Conventional Plant Breeding Program for Disease Resistance

Abstract

Disease resistance is of great concern for plant breeding programs. Diseases are a major yield-limiting factor, caused by many air born, soil born or waterborne microorganisms, which in fact are a risk for food security. Improving efficacy of management practices can increase yields, but only to a limited extent, whereas plant breeding as a technology increases yields to large extents. Advancements in new science and technology allow the development of tools whereas old ones are also refined. Most cost-effective and environment-friendly methods applied in disease resistance programs include adoption of conventional breeding approaches. There are two type of resistance, namely vertical (controlled by major genes) and horizontal (controlled by minor genes). Breeding programs change with respect to crops, diseases and pathogens. In spite of this, main objective is the accumulation of favorable gene(s) into cultivars, to deal with a given scenario. Selection, introduction, hybridization and screening are the main steps of a successful breeding program. Landraces, related species, mutations and wild relatives are the sources of resistance. They can be utilized for resistance introduction in commercial cultivars. Selection of resistant cultivar is the most robust and cheap method, allowing thereby introduction of resistant cultivar into a new region. Moreover, resistant cultivars are used to cross with local cultivars for introduction of resistance genes into them. The rapid evolution of phytopathogens and crops susceptibility pose severe issues, therefore disease resistance represents a complex aspect of any program. Being also affected by the environment it still represents a big challenge for breeders.

3.1 Introduction

Since the beginning of human civilization , agriculture is the backbone of the world’s economy. People depend on agriculture either directly or indirectly for food, feed, shelter and clothes. Therefore crop protection is of great concern for the world food security . The increase in the world population with a rapid pace will boost the demand of food and other raw materials (Miedaner 2016). Crop protection is therefore important for food security.

In nature, plants face different biotic and abiotic challenges and are affected by a variety of microorganisms, including bacteria, viruses, fungi etc. Diseases cause severe damage to crop plants and result in biomass reduction, stunting growth and ultimately plant death. However, the damage depends upon pathogen prevalence at infection by. The biggest challenge faced for food security by twenty-first century scientists is to improve yield stability through the development of disease resistant crops. . Breeding for disease resistance is not only important to avoid crop damages but also to protect the ecosystem by chemicals usually applied for disease management (Hogenboom 1993; Strange 2013). The importance of resistance as well as its stability for plant production provide an ultimate reason for disease resistance breeding (Clifford and Lester 1988).

Conventional breeding for resistance is an excellent technique to shield crops from damage, both from the ecological and economic point of view (Wolfe and Gessler 1992). Breeding strategies depend on the disease, the pathogen and the crop. The basic necessities of breeding for disease resistance are the genetic sources of resistance and the methodology for its introduction into economically important and commercially acceptable cultivars (Roane 1973). Conventional plant breeding consists of mainly three steps: (a) germplasm collection, (b) recognition of desired phenotypes and their (c) hybridization to get better cultivars (Fehr 1987; Stoskopf et al. 1993).

3.2 Disease Economic Impact

Crop epidemic diseases have caused huge economic losses and even famine. It has also been shown that most plant diseases are the result of human activities. A plant disease can be defined as any change that interrupts the plant normal development and decreases its economic value (Lucas et al. 1992). A disease interferes with the regular function of several plant parts and results in decreased yields or reduced quality. Visible reactions in plants are called “symptoms”, including wilting, stunting, yellowing, death, and whole or partial abnormal growth. Three components are necessary for a disease to occur, in any plant system:

• 1. A susceptible host plant.

• 2. A virulent pathogen.

• 3. A favourable environment.

When these three components are present at the same time (Fig. 3.1), a disease will occur (Zadoks 2001).

Fig. 3.1

A schematic representation of the three components model of disease establishment in plants

3.2.1 Examples of Plant Diseases

In 1840, an epidemic of potato late blight caused by an Oomycete (Phytophthora infestans) resulted in the Irish famine. This is still one of the most significant diseases of potato (Strange 2013.) In early nineteenth century social issues occurred in Ireland betweenEnglish land lords, who had major concern on revenues, and farmers who depended on potatoes as main source of diet for their families (Large 1940). The disease was first observed in Belgium in 1845 (Bourke 1964), and later spread to other countries i.e. England, Scotland, Ireland, France, Germany and Scandinavia. It caused million deaths and forced people to migrate to North America.

The causal agent of the brown spot of rice is the fungus Helminthosporium oryzae. In favorable conditions, this disease can result in severe damages to rice crops. In 1942, it caused disastrous consequences in Bengal,, with a dramatic impact on people. In rural areas farmers left their places and migrated to other cities searching for food and employment. They faced starvation and many people died (Padmanabhan 1973). The affected population number was two million.

In USA (1970–1971), corn leaf blight disease became epidemic with losses that were dramatic. However, the USA agricultural industry was extremely diversified, and human distress was much less than in the previously cited epidemics. Total losses were officially predictable at 1 billion USD, over the nation (Ullstrup 1972).

Cassava (Manihot esculenta) was cultivated approximately 4000–6000 years ago (Fauquette and Fargette 1990). This plant originated in South America, where it is the third carbohydrate source for importance. Its per annum production is about 136 million tonnes. In Africa it is an important crop and total yield reaches 57 million tonnes. Epidemics of the African Cassava Mosaic Virus in the continent are frequent, and prevalence may reach 80–100% of plants, with projected losses around 50% of yield (Fauquette and Fargette 1990).

Bayoud is a fungal disease caused by Fusarium oxysporum . In Morocco about ten million date palms are affected, with three million trees also killed in Algeria. This disease not only causes production losses, but also speeds up the process of desertification (Assef et al. 1986).

Cloves are used in Indonesia in the production of kretek cigarettes (tobacco mix 40% ragged clove bud) (Bennet et al. 1985). A disease known as “Sumatra disease”, caused by Pseudomonas syzygii, let down Indonesia’s plan of self dependence in cloves production. The name of this disease derived from the island where the crop is cultivated. Losses are around 10–15% of yields, about 50 million USD (Strange 2013).

A cocoa (Theobroma cacao) disease, known as swollen shoot, shows shoots that become swelled with a severe dieback. Millions of cocoa trees have been infected and died in West Africa and about 190 million trees have been eradicated to control its spread (Thresh and Owusu 1986).

3.3 Pathogens Targeted by Plant Breeders

Depending on their nature, pathogens can be seen microscopically or, in same cases, with naked eyes. They can be soilborne or airborne. The groups of disease causing agents are fungi, oomycetes, bacteria, viruses, viroids, phytoplasms, and nematodes. Plant breeders, with different degrees of success, allocated various amounts of resources to select for resistance in these categories. Plant species and germplasm differ according to their susceptibility to diseases resulting from pathogens from each group. Cereal products tend to have significant problems with airborne fungal diseases whereas, in contrast, soybean is mostly attacked by viruses.

3.3.1 Fungi

The fungi are divided into four classes that are Ascomycotina, Basidiomycotina, Mastigomycotina, and Zygomycotina, according to the morphology of sexual constitution and the sporulating organs produced subsequent to sexual reproduction (Isaac 1991). Another category, Deuteromycotina, is set aside for fungi where no sexual phase is recognized. Organisms that are detrimental to plants are grouped in five classes. Mastigomycotina includes genus Phytophthora meaning “plant destroyer”, an appropriate word for that genus.. Further important disease casused by members of this genus include the black pod disease of cocoa and blight of pigeon pea. Members of Rhizopus , a genus of Zygomycotina, cause major losses in several plants i.e. cassava, peanuts, sorghum and cucurbits. It has also importance as causing postharvest diseases in soft fruits (Michailides and Spott 1990). One of the worst pathogenic strains of known plants is Claviceps , a member of Ascomycotina. The danger of this organism is not related to damaged grain crops, but to its fungal sclerotia, which have extremely toxic compounds such as alkaloids.

Rusts and smuts are included in Basidiomycotina. Rusts and smuts are extremely specialized obligate parasites, and represent a constant danger to crops (Barnett and Binder 1973). Additionally, Basidiomycotina contains several of plant largest parasites, such as bracket fungi that damage tree species (Jonsson et al. 2005). Some fungi can also act as vectors for viruses while giving them little harm. For example, Olpidium brassicae lettuce can transmit large vascular virus (LBVV) and tobacco necrosis virus (TNV), whereas Polymyxa graminis transmits various viruses that induce significant diseases on host plants.

3.3.2 Nematodes

They can be used not only as a direct loss of crop but also as source/vectors of viruses of plant. Only two of the 17 orders of nematodes cause damages to plants (Tylenchida and Dorylaimida), either inducing direct losses or transmitting plant viruses (orders Dorylaimida and Triplonchida) (Wyss 1981). In addition, nematode feeding damages the root tissues providing entrance into the root for numerous parasites, in particular fungi. Some loss estimates can be obtained for nematodes by comparing nematicide-treated with control soils. For example, Ingham and Detling (1990) observed that, treating mixed grass prairie with carbofuran, the nematicide reduced the nematode population by about 82%, increasing production of up to 52%.

3.3.3 Protozoa and Algae

The likelihood of a protozoid origin for some severe plant diseases was not entirely documented until 1976, when they were linked to two major defects in coconut palms. McCoy and Martinez-Lopez (1982) observed nine cases of dwarf coconut palms in the USA, deadly wilted by Phytomonas staheli. Phloem necrosis in palms is currently recognized to be due to a Phytomonas (Trypanosomatidae) (Douet 1984).

Cephaleuros virescens is the causal agent of the Algal leaf spot disease. It has been associated with many disease warning sign in more than 50 high plants. In another study Tahiti lime (Citrus latifolia) showed up to 98% of leaves contaminated by an alga of this genus (Marlatt and Pohronezny 1983; Strange 1993). Other algae of genera Chlorochytrium, Rhodochytrium and Phyllosiphon are also involved in plant diseases (Strange 2006).

3.3.4 Bacteria

The bacteria causing diseases in plants were formerly classified into genera of Gram positive (i.e. Corynebacterium ) and Gram negative (i.e. Agrobacterium , Erwinia, Pseudomonas , Xanthomonas and Xylella ). Recently, this classification has been thoroughly revisited, with recommendations for classifying coryneform bacteria in Curtobacterium spp.

Other genera include Arthrobacter , Rhodococcus and Clavibacter (Davis 1986). members of the Corynebacterium-Clavibacter clade can cause diseases in a number of plants. One of the most severe one is Corynebacterium sepedonicum (Deboer and McCan 1989). Pathogenic species of Clavibacter (Raju and Wells 1986) include Clavibacter xyli subssp. Xylene , causing ratoon stunt of sugarcane. Grisham (1991) observed that this organism caused losses around 14% of cane in the 1st year of sowing, elevated to 27% in the 3rd year.

In aound 200 species of dicotyledonous plants the crown gall and root gall diseases are caused by infections by Agrobacterium tumefaciens .

3.3.5 Actinomycetes

Some members of Streptomycetes cause potato warts. The weight decrease of potatoes is minute. However, the financial failure of the grower is noteworthy because potatoes showing malicious warts are not preferred by the consumers. A similar disease in carrot was also documented (Janse 1988).

3.3.6 Mycoplasmas and Spiroplasms

This group of bacteria is characterized by the absence of a cell wall. Mycoplasmas are spherical whereas spiroplasms, as the name suggests, are spiral-shaped. They need vectors for transmission into susceptible organisms, and are responsible for diseases such as aster yellow and corn stunt. In citrus, fruit production can be decreased by 50–100% due to the ‘stubborn disease’, caused by Spiroplasma citri. This disease may be observed in 5–10% of citrus trees in California, and higher frequencies in Mediterranean countries (Smith and Banks 1986).

3.3.7 Viruses and Viroids

Plant viruses are classified into 38 groups (Boswell et al. 1986) based on morphology, RNA or DNA (single or double stranded). Serological method and nucleic acid probes are used to determine the characteristics or relatedness of plant viruses. There are more than 700 recognized viruses of plants, numerous of which have a wide host range and result in catastrophic diseases.

Viroids consist only of a circular single-strand RNA. There are at least 12 recognized root diseases induced by viroids. These comprise of economically important pathogensattackingpotato, citrus, and coconut palm trees. In Philippines, the latter destroyed more than 30 million palm trees, in spite of its simple structure that consists of around 300 nucleotides (Hanold and Randles 1991). Neither viruses nor viroids are able to proliferate in the absence of hosts.

3.4 Management of Plant Diseases

Once the causal factor of a disease is determined correctly, it is possible to develop plans for its management and control. Over the last century much research has been carried out on pathogens, diseases and management methods. Today we can take advantage of this vast amount of knowledge to sustain control programmes. Smart management of plant diseases is an economic necessity. It helps to prevent epidemics and disastrous famines. There are three basic approaches for plant diseases management i.e., chemotherapy, prevention and genetic resistance (Fig. 3.2).

Fig. 3.2

Approaches for plant disease management strategies

Chemical control against phytopathogens is an important approach. The use and misuse of chemicals (fungicides and pesticides) are known since the ‘60s, in which the dangers of pesticides were highlighted.

Prevention is based on the consideratin that the most effective disease control strategy is to keep the host and patogens far from each other. This type of management can be taken in several forms. A government unit (county, state or nation) may establish prohibition and prevention rules. Such quarantines are practiced in parallel with inspections.

The use of cultivars resistant to diseases is one of the less expensive, safest and most practical solution. The use of resistant cultivars is attractive to those who must rely on expensive pesticides to protect large tracts of low-income crops, such as wheat.Expert scientists, time and money are needed to grow resistant varieties. In crop plants, resistance is a foundation step in any disease management program.

3.5 Genetics of Disease Resistance

Van der Plank (1963) was the first to classify resistance as vertical or horizontal. Vertical resistance (VR) is also known as race specific. Horizontal resistance (HR), also called polygenic resistance, relies on genetically different and physiologically different species. Other terms used for such resistance are either quantitative or partial resistance.

3.5.1 Vertical Resistance

VR is conditioned by oligogenes and is successful against some races of a pathogen, but not all. HR, which is polygenic in inheritance, appears efficient against all races of that pathogen.. It is now clear that achieving a population resistance, where a given pathogen population cannot increase and damage the host population possessing VR or HR, or a combination of both, is a challenging task that needs much attention. In cases of outbreaks and epidemics, VR is of sufficient value in effective control measures, but it has been found unsatisfactory against widespread epidemics (Severns et al. 2014).

A variety with HR, showing most resistance to all pathogen races, does not affect the pathogen population growth from the initial inoculum level but it does reduce the rate at which such an increase normally takes place (Garrett 1999). As a multiline cultivar possesses many genes for VR, the initial inoculum of the pathogen, in course of time, becomes small. The oligogenes give VR ease of manipulation in greenhouse and field trials and were found superior in yield assessments.

Plant pathologists accustomed to work with populations. Breeders pursue a yield boom, quite unaware of the nature of adversity. In fact, the disease importance increases not only with the degree of inbreeding required for its containment, but also with the extensive use of cultivars having the same germplasm. The medial method suggested was the use of non-uniform crop varieties.

3.5.2 Horizontal Resistance

For many plant diseases the value of VR in ongoing breeding program was analyzed and found clearly inappropriate. The basic point in favor of HR breeding techniques is that the resistance effectiveness as it does not “break down”. VR instead is subject to this effect. In synthesis, while VR confers complete but non-permanent protection, HR confers incomplete but permanent protection. It is hence useful to recognize some terms introduced in HR breeding programs. A “pathodeme” is a host population in which all individuals have a given resistance in common. A “pathotype” is a pathogenic group with the same pathogenicity reaction on a particular host. When a variety pathodemes is inoculated with a variety of pathotypes, and the disease incidence displays a differential interface between pathodemes and pathotypes, the resistance and pathogenicity are called vertical. When there is no differential interaction, they are called horizontal. The pathodemes and pathotypes can also be described as vertical or horizontal. VR involves mechanisms which are within the pathogen’s capacity for change. HR, on the other hand, involves mechanisms which are beyond the pathogen’s capacity for change. The term “capacity for change” means that every pathogen can change as it has an in-built capacity within the well understood term “natural variability ”. There are, however, limits to that variability and HR involves mechanisms beyond those limits. It should be understood that change here means population dynamics and not evolution. Furthermore, VR is inherited oligogenically (i.e., controlled by a few genes for major heritable changes by looking for applied characters). HR is almost always a polygenically inherited resistance (i.e., controlled by a number of genes). However, oligogenic HR does occur in rare cases as not all the HR components are inherited polygenically. Vice versa, not all oligogenic resistance is VR. The most important point is that oligogenic HR is a qualitative inheritance, a mechanism of functioning with related final effects. As opposed to these rare cases, the general run of universal HR is quantitative. The influence of breeding techniques comparing oats and rye may well illustrate this point.

It may be difficult in some diseases to obtain sufficient HR to control a disease in natural growing conditions. It would seem best to initiate breeding with HR first and then to reinforce it with VR, should HR prove inadequate to meet the situation. For instance, a good horizontal pathodeme can be used as the basis of a multiline of several different vertical pathodemes. The result then would be a slowing down of an epidemic, as the epidemiological effects of a multiline are similar to those of HR. This approach has much merit as it is nearer natural conditions where HR is essential and VR is a supplementary protection occurring as natural multilines.

In absence of a pathogen, erosion of HR can take place in nature. There are two types of erosions, one called “phenotypic erosion” and the other known as “genotypic erosion”. Generally, in most crops, a high degree of susceptibility (the suscept-pathogen relationship) may be ascribed to an erosion of HR but it can be restored by breeding within existing local cultivars, i.e. by restoring lost genes. However, search for these local materials will have to go beyond locally available cultivars, including wild progenitors. Any factor(s) which masks HR will reduce pressure on selection for it. These factors can be fungicides and similar artificial disease control measures, or VR itself. VR can be eliminated making certain that the population does not possess genes for it. This has been found possible in the case of potato bred against Phytophthora infestans but it was not possible in wheat, where complete absence of VR to Puccinia graminis is unknown. Individuals showing hypersensitivity reactions such as ' flecking' flecking” are evidences of VR and such plants can be eliminated. Similarly, if VR confers complete resistance against non-matching vertical pathotypes, screening of the host populations can be done for a “slight disease” rather than a“no disease” condition. Also VR can be eliminated by ensuring that all individuals in the host population are susceptible to a single vertical pathotype. VR provides a complete and lasting control of a disease only when the host population flexibility is maximal, and the pathogen population flexibility is minimal.

In crops where breeding for HR is undertaken, the basic assumption should be that the existing levels of HR are due to phenotypic erosion, in which case, breeding could be confined to existing cultivars.

However, if this assumption is not warranted a search may be made beyond existing cultivars, and efforts channeled for getting together a wider genetic base. Genetic heterogeneity can be achieved by random polycross with the assistance of a male gametocide. By suitably increasing the intensity of the epidemic conditions, a sufficient selection pressure for HR can be mounted. VR has several attributes such as hypersensitivity reaction, race- or pathotype- specific effect, inheritance based on major genes resistance and non-durable resistance.

3.6 Resistance Breeding Strategies

3.6.1 Prioritize the Importance of Diseases

A significant concern in resistance breeding is to establish the suitable priority level. Breeding efforts for resistance may be unsatisfactory if the consequences are extremely damaging to other traits, e.g. yield. These special effects may occur because of genetic linkages, and are unfortunately common (Johnson 1978).

In addition, resistance breeding needs resources. Highest efficacy will be attained by placing it at a level of priority as low as reliable, by producing suitable genotypes. It can be determined by the importance of a disease and the likelihood of incorporation of a worthwhile resistance level, while conducting a breeding program considering the choices for other control schemes. Some diseases are widespread, being as such a noticeable goal to control through breeding. For other diseases, the resolution is not much clear and accurate data on theit prevalence in crops is not sufficient (Wolfe and Barrett 1979). There may be, therefore, a biased component in disease targeting. Main objective of resistance breeding is to identify diseases of importance at current genotypes have enough resistance sources. Thus breeders may need to spend energy on selection for resistance, or against high susceptibility for in fact an insignificant diseases.

The occurrence of wheat yellow rust in UK during 1970–1988 was typically low (Polley and Thomas 1991), as yellow rust was not a vital disease. Commonly less occurrence of this disease in the UK wheat crop is due to struggles by the UK wheat breeders for yield, and the National Institute of Agricultural Botany suggesting only genotypes resistant at more than a given, least possible level. On the other hand, this cannot completely exclude the threat of epidemics.

With more recent fungicides it is hard to control yellow rust in extremely susceptible genotypes. This was demonstrate by the development of an epidemic when the cultivar Slejpner became susceptible when it was commercially used (Bayles et al. 1989). Incidence of yellow rust on extremely susceptible genotypes happens regardless of availability of active fungicides, because of meteorological conditions or human factors. The potential threat of yellow rust has been famous for numerous years and resistance breeding has remained a main concern in most UK programs .

In other countries this was not the case.For example, frequent outbreaks of yellow rust on bread wheat in Italy are credited to the cultivation of extremely sensitive genotypes, lacking selection for resistance in breeding programs, in combination with much disease suitable climatic conditions, during several years (Chilosi and Corazza 1990).

Sometimes, a disease that has not even been considered important can develop in a crop. For example, due to a humid 1982 summer in the UK, the Avalon wheat genotype was considered as susceptible to ear blight, after its commercial presentation (Lupton 1983). During the development of Avalon, no selection against ear blight was made. On the other hand, a technique was later established for evaluation of susceptibility against Fusarium species by spraying the emerging spike with spore suspensions and retaining high humidity by mist irrigation (Jenkins 1984). By means of this method, bases of resistance were recognized and exploited.

3.6.2 Steps in Breeding for Disease Resistance

Collecting and maintaining genetic sources of resistance genes is the first step in breeding for pathogens resistance. The resources comprise of commercialand/or local varieties, wild related progenitors, species and related genera, mutagenesis.

3.6.2.1 Sources of Resistance Genes

A decisive factor which influences the plant breeder in the choice of breeding outlines for resistance is the knowledge about the accessibility of resistance sources. These are commonly available for many, generic diseases. On the other hand much less sources of resistance are available for specific diseases. In wheat resistance sources against rust are easily accessible, while for some diseases, such as the eyelid, it is difficult to find suitable sources. However, many sources of diseases resistance have been identified and successfully utilized by plant breeders. However, in some cases it is difficult or practically impossible to select a resistance source, because it cannot be found. This difficulty faced by the breeder and all the source of wheat disease resistance are not sufficiently documented (Scott 1981).

There are resistance sources which have not been observed in present cultivars but can be found in related species, from which they can be transferred successfully (Knott and Dvorak 1976). Availability of resistance source is indeed the most important starting point when initiating a breeding scheme. Themost suitable situation is when sufficient genetic variation/sources are available in breeding populations or cultivars. Resistance sources should be tested for other important agronomical traits and can be directly introduced in other cultivars by crossing. Some source of resistance cultivars need acclimatization when the material is imported from neighboring regions having a similar environment. Much effort is needed when the source is a non-adapted cultivar.

3.6.2.2 Utilization of Genetic Resource

Plant breeders around the globe try to collect as much as possible of broad genetic bases, and many of their work is dedicated to collecting genetic sources which likely are beneficial for them. For example, in cotton breeding for resistance to bacterial blight (Xanthomonas campestris ) R.L. Knight (1957) had to observe more than 1000 diverse accessions of wild and cultivated Gossypium spp., to find the source of resistance against the disease. Innes (1983) listed tetraploids and 2n Gossypium spp. and 2n wild species having 19 major genes, which were used to resist to blight. A trotal of 13 genes were identified in tetraploid G. hirsutum, only one gene in tetraploid G. barbadense , two in diploid G. arboretum and diploid G. herbaceum, and one gene in 2n G. anomalum.

If it is important to collect useful germplasm, another important aspect is being sure that such germplasm is conserved, well documented and easily accessible to breeders throughout the world, when needed. Techniques have been made available to conserve seeds without viability losses, kee** them in viable conditions for a long time (Roberts 1975). Tissue culture for long-term preservation is one of them, allowing preservation of vegetatively propagated species (Withers 1989). Developed and develo** countries give importance to germplasm preservation and make more efforts to provide funding and services for germplasm conservation (Hawkes 1991). However, the protection of the world genetic resources is a difficult job that goes ahead of the budget of many governments.

The International Plant Genetic Resources Board (IBPGR) was established in 1974 with the directive to encourage and synchronize the breeding work, at the international level. Collection, preservation and documentation are fundamental functions of a gene bank (Brown et al. 1989). Most of the world’s conserved genetic resources is in public sectors and was formed as the result of international agreements. Most agreements allow easy access, and without cost, to breeders. On the other hand, the Keystone Center (1991) has given emphasis to the global initiative for protection and sustainable utilization of plant genetic resources. It required joint efforts, and contribution by all members, trusting parties and institutions from all over the globe, including those that provide germplasm, information and technology, as well as financers and improvement organization.

3.7 Planned Deployment of Resistance Genes

3.7.1 Self-Pollinated Crops

In self-pollinated crops, backcross and pedigree breeding methods are used with modifications based upon breeder’s convenience. In mass selection, plants from a population are bulked for resistance to make the foundation of a variety. Their heterozygosity may provide several merits over pure line varieties for disease resistance. In pure line selection pure line are derived from the progeny of selfed homozygous plants, selected from a variety. The progeny is evaluated for resistance in succeeding generations. If it is promising, then is the progeny is multiplied to develop a new variety (Allard 1960). In line breeding plants are selected (selfed or inter-pollinated), and the resulting progenies are tested or evaluated for resistance. Hybridization involves crossing of two lines for transferring disease resistance from donor parents, combining characteristics from each parent. It allows the plant breeder to combine diseases resistance into a single variety. The F₁ genetic constitution is identical though segregation in F₂ generation occurs as well as regain of homozygosity is attained in succeeding selfed generations. Selection followed by hybridization is based on following approaches.

Pedigree selection is mostly practiced in self-pollinated crops because it gives breeders the greatest opportunity to test their selection expertise (Allard 1960). The main limitation of this method is the high amount of material that a single breeder cannot handle alone. In pedigree selection, commonly practiced crosses are between a parent selected for his desired agronomic performance and another chosen parent, having a specific weaknesses, i.e. absence of disease resistance characters.

Disease resistant plants are selected in advanced generations and records are kept for all parental and offspring associations. Information from pedigree selection is helpful to avoid selection of narrowly related individuals with a close ancestry, whose likely value is almost similar. Usually in this method selection is started in the F₂ generation. Through F₃ and F₄ generations, selection is mostly tested in the best disease resistance plants of the best families, due to a desired level of heterozygosity maintained in these generations. Selection continues to generations F₅ and F₆, focussing on to family selection, often planted as individual rows or replicated in breeding nurseries. Ultimately, the lines that are consistent for the release of fresh cultivars are tested on sick field plots, and replicated in different ecological conditions (Allard 1960).

Pedigree selection also is used in cross-pollinated crops, i.e. in maize, for improvement of lines that have known desired traits and weakness for other particular traits (Agrawal et al. 1976). Pedigree selection may start with progenies developed in cross pollinated varieties, germplasm composites, synthetic or backcross populations, and also in F₂ populations. For maize, the objective is to select pure lines with a superior combining capacity in the production of high-performance F₁ hybrids capable of supporting diseases and other stresses characteristic of the area in which the hybrids will be grown. Crops in which quality standard are required in cultivars for quality demanding consumers, backcrossing breeding method mostly are used to transfer disease resistance from sources (donors) that may be agronomically inferior for yield, and quality cultivars that have been developed by typical pedigree selection (Fig. 3.3).

Fig. 3.3

Pedigree breeding method

Bulk Selection is a desirable technique to combine the characteristics from both parents. Early segregating generations (F₂ – F₆) are bulked without selection. When homozygous plants are attained in later generation then selection is made for resistance and the plants are evaluated as in the pedigree method. Artificial epiphytotic conditions are established for selecting resistant plants (Singh 1986).

Backcross variety have been developed by crossing F1 hybrids with any of the known parent. This is useful when breeding for small grains crops. In this technique two plants are chosen and inter-mated. After regular backcrossing with one of the recurrent parent, the backcross progeny developed is almost identical to the recurrent one (Fig. 3.4). In this breeding method economically important variety, lacking a disease resistant character, is know as recurrent/recipient parent. At the same time a variety containing only a disease resistance character is known as donor parent. The élite varieties KDML105, Basmati and Manawthukha (Too**da et al. 2005) were produced for resistances to rice disease blast in South and South East Asia by practicing this breeding technique (Sreewongchai et al. 2010). Advantages of using this method include i) the intervarietal transfer of characters (disease resistance, plant height, earliness, seed size, color, shape), ii) the interspecific transmission of disease resistance characters from associated/related species to cultivated ones, iii) the transfer of cytoplasmic material from one to another variety or species, (this requires, in case of cytoplasmic male sterility, the development of transgressive segregants and the production of isogenic lines). Some of the varieties which have been developed through this method is BD 8 of cotton (resistant to wilt), MS 521, MS 541A, MS 570 A of bajra, resistant to downy mildew, the transfer of wilt resistance to alfalfa (Medicago sativa) variety California common, from the variety Turkestan.

Fig. 3.4

Back cross breeding scheme for dominant (a) and recessive (b) genes

Varieties developed by this method require several back crossings to develop a new cultivar. In general, the newly developed variety cannot be better than the donor parent, except only for the character to transmit. Hybridization must be performed for every back cross, a factor that is time consuming, expansive for handling and by the time required until the backcross is over. . Some line produced by this method show higher resistant to rust (leaf or ray rust). But they also had a yield potential 5–15% higher that the original variety (Singh et al. 2005). Certainly, a second round of crosses among lines with resistance derived from diverse donors might give advanced levels of resistance. This may be evaluated in case an additional resistance is desirable in several environments.

3.7.2 Cross-Pollinated Crops

Several methods can be employed in cross pollinated (allogamous) crops, to improve plant populations and develop disease resistant varieties.

In line breeding plants are selected (selfed or inter-pollinated), and resulting progenies are tested or evaluated for resistance (Singh 1986). In polycross, n resistant plants are selected from a heterozygous population and intercrossed, following the development of inbred lines. The progenies of a polycross are bulked, the resistant plants are selected and progenies of individual lines are tested independently (Singh 1986). Synthetic/Hybrid varieties: resistant lines, obtained through line breeding or recurrent selection, are used to produce hybrid or synthetic varieties. A synthetic variety is developed by intercrossing several selected plants that have been expected to be good combiners. Hybrid varieties are the product of controlled pollination between lines (Singh 1986). The parental lines must be maintained independently for reconstituting the synthetic or hybrid varieties.

In cross-pollinated crops, recurrent selection is also an effective method of selection for self-pollinated crops. For instance, it permits the accumulation of desirable genes to raise the level of polygenic resistance. Before commercial release of genotypes, recurrent selection provides information about partial resistance to estimate the genotypes potential. If a character, i.e. quantitative resistance, is governed by more than four genes, only a very small proportion of the progeny of a cross between a superior cultivar, susceptible, and a disease resistant donor parent, will have the required amount of resistance genes. Different cycles of recurrent selection for agronomic characters as well as required disease resistance will increase the selection efficiency. This is valid for genotypes from the population that combines better agronomic characters along with polygenic disease resistance. As observed by Eberhart (1990), “For improvement in maize population, improvement program is the foundation which leads toward maximization of durable genetic gain every year”.

Selected genotypes of both populations are mated with genotypes of pure testers of the reciprocal population, assessing the performance of resultant F₁ crosses. Formerly, best selected genotypes are crossed in all possible combinations to rise next population cycle. Tester genotypes will change in advanced selection cycles, as development of pure genotypes (Eberhart 1990). The strength of selection can be improved by accumulating the quantity of investigated genotypes assessed at the test crosses, or by reducing the selected genotypes for re-combination in the next population cycle. As suggested by Eberhart (1990), genotypes 250–400 S₂ should be assessed for selection of 6–20 genotypes for recombination for the next cycle. This will attain a 4–8% strength of selection. In the beginning, it is required to select limited desirable characters that are essential to get stress resistance and high yield. Selection of more number of characters at the same time will result in slow selection gains for each single character. Eberhart (1990) endorsed the different selection stages to attain enhancements in different aspects. The S0 plants self-fertilized in all populations can be analyzed for eradication of unwanted traits established on highly hereditary characters, for example days to maturity and disease resistance.These selections should be performed prior to production, to decrease the number of plants that will self-pollinate. In the next period, selection was done on S₁ plants for fewer heritable characters, for example resistance to insects as well as lodging resistance. The selection between test crosses should be established mainly on yields, along with root rot and stem rot resistance. The recurrent selection programs for population improvement are logically appropriate for cross-pollinated crops (Fig. 3.5). However, several schemes of recurrent selection with self-pollinated crops have been tried.

Fig. 3.5

Scheme of a recurrent selection breeding program

The use of male sterility characters was suggested to assist the recurrent selection in barley sorghum and soybean (Gilmore 1964; Doggett and Eberhart 1968; Brim and Stuber 1973). However, Matzinger and Wernsman (1968) demonstrated that constant improvements in leaf yield can be gained by repetitive mass selection during random mating cycles between selected genotypes, in a heterogeneous synthetic tobacco cultivar that is usually self-fertilized. Jensen (1970) recommended a selective pairing technique of diallel with recurrent selection, for small grain populations to assist as a complement in conventional pedigree selection procedures. Díaz-Lago et al. (2002) revealed that programs with selection in early generation for partial crown rust resistance in oats, led towards a total increase of about 42% in resistance after four cycles of population improvement, to assist as an enhancement to conventional pedigree selection scheme. However, they concluded that synchronized selection for the days to flowering would be essential as part of the supplementary resistance to crown rust was linked with late maturity.

Interspecific hybridization yields hybrids developed by crossing two species of the same genus, with the objective of transferring to a cultivated species one or few simply inherited characters such as disease resistance. Kufrijyoti is a potato variety developed through interspecific hybridization, which is resistant to late blight. Through interspecific hybridization, a resistance gene for cotton rust, due to Puccinia cacabata, has been transferred from G. anomalum and G. arboretum into G. hirusutum (Anjum et al. 1986).

Aminu (1940) reported the combination of genes for resistance to cotton leaf curl virus and other diseases between G. hirusutum and G. arboreium. Similarly, gene B6 present in the ‘A’ genome of G. arboretum, conferring resistance to bacterial blight by Xanthomonas malvacearum , was introgressed into G. barbadense (Knight 1957; Brinkerhoff 1970).

A source of common bunchy top plant resistance in G. hirsutum has been identified in “Delta Opal”, which is used to transfer disease resistance (Ellis et al. 2016). Transmission of genes between species is a very preminent technique that can result in a broad spectrum of resistance. In case of wheat, the Lr34res allele has been identified which gives resistance in maize against rust and the hemibiotrophic fungus responsible of northern corn leaf blight (NCLB) (Sucher et al. 2017). Lr34res has already been revealed to be operative for rice blast in rice (Krattinger et al. 2016) and vs different biotrophic fungi (Risk et al. 2012, 2013). Additionally, Lr34res has been linked with resistance for spot blotch (caused by the fungus Bipolaris sorokiniana ) in wheat (Lillemo et al. 2013). Oligogenic and polygenic resistance have been recognized in corn, for race specific Ht1 and Htn1 genes, against widespread NCLB races (Welz and Geiger 2000; Hurni et al. 2015).

3.8 Evaluation

The imperative step in breeding for disease resistance is to evaluate the developed germplasm, which may be achieved in either greenhouse or field conditions. Both are laborious and expensive breeding steps. While executing a backcrossing program, selected breeding material must be stabilized under greenhouse conditions. In the greenhouse the material selected from successive backcross generations are tested for pathogens resistance, and the susceptible ones are eliminated. In field evaluation, selected material is grown in disease-free and disease-infested plots, to evaluate them for resistance against particular pathogens.

3.9 Release to Growers

The final breeding step is the release of lines, which have been evaluated as disease resistant, to the growers for cultivation.

3.10 Factors Affecting Expression of Disease Resistance

Some particular causes may complicate reproduction for resistance. These factors can be biotic or abiotic (Burdon 1987), as follows.

• 1. Abiotic factors must remain within a particular range to permit the development of the Pathogenic species (Sharma et al. 2003).

  • (a) Temperature: expression of few resistant genes is restricted in case of excessively low or high temperature.

  • (b) Light: the intensity of light may disturb the efficacy of chemicals affecting as a result the pathogen resistance level.

  • (c) Soil fertility: extraordinary soil fertility produces extra succulent plants that are most vulnerable to infection. Other pathogens (opportunistic generalists) are also more effective in under-nourished plants.

• 2. Biotic factors

  • (d) Years: the response of a plant toward a pathogen can differ with time. Certain diseases are extremely effective at the beginning of plant growth than others (Burdon 1987).

  • (e) New races of pathogens: as mentioned, breeders should be awaren that there is an efficacy of resistance for certain new races of pathogens, but not for others (Burdon 1987).

  • (f) Introduced resistance: infection caused by prior pathogenic infestations can induce a systemic resistant reaction towards a later infection by other pathogens (Kathiria et al. 2013). Such cases may also occur before infection.

3.11 Advantages of Breeding for Disease Resistance

Resistant varieties offer the cheapest means of disease control, with indirect benefits as they reduce the application of fungicides, thus reducing environmental contamination. The effectiveness of resistant varieties, however, is not affected by environmental conditions. Disease resistance breeding is an important goal for plant breeders around the globe. A combination of traits is desirable instead of just targeting one trait for releasing an attractive cultivar. Performance, superior quality and resistance to epidemic diseases are major considerations in improvement programs, with the first point aiming at the most significant progress.

• 1. Resistant varieties offer the cheapest means of disease control.

• 2. They obviate the use of fungicides, thus reducing environmental pollution

• 3. Effectiveness of resistant varieties is not affected by environmental conditions.

• 4. They safeguard from the inadvertent release of varieties that are most susceptible than earlier ones.

3.12 Problems in Breeding for Disease Resistance

The problems and inconvenients occurring during the development of a new variety may be summarized as follows.

• 1. Resistance breakdown (vertifolia effect, boom and bust cycle).

• 2. Horizontal resistance being durable, but difficulty may concern the accurate and reliable assessment of the resistance level.

• 3. Sometimes there is a negative correlation between yield and disease resistance, e.g. wheat leaf rust gene Lr34 causes a 5% reduction in grain yield (Draz et al. 2015).

• 4. Introgression of multiple resistance against several diseases requires meticulous planning and far greater efforts than that needed for a single resistance.

3.13 Breeding Challenges for Pathogen Resistance

Disease resistance breeding basically varies from that applied for other characters because the induced resistance may cause alteration in the evolution as well as population of the pathogens (Van Bueren et al. 2011).Identification of resistant genes is not possible but for the plant infected in disease conducive environmental conditions (Engering et al. 2013). The development of segregating populations is necessary for breeders. The challenge is in the identification and selection of desirable genotypes in such a way that they would remain genetically in force, even many years after first release . The breeder must use reliable methods to detect variations in the level of resistance among segregates. While naturally caused infection can be utilized, artificial inoculation is often much consistent. Main issue in parenting for disease resistance is that, with passage of time, conventional crops changes the environmental conditions (i.e., different agronomic practices) and races of pathogens (Walters et al. 2013). Plant breeders should develop new genotypes with desirable resistant genes by maintaining these changes, to guarantee constant crop productivity, avoiding development of destructive epiphytes and infections, and reduction in annual yield losses . Plant breeders should not develop highly resistant cultivars that are not economically valuable, as most convenient approach is to breed for medium resistance. For the horizontal quantitative resistance, breeding and selection for better performing genotypes is the most desirable approach, subsequently representing the highest average resistance.