics’ in the first semester, only a brief discussion is followed for your review and better understanding. 3.2 Character When we call ‘character’ or ‘trait’ in genetics, we mean any morphological, anatomical, biochemical or behavioural feature of an organism. For instance, flower colour, blooming period, leaf size, size of guard cells in stomata, vitamin C content, disease resistance etc. A single gene or a number of genes may govern the development of a character and, often it is influenced by the environment. Characters may be qualitative or quantitative.

4.1 Introduction Many important traits such as yield, quality and some forms of disease resistance are controlled by many genes and are known as quantitative traits or characters (also called ‘metric’,‘polygenic,’ ‘multifactorial’ or ‘complex’ traits). The regions within genomes that contain genes associated with a particular quantitative trait are known as quantitative trait loci (QTLs). The identification of QTLs based only on conventional phenotypic evaluation is not possible. A major breakthrough in the characterization of quantitative traits that created opportunities to select for QTLs was initiated by the development of DNA (also called molecular) markers in the 1980s. One of the main uses of DNA markers in agri-horticultural research has been in the construction of linkage maps for diverse crop species. Linkage maps have been utilised for identifying chromosomal regions that contain genes controlling simple traits (controlled by a single gene) and quantitative traits using QTL analysis. The process of constructing linkage maps and conducting QTL analysis–to identify genomic regions associated with traits–is known as QTL mapping (also called ‘genetic,’ ‘gene’ or ‘genome’ mapping). DNA markers that are tightly linked to agronomically important genes (called gene ‘tagging’) may be used as molecular tools for marker-assisted selection (MAS) in plant breeding. MAS involves using the presence/absence of a marker as a substitute for or to assist in phenotypic selection, in a way which may make it more efficient, effective, reliable and cost-effective compared to the more conventional plant breeding methods. The use of DNA markers in plant (and animal) breeding has opened a new realm in agriculture and horticulture called ‘molecular breeding’.

5.1 Introduction The development of quantitative trait loci (QTL) mapping methods to identify genes or QTLs controlling quantitative traits was a landmark achievement in plant genetics research in the late 1980s. Since then literally thousands of research papers have reported the identification of genes or QTLs for important traits across a diverse range of plant species. This wealth of genetic information was built on the foundation of decades of research in crop molecular genetics and genomics. The selection and enrichment of QTLs within breeding material was the inevitable next step from QTL discovery to application, and there have been numerous reports of successful tracking of genes and QTLs within breeding programmes. DNA (or molecular) markers have enabled selection of major genes or QTLs for critical or important traits in a process called marker-assisted selection (MAS), which has revolutionized plant breeding. DNA markers are used as tools by breeders to improve the accuracy or efficiency of selection as well cost and time efficiency. Apart from MAS, DNA markers have numerous applications including DNA fingerprinting, genetic diversity analysis and parental characterization. Recent developments in genotyping platforms and systems to implement molecular breeding schemes offer new tools for modern plant breeders. Single nucleotide polymorphism (SNP) markers are biallelic, co-dominant markers which are abundant in the genome. Insertion-deletion (Indel) markers are also prevalent and can be screened using high-throughput genotyping platforms. These platforms are cost-efficient, can handle large sample sizes and provide fast data turn-around time. The availability of genome sequences and genomic resources continues to provide a wealth of SNP and Indel markers which will undoubtedly be the marker type of choice for decades to come. The availability of high-throughput SNP platforms in conjunction with advances in computational methods has also led to the molecular dissection of traits using genome-wide association studies (GWASs) across diversity panels and the development of genomics-based molecular breeding strategies. Association mapping (AM) has now emerged as a standard method for gene and QTL discovery for major crops.

6.1 Introduction The process by which living beings give rise to the progeny of similar kind is called reproduction. Reproduction allows both multiplication and maintenance of a genotype/line/cultivar/species. So, the process of reproduction is also called propagation, and the plant part used for this purpose is called propagule. The way progeny originate is known as mode of reproduction (also called breeding system or reproductive system). The mode of reproduction of a crop determines its genetic composition which, in turn, is the deciding factor to develop suitable breeding methods. Knowledge of mode of reproduction is also essential for its artificial manipulation to breed improved types. The methods to be adopted for multiplication and maintenance of improved cultivars are also governed by the mode of reproduction. Especially in undertaking breeding investigations with new plants the nature of reproduction must be known before efficient breeding plans can be developed. The mode of reproduction has been well established for most of our important crop species. 6.2 Mode of Reproduction Mode reproduction in crop plants may be sexual or asexual. In sexual reproduction (also called amphimixis), specialized reproductive cells called gametes are formed by the process of gametogenesis. Fusion of the male and female gametes leads to the development of an embryo and eventually the seed. In asexual reproduction, fusion of the male and female gametes does not occur, and new plants arise from unfertilized gametes (but not from zygote), or from specialized vegetative organs such as rhizome, tuber, bulb, corm, runner, sucker, stolon, bulbil etc., or by various artificial means of propagation such as rooting of stem and root cuttings, layering, grafting, gootee, etc., or tissue culturing.

7.1 Introduction Breeding plans are based on controlled mating (i.e., mating between selected strains) and selfing of selected strains or a combination of both. Continued selfing is practised to isolate purelines and inbreds. On the other hand, crossing (hybridization) is necessary to produce hybrids and synthetics. In crossing, self-pollination is prevented in the female parent. Male sterility and self-incompatibility easily exclude self-pollination, and so they are used in hybrid seed production. 7.2 Male Sterility Koelreuter (1763) for the first time reported male sterility in flowering plants. Male sterility is a reproductive deficiency of some plants in which male organs in bisexual flowers become defunct. It relates particularly to nonviable pollen grains that are formed through a chain of vital processes during microsporogenesis. These processes are so delicately balanced under genetic control of many loci that mutation of any one locus may lead to the formation of non-functional microspores, and hence male sterility. In male sterility, pollen grains are non-functional (inactive); but the female gametes (egg cells) are normally functional.

8.1 Introduction In pre-historic times, people lived as hunters and gatherers. Then, gradually they began to produce the crops they ate on piece of land, and farming was born. Wild plants have certain traits that keep them protected and productive without human intervention. However, most of them are not desired for food or other use by humans. By spontaneous mutagenesis and hybridization, occasionally variant plants were found that lacked some of the undesired traits, such as bitter taste, thorns, or had particularly attractive features, such as larger fruits and more regular tuber shape. Consequently, as time passes such variation was picked up by humans by selection of such variants, keeping and advancing them. Thus, plant domestication is the process of bringing wild species under human management. In other words, plant domestication is the process by which genetic changes (shifts) in wild plants are brought about through a selection process imposed by humans. It is a method of plant breeding in the sense that, when successful, it provides domestic types that are superior to ones previously available. Pre-historic man domesticated virtually all of our present-day crops. But, domestication of wild species continues even today and is likely to continue for a long time in the future. For example, in many countries there is an increasing emphasis on bringing forest trees producing timber, etc. under human management. A similar trend is seen for medicinal plants and plants producing specific compounds of interest, e.g., hydrocarbons, oils, etc. Kala jeera (Bunium persicum), a perennial spice, was domesticated during 1990s in Himachal Pradesh; it is being cultivated as an orchard crop. One important aspect of domestication at present is the use of particular genes from wild relatives in the improvement of cultivated species. When a plant breeder transfers one or a few desirable genes from a wild relative to a cultivated type, he is, in a sense, domesticating the wild species in part.

9.1 Introduction The sum total of genes in a plant species is called as plant genetic resources (also called germplasm, gene pool, or genetic stock). In other words, plant genetic resources refer to a whole library of different alleles of a plant (crop) species. Germplasm is the lifeblood of plant breeding without which breeding is impossible to conduct. It is the genetic material that can be used to perpetuate a species or population. It not only has reproductive value, but through genetic manipulation (plant breeding), germplasm can be improved for better performance of the crop. Germplasm provides the materials (parents) used to initiate breeding programme. Sometimes, what a plant breeder does is to evaluate plant genetic resources and make a selection out of existing biological variation. Promising genotypes that are adapted to the production region are then released for cultivation by the farmers. Other times, a plant breeder generates new variability by using different methods such as hybridization, mutagenesis and more recently gene transfer. This base population is then subjected to appropriate selection methods, leading to the identification and further evaluation of promising genotypes for release as cultivars. When a plant breeder needs to improve crop plants, he has to find a source of germplasm that would supply the genes needed to undertake the plant breeding programme. To facilitate the use of genetic resources (germplasm), germplasm (gene) banks are given the responsibility of collecting, evaluating, cataloguing, storing and managing large numbers of germplasm. This strategy allows a plant breeder ready and quick access to genetic resources when he needs it. The fact that Sir Otto Frankel coined the term ‘genetic resources’ only in 1968 shows that the plant breeders, though aware of the gradual loss of germplasm, failed to recognize the urgency of protecting the genetic resources of crop plants prior to a point of no return.

10.1 Introduction Plant breeders come across two categories of characters (traits) for improvement, namely, qualitative characters and quantitative characters. Red vs white flower, round vs wrinkled seed, determinate plant growth vs indeterminate plant growth etc. are examples of qualitative trait differences. There is no overlapping of characters and no confusion during classification. Such trait differences are usually governed by one or two gene pairs, each with large effect that can be measured even in the presence of segregation at other loci and even in the presence of effects of environmental factors. These characters are very less influenced by the environmental factors. On the other hand, most of the traits of economic importance like yield of fruits of vegetable and fruit crops, yield of vegetative parts in fodder crops, yield of lint in cotton, yield of grains in cereals, pulses, oilseeds etc., plant height, days to maturity etc. are examples of quantitative characters. Variation observed for such traits is continuous. Again, there is overlapping of trait differences. So, one cannot assign individuals to a specific class unambiguously. Such characters are influenced by environmental factors, such that phenotypes are not same when grown over locations and/or seasons. When different plants/lines of a species exhibit trait differences, it is called variation. Variation is essential for any improvement in a crop. It may be present in the population to be improved or else it may be created by different means such as hybridization, mutation, polyploidy, domestication, plant introduction, somaclonal variation, genetic engineering etc. Now, we shall discuss the types and estimation of variation.

11.1 Introduction In chapter 10, we have discussed the different types of variation, namely, genetic, environmental and genotype × environment interaction variations. We have also learnt how to estimate the phenotypic variance and its components including genotypic (also called genetic), environmental and g × e interaction variances from trial data. Now in this chapter, we shall discuss on the genetic components of polygenic (quantitative) variation and its implications on breeding strategies. 11.2 Genetic Components of Polygenic Variation In this chapter whenever we call genetic variation, we mean polygenic (quantitative) variation, and we know that variation is usually measured in term of variance. However, variation, variability and variance are almost used synonymously. The genetic variance has been classified into different components by various workers. Fisher (1918) divided genetic variance into three components: additive, dominance and epistatic (interaction) variances. Wright (1935) classified genetic variance into two components: additive variance and non-additive variance (dominance and epistatic variances). Mather (1949) classified genetic variance into two components: heritable fixable variance (additive variance and additive × additive epistatic variance) and heritable non-fixable variance (dominance variance, and additive × dominance and dominance × dominance epistatic variances). Later, Hayman and Mather further divided the epistatic variance into three categories: additive × additive, additive × dominance and dominance × dominance.

12.1 Introduction Allowing certain plants from the population to reproduce, while barring others, comprises selection. This permission for reproduction may be granted by nature or by the plant breeder. In the other words, both nature and breeder exert selection pressure. Natural selection operates through differences of fertility among the adult individuals of parent generation as well as through differences of viability among the individuals of offspring generation. Artificial selection, i.e., the selection from action of the plant breeder in the choice of parents, produces its change of gene frequency by separating the adult individuals of parent generation into two groups, viz., the selected and the discarded, that differ in gene frequency. So, selection simply implies the retaining of desirable types or culling of unwanted or undesirable types.

13.1 Introduction F1 plants produced by crossing two parents with contrasting characters are called hybrids. Hybrids generally exhibit increased vigour and fitness over the parents. This phenomenon is called hybrid vigour or heterosis. Thus, heterosis is the phenomenon in which the hybrid of two genetically dissimilar parents shows increased vigour at least over the mid-parental value. Heterosis is just the reverse of inbreeding depression, which results after selfing the plants of the cross-pollinated crops. Kolreuter (1761-66) was the first to report hybrid vigour in the hybrids of tobacco, Datura, etc. Most of the early plant hybridizers including Mendel (1865) had noticed this phenomenon. Shull (1914) coined the term heterosis from two Greek words, hetero (different) and osis (condition), to replace his own earlier word ‘stimulus of heterozygosis’. In current usage, heterosis and hybrid vigour are used as synonyms and interchangeable. 13.2 Types of Heterosis Depending on the nature, origin, adaptability, reproducibility and non-reproducibility, heterosis can be categorized into two: (1) euheterosis (true heterosis) and (2) pseudo-heterosis (false heterosis, i.e., luxuriance).

14.1 Introduction The mating or crossing of genetically dissimilar individuals is called hybridization. Hybridization results in recombination that in turn widens the spectrum of variation among individuals. So, the reason for genetic diversity in progenies of crosses is the formation of new combinations of genes. This newly created variability is then channelized into development of better cultivars. The importance of pure line selection as a method of breeding started decreasing when plant breeders felt that the genetic variability existing in the land races of self-pollinated crops had been almost completely exploited and there was little chance for further improvement in these crops by using pure line breeding. Therefore, no option was left for plant breeders except to cross diverse individuals and combine together desirable characters in a single genotype from two or more parents. The planned hybridization which could avoid self-pollination and chance cross-pollination, soon became the main feature of almost all plant breeding programmes.

15.1 Introduction Plant breeding aims at developing genetically improved crop cultivars with economic benefits for small-scale and commercial farmers. Population growth, dwindling agricultural land and global climate change present increasing risk to crop production. Consequently, plant breeding aims to constantly develop crop cultivars with improved yield and quality and tolerant to drought, diseases and pests. Use of genetically improved crop cultivars and better management practices are among the best strategies to increase food production and meet a projected doubling of food demand in the next 40 years. Both the public and private plant breeding sectors face several constraints, including a shortage of professional plant breeders and breeding technicians, limited budget, inadequate facilities and lack of access to information. Successful plant breeding requires adequate infrastructural investment, in addition to the actual breeding activities. The benefits of plant breeding research and development can only be realized on a long-term basis because of the inherent nature of the crops and the eminent breeding procedures involved. Plant breeding involves two main activities, i.e., pre-breeding/ germplasm enhancement and cultivar development per se. These interdependent activities are the controlling factors that determine the pace at which cultivars are released timeously and consistently to farmers. The two phases, in turn, depend upon various factors, e.g., breeding goals, genetics and agronomy of the crop, breeder’s long-term objectives, availability of testing facilities and national cultivar-registration requirements. Despite these factors, there are certain clear steps and breeding procedures found in any conventional breeding programme. These include choice of parents, making crosses among chosen parents, and selection from recombined parents followed by extensive field testing of the candidate cultivars. Maintenance, multiplication and distribution of the seed are the ultimate stages of a breeding programme. Systematically outlined conventional breeding procedures, timeframes and estimated breeding generations are essential to objectively consider the ultimate timescales required to release new and improved cultivars of all crops. The information may assist plant breeding- students, educators, researchers, project advisors, administrators and funding agencies. Dear students, in this chapter we outline the timeframes of conventional breeding procedures of clonally (also called vegetatively) propagated, self-fertilizing (also called self-pollinated) and cross-fertilizing (also called cross-pollinated) crops.

16.1 Introduction Plant introduction is the process of introducing plants from their growing locality to a new locality. Introduction of plants from a foreign country is called foreign introduction or exotic collection. Introduction from one state to another within a country is called indigenous collection or indigenous introduction. With introduction, the process of acclimatization is associated. Acclimatization is the adaptation or adjustment of an individual plant or population of plants under the changed climate for a number of generations. Plant introduction is an oldest method of plant breeding. It is used in self-pollinated, cross-pollinated and asexually propagated crops. The material of seed-propagated crops is introduced in the form of seed and that of vegetatively propagated crops in the form of cuttings or propagules. The introduced material may be a new crop, a wild relative or a new cultivar of a crop already grown in the area. There are five important sources of plant collection, namely, (1) centres of diversity, (2) gene banks, (3) gene sanctuaries, (4) seed companies, and (5) farmers’ fields.

17.1 Introduction Self-pollinated vegetable, spice and ornamental crops may be heterogeneous. It is exemplified by landrace cultivars. They may have originated from single plant selections but have been grown over a long period of time. Landrace cultivars are a mixture of genotypes, perhaps because of breeders’ lack of appreciation of selection techniques to produce a pure line, spontaneous mutations, chance hybridization, or a combination of factors. Natural selection in landraces has resulted in a cultivar that is well adapted to the local environment. Depending on amount of human selection, differences among genotypes in a landrace cultivar may be small and inconspicuous. On the other hand, a lack of human intervention may mean that differences among plants in a landrace cultivar will be conspicuous. After years of self-pollination, individual plants are homozygous. Selection of such individuals would result in a true-to-type reproduction of their phenotype within the limitations imposed by the environment.

18.1 Introduction The genetic variability present in populations of self-pollinated vegetable, spice and ornamental crops is rapidly exhausted by pureline selection. For further improvement, genetic variability must be created. This is generally achieved by hybridization. After the cross has been made, F1 is grown and seeds set on it are harvested. This makes the seed source for raising F2 population, and so on. The segregating populations from crosses are handled according to a suitable method. The three basic methods available for this purpose are: (1) pedigree method, (2) bulk method, and (3) backcross method. There are also certain modifications of these methods. 18.2 Pedigree Method Pedigree method is developed from the pureline system and widely used method of plant breeding for self-pollinated crops. A main difference between pedigree selection and mass selection or pureline selection is that hybridization is used to create variability for the base population in case of the former, whereas in mass and pureline selections variability is naturally present in the base populations. The pedigree method was first described by H.H. Lowe (1927). This method predominated the crop improvement programme throughout the world until 1980s. Pedigree method is common in horticultural crops, especially where readily identifiable qualitative traits are involved. Vegetable crops in which pedigree system is used include tomato, cucumber, pepper, pea, lettuce, snap and field beans, all self-pollinated crops. In general, selection is done on F2 plants. Yield is important in many horticultural plants, but quality is equally or even more important. Quality may be associated with identifiable traits, making the pedigree system ideal for self-pollinated vegetable crops.

19.1 Introduction In self-pollinated crops, the methods of selection aim at improving individual plants. On the other hand, in cross-pollinated crops they aim at improving a population of plants. A population is a large group of interbreeding individuals. Hence, selection is called population improvement in cross-pollinated crops. Selection in self-pollinated crops results in isolation of pure breeding lines which is the end product. But in cross-pollinated crops, it results in an improved population which is used as the commercial cultivar. Improved inbred lines (also called inbreds) for producing hybrids can be obtained from such populations. Again, like many rounds of selection being practised in different inbreeding generations in self-pollinated crops we are also practising many rounds of selection in cross-pollinated crops. But, unlike self-pollinated crops selection in cross-pollinated crops is followed by intermating to develop a new population before starting another round of selection. One cycle of selection consists of selection of individual/family and intermating of the selected units. Such cycle is repeated till we get the improved population. This method of practising the cycles of selection and recombination in a population is called recurrent selection or population improvement. Frey (1983) prefers the use of recurrent selection for closed populations where no new germplasm is added to the population during selection. Population improvement was used for a group of breeding techniques where all aspects are similar to recurrent selection but with the provision of adding new sources of germplasm whenever feasible. It is only a matter of coincidence that past history of application of recurrent selection has been limited to closed populations, but its basic aim has always been the accumulation of favourable genes, without any restriction on the migration of new genes during the course of selection. Apart from a slight nuance, population improvement and recurrent selection are two titles of the same principle and procedure of manipulating the genetic potential of populations. Recurrent selection can also be applied in self-pollinated crops.

20.1 Introduction A hybrid cultivar (also called hybrid) is the F1 progeny of a planned cross between inbreds, cultivars, clones or populations. Depending upon the breeding approach, the hybrid cultivar may involve two or more parents. A critical requirement of hybrid production is that the parents are divergent. This divergence is the cause of superior performance of hybrids. The outstanding performance of crops is due to the exploitation of the phenomenon of heterosis (hybrid vigour) which is high when parents are divergent. Much of what we know about heterosis breeding (also called hybrid breeding) came from the work on maize hybrid cultivar development. However, commercial hybrids are now available in many crops including self-pollinated crops.

21.1 Introduction There are a number of field, vegetable, fruit and ornamental crops that are cultivated using asexual or vegetative parts such as stems, roots, modified flower etc. This is a heterogeneous group of plants and can be further categorized into four groups for ease in understanding the breeding methods applied to them. They are: Group 1: Flowerless or Sterile This group either does not bear flowers or if bears, they are sterile and do not set seed, e.g., ginger, mango ginger, turmeric, garlic, betel, many yams, etc. Group 2: Apomicts Apomixis has been reported in over 300 genera. But stable apomixis has been reported only in a few cultivated plants like meadow grass, citrus, mango, raspberry, etc. Group 3: Flowers but Seed-Set Rare In this group flowering takes place under specific situations but seed-set is limited, e.g., potato, sweet potato, sugarcane, etc.

22.1 Introduction Mutations are sudden heritable changes in the genotype of an organism. De Vries (1900) for the first time used the term mutation (mutare in Latin means ‘to change’) for the appearance of new types in evening primrose (Oenothera) plant. In 1901 he put forth the idea of producing mutations artificially for use in crop improvement. Alberto Pirovano (1922) was first to use X-rays and ultraviolet rays for inducing mutations in plants, but his work remained unknown. So, Muller (1927) became the first known to induce mutation in Drosophila fly using X-rays. Though Stadler (1928) had started working simultaneously on barley and maize and induced mutations, he was late in reporting mutation due to longer life cycle of these plants compared to Drosophila. Mutation may be gene mutation (the result of change in the nuclear gene or plasma gene) or chromosomal mutation (change in chromosome number, structure or chromosomal aberrations of various types).

23.1 Introduction An organism or individual having more than two basic sets of chromosomes is called polyploid and the condition is known as polyploidy. Polyploidy is an important tool to increase genetic diversity by altering the chromosome number (2x) and consequently the number of genes within a single cell. Polyploidy has been one of the important mechanisms in the evolution of many cultivated crop plants. 23.2 Types of Polyploidy 23.2.1 Autopolyploidy The condition that arises due to multiplication of the same chromosomes of a single species is known as autopolyploidy (also called ‘simple polyploidy’ or ‘single species polyploidy’). Autopolyploids have generally larger leaves, stem and other vegetative parts and flower, fruit and seeds than their normal diploids.

24.1 Introduction When crosses are made between two different species of a genus or between two different genera, they are known as distant hybridization (also called wide hybridization). It includes both interspecific and intergeneric hybridization. Thomas Fairchild (1717) was the first man to do distant hybridization. He produced a hybrid between two species of Dianthus, viz., D. caryophyllus and D. barbatus (Carnation and Sweet William). Intergeneric hybrid produced by Karpechenko, a Russian scientist, in 1928 is Raphanobarssica. It is the amphidiploid of cross between radish (Raphanus sativus) and cabbage (Brassica oleracea var. capitata). Unfortunately, it had roots like cabbage and leaves like radish. Triticale was produced by Rimpau in 1890 itself. It is an amphidiploid obtained from a cross between wheat and rye (Triticum and Secale). Another example is Saccharum nobilisation involving Saccharum officinarum, S. barberi, S. sinensis, S. spontaneum. Wide hybridization has been used in the genetic improvement of some crops. It is an effective means of transferring desirable genes into cultivated plants from related species and genera.

25.1 Introduction The method of selection in which a gene/QTL (Quantitative Trait Locus) is selected on the basis of the genotype of the molecular marker (also called DNA marker) linked to this gene/QTL is known as marker-assisted selection (also called marker-aided selection). The idea of marker-assisted selection (MAS) was first advocated by Tanksley (1983). MAS can be used in combination with the conventional breeding methods or novel breeding schemes could be devised to take full advantage of the marker data. MAS has been widely used for introgression of the desired genes and QTLs using backcross programmes. 25.2 Marker-Assisted Backcrossing (MABC) The backcross programme based on molecular marker is usually called marker-assisted backcrossing (MABC). MABC has three activities: (a) foreground selection, (b) background selection and (c) recombinant selection. 25.2.1 Foreground Selection The use of molecular marker to select the gene/QTL being introgressed is known as foreground selection. The objective of foreground selection is to select the target gene, i.e., the gene being introgressed, without phenotypic evaluation for the trait governed by the target gene. Foreground selection for a gene/QTL will be highly desirable in a variety of situation, some of which are listed below:

26.1 Introduction We have already discussed the basics of tissue culture techniques in Chapter 2. Plant tissue culture techniques in combination with recombinant-DNA technology are essential requirements for development of transgenic plants (will be discussed in next chapter). However, tissue culture techniques like anther, pollen, ovule and meristem culture can themselves be used for improvement of different traits or as an aid to conventional breeding methods. In recent years, isolated microspore culture has been preferred as a breeding tool and an experiment system for various genetic manipulations. Besides, using protoplast fusion and hybrid embryo rescue, distant hybridization has been successfully achieved in many crops. Protoplast fusion technique can be used for the transfer of cytoplasmic male sterility from one species to another in very short duration. Somaclonal variation generated during tissue culture can also be utilized for recovery of variants showing disease resistance or other desirable characters.

27.1 Introduction Crop improvement depends on genetic variation present in nature or created by hybridization followed by segregation and recombination. Again, gene transfers are possible only from the lines and species that are sexually compatible with the concerned species. Interspecific gene transfers pose many problems, including the loss of F1 hybrids during embryo development due to abortion of the endosperm in the developing hybrid seeds. Embryo rescue technique was developed to rescue such interspecific hybrid embryos, and it has been widely used for this purpose. It is to be mentioned that embryo rescue can be used only in such cases where sexual hybridization is successful in producing zygotes that begin to develop into embryos. Besides, the technique of somatic hybridization by protoplast fusion was developed to enable gene transfer from the species that do not produce zygotes on hybridization. This method has been extensively used and some useful lines have been derived. But this method is limited to utilization of genes present in plant species. Again, the results of somatic hybridization are unpredictable since many somatic hybrids fail to regenerate complete plants and the transfer of specific genes or groups of genes depends entirely on chance. The recombinant DNA technology (also called genetic engineering) has permitted the transfer of genes from any organism into any organism. Besides, chemically synthesized genes can be transferred and integrated into genomes of various organisms to enable the expression of these genes. A gene transferred into an organism by genetic engineering is called a transgene. 

28.1 Introduction The stress that is caused by biological agents or factors such as diseases, insect-pests and parasitic weeds is called biotic stress. The term disease can be broken into two words: “dis” (means negative, reverse or opposite) and “ease” (means comfort, or freedom from pain or discomfort). Hence, plant disease can be defined as any harmful alteration from the normal functioning of physiological processes. Diseases may be bacterial, fungal or viral. A wide range of insects infests various crop plants. The extent of damage caused to crop plants by various organisms is usually in the order fungi > bacteria > viruses > nematodes = insects. But the relative importance of these organisms varies to a great deal in different crops. Breeding of cultivars resistant to diseases and/or insect-pests is the cheapest, safest and most dependable means of limiting the losses due to them. Resistant cultivars form an important component of integrated management of diseases and insect-pests. 28.2 Breeding for Resistance to Biotic Stresses-Diseases Agrios (1970) has defined disease as: “Disease is a series of invisible and visible responses of plant cells and tissues to a pathogenic microorganism or an environmental factor that result in adverse changes in form, function or integrity of plant and may lead to partial impairment or death of the plant or its parts.” The organism causing disease is called pathogen, while the plant affected by the disease is called host. The principles underlying breeding for resistance to diseases are much the same as for other characters, except for one important difference, i.e., the diseases caused by pathogens are the product of interaction between two genetic systems, that of the host and that of the parasite. Both systems are capable of variation and evolution and affect the interaction between host and pathogen. Here the breeder is required to deal with the heritable traits of both the host plant and the pathogens invading it.

29.1 Introduction An environmental factor that interferes with the complete expression of genotypic potential of a crop is called stress. The stresses may be biotic (pathogens, insect-pests, etc.) or abiotic. The main abiotic stresses are drought, mineral deficiency/toxicity and heat or cold. The losses due to abiotic stresses can be minimized by: Crop management: The degree of stress can be reduced by suitable agronomic/soil management practices, e.g., irrigation to relieve drought stress, soil amendments to reduce salinity. Development of resistant cultivars: This offers the cheapest, easiest to apply and most eco-friendly approach to reduce losses due to any stress. Indirect breeding: Evaluation of materials under stress often helps in identification of a resistant line that may become an important commercial cultivar. ???????Direct breeding: It is deliberate breeding of materials for stress resistance. When a genetically variable material is grown under the stress environment, selection can be based on survival, yield and other traits contributing to stress resistance.