Chapter 3
Breeding Objectives

3.1 Introduction

The first exercize that must precede any of the breeding operations (and indeed a task that should be continually updated) is preparing a breeding plan or setting breeding objectives. Every breeding programme must have well defined objectives that are both economically and biologically feasible. It can be argued that instead of ‘breeding objectives’, which implies that such objectives are useful only for breeding, a more appropriate name would be ‘cultivar improvement objectives’, because this reflects the benefit of changing a trait by any means.

In practice, many new cultivars fail to be commercialized successfully after they are introduced to large-scale agricultural production. In some cases these failures are associated with the programme having the wrong economic objectives. Similarly, many excellent new genotypes fail to become successful cultivars because of some unforeseen defect which was not considered important or was overlooked in the breeding scheme.

Objectives, then, are the first of the plant breeder's decisions. The breeder will have to decide on such considerations as:

• What political, social and economic factors are likely to be of greatest importance in future years?
• What criteria will be used to determine the yielding ability required of a new cultivar?
• What end-use quality characters are likely to be of greatest importance when the newly released cultivars are at a commercial stage?
• What diseases or pests are likely to be of greatest importance in future years?
• What type of agricultural system will the cultivar be developed for?

All these will need to be considered and extrapolated ahead to a time that is likely to be 8 to 14 years from the onset of the breeding process. It should also be noted that politics, economics, yield, consumer preferences, quality and plant resistance are not independent factors, and that interactions between all these factors are likely to have an effect on the breeding strategy. It is only after answering these questions that breeders will be able to ask:

• What type of cultivar should be developed?
• How many parents to include in the crossing scheme? Which parents to include? How many crosses to examine? To examine two-way or three-way parent cross combinations and why?
• How should progenies progress through the breeding scheme (pedigree system, bulk system, etc.)?
• What characters are to be selected for, or against, in the breeding scheme, and at what stage should selection for these characters take place?
• How to release the variety and promote its use in agriculture and its benefits to end-customers?

3.2 People, politics and economic criteria

The final users of almost all agricultural and horticultural crops are consumers (humans or other animals) who are increasingly removed from agricultural production systems. In 1863, the United States Department of Agriculture (USDA) (www.usda.gov) was created, and at that time 58% of the US population were actually farmers. Indeed, only a few decades ago the vast majority of people in the Western world were directly involved in agricultural and food production. However, in 2010, less than 1.5% of the US population was directly involved with agriculture. This past century, therefore, has resulted in a dramatic shift away from working on the land to living and working in cities. Agricultural output has, and continues to, increase almost annually despite fewer and fewer people working directly in agriculture. The major consumers of agricultural products are therefore city dwellers who are remote from agricultural production but obviously have a large influence on the types of food that are purchased. In addition, these non-agriculturists have a tremendous influence on the way that agricultural products are grown and processed, and plant breeders would be foolish not to consider end-users' likes and dislikes when designing future crops. Although it is the case that, in developing countries, the proportion of the population involved in agriculture is generally higher than in developed ones, nevertheless in 2012 it was announced that for the first time in history more than 50% of the world's population lived in urban areas.

Despite an overall shortfall in world food supply, many developed countries have an overabundance of agricultural food products available, and consumers have become used to spending a lower proportion of their total earnings on food than ever before. In addition, consumers have become more interested in the way that food products are grown and processed. Many consumers are interested in eating ‘healthy’ food, often grown without agrochemicals and without subsequent chemical colourings or preservatives. Obviously breeding for cultivars that are resistant to diseases, which can be grown without application of pesticides, fits the needs of these consumers. The desire of customers for what they call ‘more natural’ food has, in recent years, had a large impact on agriculture and intercountry trade in agricultural commodities, particularly with the advent of large-scale commercialization of genetically modified organisms (GMOs).

The development of recombinant DNA techniques that allow the transfer and expression of a gene from one species, or organism, into another represented a breakthrough in modern plant breeding, and offers enormous potential advances in crop development as it increases the genetic variation available to plant breeders. However, the first GMO crops to be commercialized conveyed advantages more appreciated by the farmer growing them than by end-users. In general this technology has had a mixed reception by consumers. The reasons for this are numerous, but are related to a general mistrust among consumers regarding the health and safety of these novel products. In addition there are concerns amongst many groups that there might be environmental risks associated with GMO crops, and that transgenes might escape into the ecosystem as or by intercrossing with related weeds or wild species. Other issues obviously are involved in this barrier of acceptance, including free trade agreements and monopolies of transformation technology by a few companies worldwide. As scientists, we must also accept that we do not know all the possible facts or outcomes. None the less, during the 2011 growing season, over 10% (i.e. 160 million hectares) of the world's 1,389 million hectares of total crop-land planted were cultivated with transgenic cultivars, and the rate of adoption of this technology by large and small farmers shows no sign of slowing down thus far.

How many plant breeders, say, 10 to 15 years ago had the insight to foresee such public opposition in acceptance of GMO products, that many consider as showing “a significant advantage over proceeding cultivars”? However, as noted, almost all of the first GMO crops had genetic advantages that were “hidden” to the final consumer. Nevertheless, on closer inspection, research recently carried out at Iowa State University in the US suggests that world prices of corn, soybeans and canola would probably be, respectively, 6%, 10% and 4% higher on average than 2007 baseline levels if GMO cultivars of these crops were not available to farmers.

Therefore, even though the most direct beneficiaries of the first wave of GMO crops have been farmers and biotechnology-based private breeding companies, there are already spillovers directly benefiting the purchasing power of end-consumers. The main reason why the first GMO releases had grower advantages rather than benefits to the end-user is the sheer genetic complexity of modifying the metabolic pathways involved in quality traits important for final consumers. Nevertheless, the first GMO cultivars with improved oil fatty acid profiles, enriched with omega-3 fatty acids (associated with a reduced cardiovascular risk) which show a clear advantage for end-users, are now commercially available. In addition, transgenic maize hybrids tolerant to drought are already at the commercialization stage in the US, which will provide benefits to farmers by stabilizing the production of grain under water-limiting growing conditions, but could also contribute to a more efficient use of an ever-more valuable resource, water.

Including recombinant DNA technologies as tools in cultivar development is one issue that many breeders and breeding programmes are at present giving serious consideration. Consumers, farmers or housewives, also have a tremendous impact on all aspects of everyday life, as they are usually involved in democratically electing politicians that govern the nations of the world.

Many people would consider it impossible to try to predict what is in the mind of a politician. Politicians and political forces will, however, continue to be a large determining factor in shaping agriculture. For example, there may be a very cheap and ‘safe’ chemical available that controls a certain disease in your crop of interest. With this in mind, the breeding objectives may not include selection or screening for biological resistance to this disease. Several years into the breeding scheme, it may be demonstrated that the use of this chemical is harmful to the environment and government policy responds by withdrawing the use of the chemical, and suddenly the need for resistance to this disease in breeding lines is vital. As an example, it is likely that over the years the majority of organophosphate-based insecticides will not be registered or re-registered for application to many of the crops that today depend on them for successful production. It has further been suggested that over 80% of all agrochemicals used in the US might not be registered or re-registered for use in agriculture at some point in the future. Another example of the far-reaching influence of political decisions on breeding outcomes is the current debate of food versus fuel. Through the development of economic incentives like subsidies, politicians can raise (or reduce) the demand for a given type of crop, and thus affect the breeding approach required to fulfil these requirements.

Many soil fumigants are highly toxic, volatile chemicals that, amongst other things, have adverse depletion effects on our atmosphere. As a result many governments worldwide have banned the use of soil fumigants such as methyl bromide. One possible alternative to using synthetic fumigation is Brassicaceae cover crops (plough-down crops) or high glucosinolate-containing seed meal soil amendments, an approach called biofumigation. Glucosinolates per se are not toxic, but when mixed with water in the presence of myrosinase they degrade into a number of toxic compounds including isothiocyanates and ionic thiocyanate. Past research has shown that different Brassicaceae species produce different quantities and types of glucosinolate which have greater or lesser pesticidal activity on different pests. Far-sighted plant breeders have recognized the potential of biopesticides and have found that interspecific hybridization between different Brassicaceae species offers an opportunity to develop ‘designer glucosinolate’ plants with specific pesticidal effects. It is fascinating to note that some hydrolytic byproducts of specific glucosinolates have also been shown to play a significant cancer preventative role, and very recently broccoli cultivars that contain higher levels of those glucosinolates have been made available to farmers, as a means to improve the diet of end-users and to encourage the adoption of healthier dietary habits.

Government agencies (e.g. the Food and Drug Administration in the US (www.fda.gov), or the European Food Safety Authority in Europe (www.efsa.europa.eu)) can greatly influence consumer acceptance and choice. One recent example of this relates to trans fats in cooking oils. Research has shown that hydrogenated vegetable oils which contain trans fats have adverse effects on human health when included in diets. Indeed, the Food and Drug Administration now requires trans fat content to be listed on all food products. Traditional vegetable oils like oilseed rape (canola) and soy, although relatively low in saturated fats, are usually hydrogenated to avoid off-flavours in high-temperature frying and to increase the shelf life of the oil products. Rancidity and off-flavours in vegetable oil are caused by high concentrations of polyunsaturated fats. This has greatly raised the consumer awareness of trans fats, and as a result there is now high demand for vegetable oils which have a low polyunsaturated fat content. Perceptive canola and soy breeders had anticipated trans fat labelling and had low polyunsaturated (high oleic acid) cultivars of canola and soy available to meet market needs. These low polyunsaturated fat cultivars produce oils that show higher thermal stability, lower levels of oxidation products, and increased shelf life with minimal hydrogenation. Because health-conscious consumers and food companies want to avoid trans fats in foods, farmers willing to grow these soybean cultivars under contracts can often receive a premium price for their crop compared to other cultivars.

Political pressure can also have an influence on the types of crops that are grown. Within several countries in the world, and also groups of countries (e.g. the European Union), the farming community are offered subsidies to grow certain crops. As a result, over-production can occur, which can affect the world price of the crop, and hence influence the economics of farming outside the subsidized regions. If crop subsidies are reduced or stopped, this can also have a similarly large but opposite effect on the economics and hence directly affect acreage of the crop in these other regions. Crop price is always driven by demand, greater demand resulting in a higher price. However, this can give rise to increased acreage, which may then mean over-production, which in turn usually leads to reduced crop prices.

The US, like many other Western countries, has become increasingly dependent upon imported oil to satisfy energy demand. It is possible to substitute oils from fossil fuels with renewable agricultural products (Figure 3.1). Therefore, bio-ethanol and biodiesel fuel, lubricating oil, hydraulic oil and transmission oil can all be derived from plants. At present the agricultural substitutes are still higher in cost than traditional fossil-derived equivalents. However, in the future this may change either as a result of a change in fossil oil costs or in further breakthroughs in either increasing crop productivity or the processes needed to obtain these substitutes from agriculture. Governments in several countries have mandated that liquid fuel should contain a certain proportion of biodiesel or bio-ethanol, and public transport vehicles in inner cities are being encouraged to use biofuels as these have fewer emission problems. Similarly, in many countries (particularly Northern Europe) governments are legislating that certain operations (e.g. chainsaw lubricants) should use only biodegradable oils. Also taxation decisions made by relevant countries can affect the relative cost and hence use of fossil- and plant-derived fuels and oils.

Figure 3.1 Volkswagen Beetle (‘Bio-Bug’) powered by biodiesel produced from mustard oil.

The recent spike in food prices due to climatic disasters such as severe drought spells in Russia and Australia, and diminishing grain stocks, triggered rioting and civil unrest in many countries. This is a sober reminder about the importance of a supply of cheap food and the close link existing between food stability and political stability. Additionally it highlights the overreaching impact plant breeding imparts, which extends well beyond the purely agricultural realm. This further evidences the impact that plant breeding has on food production, the quality of livelihoods and even on political stability in many parts of the world.

Economic criteria are important because the breeder must ensure that the characteristics of cultivars that are to be developed are the ones that will satisfy not only the farmers, but also the end-users, and that can be produced in an agricultural system at an economic level. The supply of a product and the consumer's demand for that product are inter-related. If there is over-production of a crop then there is a tendency for the purchase price to be lower. Conversely, of course, when a product is in high demand and there is limited production, then the product is likely to command high premiums. In general, however, there is a tendency for an equilibrium: that farmers will only produce a volume that they think they can sell according to the needs of the end-user.

Although plant breeding is influenced by economic activity, unfortunately financial concerns are rarely considered in setting breeding objectives or setting a breeding or selection strategy. It is often assumed that increased yielding ability, better quality and greater disease or pest resistance are going to be associated with improved economics of the crop. Unfortunately this topic has been examined by very few researchers and is an area where greater examination would increase the probability of success in plant breeding and therefore its contribution to society and mankind.

Private breeding companies have developed economic breeding objectives that have had greatest influence on breeding objectives or strategy. This is perhaps not surprising as these groups require developing better cultivars and selling seeds or collecting royalties on these genotypes in order to sustain the ever-increasing research and development expenses required to survive in the industry. This, for example, has been one of the main drivers to develop so-called hybrid cultivars, which generally allow farmers to achieve higher levels of yield and greater uniformity than with other types of cultivars, but require fresh seed to be purchased every growing season.

Public breeding programmes have in the past been better placed to carry out breeding with objectives that might be considered to have a greater social than economic impact, for example breeding varieties that might suit small-holder growers, concentrating on species where there was a limited seed market, or crops with small overall acreages. They also usually were associated with universities, colleges or government departments which had, as a background, research at a more fundamental level or which could be carried out over a longer timescale without immediate financial return. This gave them greater freedom to carry out research into aspects that were not necessarily ‘mainstream’ to the variety production process and investigate such aspects as wild germplasm characteristics, plant breeding strategies, novel crops or novel uses for crops. This has, however, become much less the case in recent times, with more pressure being exerted in public systems for near-market research to be privatized and for public research to be self-funding. So, for example, they are often encouraged to develop breeding material which can be licensed to private breeding companies. Therefore the differences between the two types of breeding programme have been severely diminished.

3.3 Grower profitability

In general yield is the most important character of interest in any plant breeding programme. Therefore, increasing crop yield will always be a sensible strategy. There are rare cases, however, when farmers are willing to trade-off yield with quality, if the end product premium can offset the reduced productivity. One such case is the production of grapes for premium wine-making, where farmers deliberately avoid maximizing production in order to reach the quality standards and higher prices under which their grapes are purchased by wineries. In general terms, though, there would be only limited use for a new cultivar unless it has the potential to at least yield at a comparable level with existing varieties, unless, as noted above, the harvestable product fits a particular niche market and hence can attract a higher ‘per unit price’. Plant breeders tend therefore to select for increased profitability. Farmers' profits are related to input costs and gross returns on the crop. Plant breeders can increase grower's profitability by:

• increasing the yield per planted area, assuming input costs remain constant;
• expanding the region of crop production;
• reducing input costs while maintaining high yield per unit area (input costs will include herbicides, insecticides and fungicides);
• increasing the inherent quality component of the end product so that growers receive a higher unit price when the harvestable product is sold.

All crops have restricted ranges of environments to which they are adapted. Bananas and sugarcane are unlikely to be grown as commercial crops in the Pacific Northwest region of the US or in northern Europe. However, one attribute to increasing yield may be related to increasing the range of environments in which a crop can be grown. For example, the development of earlier maturing Brassica napus lines has extended the canola (oilseed rape) acreage in Canada to include regions further west than was previously thought possible. A similar extension of adaptation must have been involved with movement of wheat and maize to northern temperate regions over the past decades. For example, potato production in many world regions is difficult, as healthy seed tubers cannot be produced or made available when required for planting. Developing potato cultivars that are propagated from true botanical potato seed (TPS) would overcome many difficulties that occur in these regions. Few potato diseases are transmitted through TPS. In addition, small quantities of TPS would be required for planting compared with traditional seed tubers, which are bulky and usually require refrigerated storage. Further examples of the expansion of cropping enabled by plant breeding are the expansion of soybean production in North Dakota from 2.5 million acres in 2002 to 4 million acres in 2010, the development of corn hybrids able to perform well in the summer crop known as ‘safrinha’ in Brazil and Paraguay, and the development of short-cycle wheat varieties in Argentina enabling a second summer crop of soybeans or maize. The latter example not only brings about economic benefits to farmers; in addition it creates alternative crop rotations which enhance soil organic matter content and a more efficient use of fertilizers.

These examples are, however, perhaps exceptions, and it should be noted that the majority of breeding programmes are concerned with increasing yield potential within an already well-established growing region.

Crop profitability is based on net profit rather than gross product. By reducing input costs or labour requirements and at the same time maintaining high yield per unit area, breeders can increase crop profits. Input costs in crop production include herbicides, insecticides and fungicides. Therefore developing cultivars that are more competitive with weeds, resistant to damage by insect pest, or have disease resistance, reduces inputs and alleviates the need to purchase and apply chemicals. This rationale has supported the development of herbicide-tolerant and pest-resistant crops through plant breeding in many crop species. In the case of these herbicide-tolerant crops, which have been developed not only through biotechnology but also through traditional means, they have in addition supported the use of herbicides with a lesser environmental footprint, such as glyphosate.

Other inputs will include nutrients (mainly nitrogen) and water (which can have a high price in irrigated farming regions). It follows, of course, that developing cultivars that require less nitrogen or are more tolerant to drought and other stress factors will result in greater profitability to growers and will also contribute to stabilizing food supply.

3.3.1 Increasing harvestable yield

Yield, in the eyes of breeders, is considered to have two main components: biomass, the ability to produce and maintain an adequate quantity of vegetative material, and partition, the capacity to divert biomass to the desired harvestable product (seeds, fruits, or tubers etc.). Therefore, the partitioning of assimilate is very important in obtaining maximum yielding ability. Partition, in general, takes the form of enhancement of yield of desired parts of the plant product at the expense of unwanted plant parts (sometimes referred to as increasing the harvest index, defined as the ratio between harvestable dry matter and total dry matter). This can take three main forms:

• Vegetative growth is reduced to a minimum compared to reproductive growth. In many crop species plant breeders have selected plants that have short stature, or indeed are dwarf mutants. This was mainly driven by the need to reduce lodging (plants falling over before harvest) under increasing levels of applied nitrogen. However, short plant stature also allows more convenient harvest and sometimes (e.g. in fruit trees) allows for mechanical harvest, hence avoiding more expensive harvest by hand-picking. This strategy has been adopted in breeding objectives of many crops such as wheat, barley, oats, sunflower, several legumes, along with fruit trees like apple, orange, peach and cherry. In the case of rice and wheat, the exploitation by breeders of naturally occurring dwarfing alleles enabled the Green Revolution.
• Reproductive performance is suppressed in favour of a vegetative product. This has been applied to a number of vegetatively reproduced crops where sexual reproduction has been selected against in plant breeding programmes in favour of vegetative growth (e.g. potato, sugarcane, sugar beet and various vegetables). The rationale behind such efforts has been to divert the energy naturally used to develop and maintain reproductive organs towards those organs needed and appreciated by customers.
• Vegetative production to different vegetative parts can be used to increase yield of root and vegetable crops like potato, rutabaga (swede) and carrot. In this case, the breeder's task is to maximize the partition towards one type of vegetative yield (e.g. tubers in the case of potato) while maintaining the minimum biomass of unused plant parts (e.g. the haulm of potato).

3.3.2 Selection for yield increase

It is perhaps ironic that harvestable yield is arguably the most important factor in all plant breeding schemes, and yet it is possibly the most difficult to select for. Increasing yield is complex and involves multiple modifications to the plant's morphology, physiology and biochemistry. Yield is, not surprisingly, quantitatively inherited (i.e. under the control of many genes, each with small phenotypic effect) and highly modifiable by a wide range of environmental factors. Evaluating accurately the genotypic response to differing environments and genotype–environment interactions are the major limiting factors to maximizing selection response in plant breeding. Despite advances in molecular marker selection (mainly quantitative trait loci, and more recently haplotypes and the development of molecular markers-based breeding values used in genomic selection efforts), increased yield is achieved by evaluating the phenotype of breeding lines under a wide range of rather atypical environments, sometimes called the target population of environments.

Yield potential will be one of few characters that is evaluated (or at least considered) at virtually all stages of plant breeding programmes. Plant breeding schemes begin with many (often many thousands) genotypes on which selection is carried out over years and seasons until the ‘best’ cultivar is identified, stabilized and increased. Usually the size of plots used for field evaluation trials increases with increasing rounds of selection. On completion of the selection process, surviving breeding lines must have produced phenotypically high yield in small unreplicated plots (often a single plant), and a variety of increasing plot sizes associated with advancing generations in the selection scheme. Towards the most advanced stages, a few breeding lines will be grown in farm-scale tests. Irrespective of the crop species involved, most plant breeders have been successful by selecting for yield per se of the plant part of importance, rather than by selecting for modified assimilate partition within a new crop cultivar, albeit that selection for the first resulted in a difference in the second. A number of different plant breeders have selected for yield components (i.e. attributes that contribute to total yield such as number of ears per plant, number of seeds per ear and seed weight in the case of cereals, or number of tubers per plant and tuber weight in potato) rather than for yield itself. In most of these cases, however, there has been little achieved in respect of increasing overall yield. The reasons behind this failure are complex, but one factor is related to the negative relationships between many yield components. Therefore positive selection for one component is counterbalanced by a negative response in another. One of the few examples of successful selection based on partitioning has been the efforts of the International Maize and Wheat Improvement Center (commonly called by its Spanish acronym CIMMYT for Centro Internacional de Mejoramiento de Maíz y Trigo) to improve drought tolerance in tropical corn, where the trait selection imposed is directly involved in increasing the partitioning of dry matter into kernels, resulting in corn breeding lines able to produce more kernels, and therefore more yield, under a severe stress at flowering.

It is the actual yield obtained by the farmer that is clearly an important criterion, and therefore factors such as ‘harvestability’ come to the fore. Mechanical harvesters now carry out many harvest operations. If a given genotype is not suited to mechanical harvest, its usefulness can be greatly limited. Therefore characters such as plant lodging, precocious sprouting, seed shattering or fruit drop are all factors that will reduce the harvestable yield.

In many instances the uniformity of morphological characters (seed/tuber/fruit – size, shape, colour, etc.) have a great effect on ‘useable yield’. Obviously, the end-user has a preference for a product which has a certain size, shape or colour, and any deviation (either genetic or environmental) from this appearance will reduce useable yield. Similarly, if a crop product is prone to develop defects when processed, or in storage, this will affect useable yield as the defects will not meet the required legislative standards, or customer expectations, and will need to be culled out. A secondary factor regarding defective products is related to the cost that is incurred in having the defective fruits/tubers/seeds removed.

Uniformity of yield is more difficult to evaluate than yield itself. Often it is not possible to evaluate product uniformity with any accuracy in small plot trails, and therefore many potentially highly uniform breeding lines may be wrongfully discarded in the early stages of selection. At the same time, it is important to consider that in cases like tomato and other horticultural crops, uniformity is of paramount importance to the vast majority of consumers purchasing them at retail points such as in supermarket outlets. Uniformity can also be important to processors or corporate customers such as restaurant chains.

Research by crop physiologists has provided a great deal of information regarding plant growth models for yield, and we have developed the ability to predict actual yield from a wide range of different physiological measurements. In the latter half of the last century, many plant breeders believed that input from crop physiologists and physiological biotype models of our crop plants would assist plant breeders to identify superior cultivars. Crop physiologists believed that photosynthetic or net assimilation rates could be used as selection tools to increase plant productivity and hence increase yield of crop plants. Some successes do exist, and an example is afforded by lupins. Physiologically-based research and modelling led to the proposal it would be beneficial to aid the development of the crop into northern Europe to breed for a particular crop architecture, using genotypes with a determinate growth habit. Suitable mutants were found, and indeed proved to be a marked improvement on the traditional lupin types in the new target environments. Despite the success in lupin, however, the impacts of physiological biotype models in plant breeding are rare. More progress has been observed with the use of crop models to support environmental classification approaches. For instance, work carried out in Australia at the University of Queensland has shown that the crop model APSIM is able to model the interaction of crops like wheat with its environment, and to establish environmental classifications able to reduce the relative effect of Genotype × Environment interactions and therefore to increase expected genetic gains and suggest breeding approaches.

3.4 Increasing end-use quality

Regardless of the yielding potential of a newly developed cultivar, success of a new cultivar will also be determined by the end-use quality of the saleable product. Demand for sale of year-round fruits and vegetables has resulted in food products being shipped greater and greater distances to arrive fresh almost on a daily basis. In addition, greater emphasis is now, and will continue, to be placed on storage of perishable agricultural products to make them available at times of shortage of local supplies or, as noted above, simply to make them available on a year-round basis.

There are two main types of end-use quality:

• Organoleptic – consumer acceptance or preference for taste, size, texture and colour. Although many people differ in their preference, there is often general agreement within taste panels as to preference towards certain levels of expression of these attributes, thus ‘liking’ some genotypes over others (even disregarding ‘off-tastes’). Similarly, the visual appearance of a product (particularly with fruit, vegetables and pulses) can have a large influence on which ones are preferred over others (Figure 3.2). An increasingly important factor for today's agricultural products is their ability to be stored for long periods without loss of quality. Hence many vegetable or fruit crops have a certain ‘harvest window’ where the majority of the crop is harvested. The end-user, however, demands that the product retains its quality characteristics over whatever storage period is necessary before it reaches the consumer.
• Chemical – where quality is determined by chemical analyses of the harvestable product. This is perhaps easily understandable in, say, oil crops, where the quality of the oil can be determined with great accuracy by determination of the oil fatty acid profile, or in the pharmaceutical (or farm-aceutical) industry where the quality of drugs is chemically determined. However, this is also true for fibre plants like cotton, as well as fodder crops where protein content and digestibility are determined by analytical methods. Increasingly, the ‘functionality’ (in other words, what positive effects it can have on health) of any human food is also of interest, and consumers are turning towards taking this into account in choice of purchases.

Figure 3.2 Visual appearance of saleable products is an important characteristic for breeders of fruits and vegetables.

Several crop species have been utilized for a range of different uses according to variation in their physical or chemical characteristics. Take, for example, a potato crop. The end-uses of potatoes are either as raw tubers to be cooked or through industrial processors, via retail purchasers. The needs and requirements of a potato will be different depending upon the use that the product will be put to. For example, potatoes can be boiled, mashed, baked, chipped, canned, dried or fried. Each cooking method (or use) will demand certain quality characteristics. Boiled potatoes need to remain relatively firm and not disintegrate on boiling. This trait is related to the ‘solids’ content of the tubers, the lower proportions of solids being associated with less disintegration. Conversely, potato chip (crisp) processors do not wish to purchase potatoes with low solids as these have a higher water content, which has to be turned into steam (and hence waste) in the frying process. ‘Chippers’ also require potatoes with low reducing sugar content, which ensures that the chips (crisps) produced will have a pale golden colour.

Many crop species therefore have several end-uses, and specific quality characteristics will be required in cultivars bred for these uses. Cultivars of bread wheat are required to have hard seed and high seed protein, while those of biscuit wheat should have soft seed and low protein content. Canola (edible rapeseed oil) needs a fatty acid composition low in erucic acid (22:1 fatty acid) and high in oleic acid (18:1), while industrial rapeseed cultivars need to have oil that is high in erucic acid content. The determination of most quality traits is genetic, although the growing conditions of soil type, climate, irrigation management and nitrogen application can all have large influences on the level at which these characters are expressed and hence on the final crop quality. Similarly, mechanical damage (particularly in vegetables and fruits) and crop disease can both greatly reduce the overall quality of the product irrespective of what the end use will be.

Determining ‘desirable quality’ characteristics can be difficult and requires close integration of the breeding team with end-users and processors. In some countries (e.g. the US) government authorities have laid down rules for quality standards. In these cases it is often easier to set standards for the acceptable level of quality required from breeding lines. Caution, however, needs to be exercized since it is unlikely that these standards will remain constant over time; indeed, they may change dramatically even before the new cultivar is even released.

3.4.1 Testing for end-use quality

If new cultivars are released that have special quality characters, there may be justification and economic merit in introducing this as a ‘specialty’ product, even if the overall yielding ability is not high. This would be justified if economic returns were sufficiently enhanced such as to overcome the deficiencies in total yield. It should also be noted that competitors and other breeders will, of course, be quick to notice the market opportunity that has been opened and will focus on rapidly superseding such introductions, perhaps overcoming any of the obvious defects present in the original cultivar (e.g. pink grapefruit).

It is usually difficult (and most often impossible) to simulate an exactly similar processing operation as carried out commercially on a very large number of breeding lines and at the speed required in a plant breeding programme. For example, in order to obtain the true quality potential of a new potato line with regards to French fry production (taking into account quality of end product, oil uptake, ease of processing, etc.), it would be necessary to produce several hundred tons of tubers and make French fries from them in a commercial processing plant. Similarly, in order to determine malting potential of barley for whisky (including all operations through to consumer acceptance) would require large quantities of grain and considerable time. Obviously both these would be impossible or too expensive in all but the very last stages of a breeding scheme. The basic features of any effective quality assessment in a plant breeding programme is that they should be quick, cheap and use very little material. These three criteria are important because:

• A plant breeding programme will involve screening many thousands of breeding lines each year or growing cycle.
• A plant breeder is often working against time. Many quality traits are assessed post-harvest and it is often important to make selection decisions quickly, before large-scale quality is determined. Moreover, many breeding programmes use off-season nurseries (i.e. in the southern hemisphere during the northern hemisphere's winter) to shorten the time needed to release new cultivars, which further constrains the time available to run quality tests on breeding lines before advancement decisions are made.
• In most stages of a plant breeding scheme there are only limited amounts of material available for testing. In addition, this is often the reproductive parts of the plants (seeds or tubers) that are used for testing, and so a further complication is that many of the quality tests available are destructive of the very parts of the plant that are required to be grown to provide the next generation for selection.

It is clear, therefore, that it is important to determine at what stage in the breeding scheme it is best to begin various quality screens. Obviously, quality evaluation should be included as early in the selection process as possible to avoid discarding some breeding lines carrying high-quality characteristics. However, often this decision must be based on the cost of the test, volume of material needed, accuracy of the test, and the importance of the quality trait for the success of any new cultivar.

Taste panels (groups of experienced (or sometimes inexperienced) people who assess the food quality of new products) are often used. It is, however, impossible to compare more than a modest number of types or breeding lines with a taste panel. These tests must also include some standard control lines, for comparative purposes, which further reduces the number of new lines that can be tested.

Most other quality assessments are, at best, estimates of what will happen in the ‘real world’. They tend to be mini-reconstructions of parts of a larger scale commercial process or operation. When carrying out these assessments, great care should be taken to ensure that the test follows as accurately as possible the actual process as it is carried out in industry. It is therefore essential that good links are set up with industry partners and that the breeding programme tries to integrate ideas from the processing industry into the breeding strategy as much as is feasible. This will also allow experiments to establish the levels of relationship (the correlations) between the ‘lab tests’ and the behaviour of the lines in commercial practice.

In other instances it is easier to record a related character than to record the trait itself. For example, in canola breeding it is desirable to have low glucosinolate content in seed meal. Glucosinolate breakdown products are highly toxic and can cause dietary problems when seed meal is fed to livestock. Determining glucosinolate content is an expensive, two-day process requiring rather sophisticated equipment such as gas chromatography. A much quicker and less expensive alternative is available. One of the breakdown products of glucosinolates is glucose. It is possible to obtain a good estimate of glucosinolate content simply by crushing a few seeds, adding water and estimating glucose concentration, using glucose-sensitive paper. Similarly, malt barley breeders evaluate and select breeding lines for seed nitrogen content and soluble carbohydrates, which are highly related to the malting quality traits of malt extract and oligosaccharides, but these latter two characteristics are difficult to assess with small quantities of seed. Finally, the quality objectives of forage/fodder breeding programmes are biological in character and would ideally be met by testing the growth of animals fed on the breeding lines, but these large-scale feed studies are virtually never carried out, for reasons of time and cost. It should always be remembered, however, that these quality determinations are, at best, predictions, and in many cases, only a crude estimate of the character that is actually to be selected for.

Plant breeders seek to predict quality, however complex, by relatively simple and cheap measurements or organoleptic tests. Often small-scale testing units based on the larger operation are used, but in many cases quality assessment is determined by the correlation or relationship between an easily measured character and the more difficult to assess trait. However, before a new cultivar is released into agriculture it is desirable that new genotypes be actually tested on a commercial scale process. So wheat should be milled in a commercial mill, barley should be malted and beer made, potatoes should be fried and sold in fast food stores, onions stored in commercial storage and fodder fed to livestock before the product is released.

It is only after several rounds of testing at the commercial level that a secondary factor can be accurately estimated – that is, the uniformity of quality. Uniformity of quality is as important as the actual quality character itself. A cultivar that produces excellent quality in one environment or year but unacceptable quality in others will have little merit in commercial production. Unfortunately, uniformity in quality (although one of the most important characters of a new cultivar) is difficult to assess within the restrictions of a feasible sized breeding scheme.

Overall, quality is what creates the demand for a product and what allows differentiation in the market, thus reducing the commoditization that often leads to low prices. It is the end-user who will mostly determine whether that crop will be grown in future years. It is a very naïve breeder who ignores the fact that consumer preference is continually changing and that the quality standards of today may be superseded by a new set of standards in the future. It is therefore imperative to organize a breeding scheme to be flexible and to try to cover as many potential aspects of yield, quality and other factors which may be important in the next two decades.

3.5 Increasing pest and disease resistance

A major limiting factor affecting both harvested yield and end-use quality of agricultural and horticultural crops is infection or infestation by plant pests and diseases. Breeding cultivars that are genetically resistant to pests and diseases is still a primary objective of plant breeding.

The development of resistant cultivars involves consideration of the genetic variability of the pest or disease as well as the variability in resistance (or sometimes tolerance) that exists within the crop species (or related species from which resistance can often be obtained). The durability of resistance of developed cultivars can be affected by the emergence of new races of the disease/pest that are able to overcome the resistance mechanism in the host plants. It has been argued that the environmental changes brought about by global warming will also affect the dynamics of plant interactions with pests and diseases, perhaps rendering crops more or less susceptible to these biotic stresses. Thus the longevity of disease resistance that can be achieved in a new cultivar is often as important as the extent, or degree, of resistance that the new cultivar actually exhibits. In many cases the source of alleles conferring disease resistance have been from genetic resources such as landraces, old cultivars or materials kept by small farmers, which highlights the importance that the conservation of genetic resources represents for plant breeders.

The major forms of disease and pests include: fungi (air- and soil-borne), bacteria, viruses, nematodes and insects. However, this is not an exhaustive list. Other damage can occur (e.g. bird damage and mammal foraging), although in many cases it is difficult to imagine how biological plant resistance can greatly reduce such damage (cashew trees being knocked over by hippopotami is difficult to breed against!).

It can be assumed that pests and diseases will cause damage, and almost all important diseases have been given attention by plant breeders. Crops differ greatly in the number of diseases that attack them and similarly in the exact damage that infection can cause. Small grain cereals are particularly susceptible to air-borne fungal epidemics; most Solanaceous crops are especially affected by viruses; while cotton is particularly affected by insect attack.

It is difficult to assign importance to any class of plant diseases. In some cases there are interactions between diverse species preying on plants. For instance, the damage created by an insect chewing on a growing corn kernel can pave the way for opportunistic fungi to colonize such damaged tissues, further increasing the potential economic losses incurred. In economic terms the soil- and air-borne fungi may be more important than all other diseases, so much so that many breeding textbooks consider breeding for disease resistance to actually be simply breeding for resistance to fungal disease. Because of the harsh tropical environments, namely both high temperatures and humidity, breeding tropical crops is, to a larger extent than breeding for temperate crops, fundamentally breeding to better withstand diseases and pests. This is, of course, an over-generalization, and there is no doubt that other disease types also have potentially significant impacts on breeding objectives and goals, depending on the crop being bred. Indeed, it is recognized that virus diseases and many soil infestations are problematic because there are few treatments (especially agrochemicals) that can be used to treat crops once plants become infected.

Any breeder trying to develop new cultivars with specific disease resistance must have knowledge of the particular disease or pest and its effect on the crop. One of the obvious and most important effects of almost all crop pests and diseases is reduction in yield. This is caused in four main ways:

• Destruction of leaf tissue and hence reducing plant photosynthetic capacity or efficiency (e.g. many rusts, mildew and blight).
• Stunting plants by metabolic disturbance, nutrient drain or root damage (e.g. many viruses, aphids or nematodes).
• Reducing plant stands by killing whole plants and leaving gaps in the crop which cannot be compensated for by increased productivity of neighbours (e.g. vascular wilts, soil-borne fungi and boring insects).
• Killing parts of plants (e.g. boring or feeding insects).

Killing plant tissue or causing reduced plant vigour can reduce yields per se, although reduced yield can result from other factors like increased weed infestation through reduced crop competition.

Other impacts of plant pests and diseases relate to damage to the end-use product of the crop. These infestations are often initiated in the field but often become more apparent after harvest (e.g. cereal smuts, various rots and insect boring of fruits and tubers), but can also arise during postharvest life. Many pests/diseases also reduce the quality of harvested crops (e.g. insect damage in fruit or fungal blemishes in fruit or tubers). Some can even lead to the accumulation of potentially carcinogenic compounds like mycotoxins in grains.

The first task, which must often be carried out prior to screening for natural resistance to diseases, is to determine:

• Which diseases can affect the crop?
• What is the effect of these diseases, for example on yield or quality?
• From amongst the several diseases that can attack a given crop, which are the most relevant and damaging, and which are likely to become so?

Others who have been working with the crop in particular areas can often answer the first question. For example, if a relatively well established crop is to be bred (e.g. wheat in the Pacific Northwest of the US), there will already be a large body of data that have been collected regarding particular diseases and an indication of the frequency of disease attack.

The exact yield, quality or economic effect that different pests or diseases have on a crop can be used to partition the degree of effort that is exerted in breeding for resistance. Obviously, if a particular disease does not exist within the region there may be little point in devoting a large effort towards screening for natural resistance, unless this situation is predicted (e.g. due to climate change) to alter in coming years. Similarly, if a certain pathogen does not recognize your crop as a host, any attempt to increase resistance would be a waste of time and effort. In reality, the availability of a cheap and effective control measure will also decrease the priority a breeder assigns to tackling the resistance or tolerance to that particular disease or pest, unless there is an environmental priority involved.

The most common means to determine the effect of a disease is to grow a series of genotypes under conditions where disease is artificially managed. In most cases the simplest way that this is done is to grow plots where disease is chemically controlled next to others where disease is allowed to occur naturally (or indeed artificially infected to ensure high disease pressure). In the case of wheat and rust tolerance, differential genotypes carrying loci conferring resistance to specific rust races can be used to gain insight about the complex of rust races existing in a given growing region, and therefore help to predict which resistance loci are needed to withstand that rust population in that particular region.

For example, the effect on yield caused by infestation by cabbage seedpod weevil (Figure 3.3) on four Brassicacea species (Brassica napus, B. juncea, B. rapa and Sinapis alba) was examined in field trials in 1992 and 1993. Forty genotypes were grown in a pseudo-split-plot design where each entry was grown under three treatments: full weevil control with several insecticides, partial control with one insecticide, and no chemical control of the pest (Figure 3.4). The results differed between the four species investigated. However, without chemical control three of the four species showed yield reductions (some to a large degree). It is also obvious that Sinapis alba has more insect resistance (or tolerance) than the other species, and indeed offered breeders a source of resistance through intergeneric hybridization (see later). Additional data regarding cost of chemical application, and so on, can then be used in coordination with these data to estimate the actual economic effect of this pest on Brassica crop production.

Figure 3.3 Cabbage seedpod weevil larvae damage of canola seeds.

Figure 3.4 Seed yield (t ha⁻¹) from four Brassicaceae species as affected by late-season insect infestation when grown with full insect control, partial insect control and no insect control.

A major difficulty in carrying out effective disease impact trials is to remove variation in as many other factors that may interact with those under study as possible. For example, if the effect of a particular air-borne fungus is to be studied, then attempts must be made to ensure that other yield-reducing factors (e.g. other air-borne fungi or other pests and diseases) are kept under control in the trial.

3.6 Types of plant resistance

It has been claimed that for each gene in the host that controls resistance there is a gene in the pathogen that determines whether the pathogen will be avirulent (unable to overcome the resistance and hence unable to infect or injure the host) or virulent (able to infect or injure the host). This gene-for-gene hypothesis, first postulated by H.H. Flor over half a century ago, has been likened to a set of locks and keys. A simple example of this lock and key situation is shown in Table 3.1. In the first example, the host plant genotype has no resistance genes, so any pest genotype will be able to infect the host plant irrespective of the presence or absence of virulence alleles. In the second example, the host plant has one (or two) dominant alleles for resistance to pest A strain (i.e. A_bb), and as the pest genotype has no virulence genes, the plant is resistant to the disease. In the third example, the host plant again has one (or two) dominant resistance alleles against the A strain of pest, but now the pest genotype is homozygous recessive (i.e. two copies) of the virulence gene (a′a′) and therefore unlocks (or can overcome) the resistance gene (A) in the host plant, and the plant is susceptible to the disease. In the last three examples the host plant has one or more copies of the dominant resistance alleles to both pest A and B strains, (i.e. A_B_). When the pest genotype is homozygous for the recessive virulent alleles a′a′ but has no b′ virulence alleles (i.e. a′a′B′B′) the plant is resistant to the disease, as the pest opened (or overcame) the A resistance gene, but could not open the B resistance gene. Similarly, when the pest genotype is homozygous for the recessive virulent alleles b′b′ but has no a′ virulence alleles (i.e. A′A′b′b′) the plant is also resistant to the disease, in this case because the pest opened (or overcame) the B resistance gene, but could not open the A resistance gene. In the last example, the pest genotype is homozygous recessive for both the a′a′ and b′b′ virulence alleles (i.e. a′a′b′b′) and can open (or overcome) both the A and B resistance genes in the host, and hence the host plant is susceptible to infection by the disease.

Table 3.1 Possible phenotypic plant responses (i.e. resistant to disease or susceptible to disease) in various combinations of dominant alleles conferring single gene plant resistance (capital letters A or B represent resistance genes), and recessive alleles conferring susceptibility (a or b) and the ‘matching’ alleles in the pest where a′ or b′ confer virulence and A′ and B′ give avirulence.

Plant genotype	Pest genotype	Plant response
aabb	Any virulence gene	Susceptible
A_bb	No virulence gene	Resistant
A_bb	a′a′B′B′	Susceptible
A_B_	a′a′B′B′	Resistant
A_B_	A′a′b′b′	Resistant
A_B_	a′a′b′b′	Susceptible

However, the situation is far from being this simple. Resistance to pests or diseases can be the result of either qualitative (single gene) or quantitative (multiple gene) determination. Resistance that is controlled by a single gene will result in distinct classes of resistance (usually resistant or susceptible) and are referred to as specific or vertical resistance. Resistance that is controlled by many genes will show a continually variable degree of resistance and is referred to as non-specific, field, general or horizontal resistance. Throughout this text the terms used will be vertical or horizontal resistance.

Vertical resistance is associated with the ability of single genes to control specific races of a disease or pest. The individual alleles of a major gene can be readily identified and transferred from one genotype to another. In many cases the source of the single gene resistance is derived from a wild or related species, and backcrossing is the most common method to introduce the allele into an elite commercial background. Segregation of single genes can be predicted with a good degree of reliability, and the selection of resistant genotypes can be relatively simply achieved by infection tests with specific pathogen races.

The primary disadvantage of vertical disease resistance is that new races of the pathogen are quite likely to arise that will be able to completely overcome the resistance. These new races may, in fact, have existed at a low level within the population of the pathogen before the resistance was even incorporated into the new cultivar or that cultivar was grown in agriculture. Thus, of course, the ‘resistance’ can be overcome relatively quickly. In addition, introduction of vertical resistance will increase the selective advantage of any mutant that arises in the pathogen population which can overcome the resistance. And as only a single mutation is required, the pathogen population may be many millions in size, so such a mutant will arise! New races of pathogen have overcome vertical resistance to air-borne diseases particularly quickly. Other cases, for example the single gene (H₁) in potato which gives vertical resistance to potato cyst nematode (Globodera rostochiensis), have proved very durable, probably as a result of the much lower degree of mobility of the earth-dwelling nematode pest.

One technique used by plant breeders is to pyramid single gene resistance where there are a number of qualitative genes available. This technique was attempted in potato for late blight (Phytophtora infestans) using a series of single resistance genes (R genes) derived from the wild potato species Solanum demissum. To date, nine R genes have been identified, and up to six of these combined into a single potato clone. However, the late blight pathogen was able to overcome the pyramiding of R genes quickly and the technique was not successful. Pyramiding single gene resistance to diseases and pests, with the use of molecular markers, which avoids the need to have suitable virulent pathotypes to screen for multiple resistance genes, has recently kindled interest.

Horizontal resistance is determined by many alleles acting collectively, with each allele only having a small contribution to overall resistance. Because of the multiplicity of genes involved, horizontal resistance tends to be far more durable than vertical resistance. The advantage of horizontal resistance is in its ability to control a wide spectrum of races, and new races of the pathogen have difficulty overcoming the alleles at all loci controlling the resistance. The main disadvantage of horizontal resistance is that it is often difficult to transfer from parent to offspring. The probability of transferring all the resistant alleles from a resistant parent to a susceptible one is generally very low. Breeding for horizontal resistance therefore tends to be a cyclic operation with the aim of increasing the frequency of desirable resistant genes.

3.7 Mechanisms for disease resistance

Two main disease resistance mechanisms exist. These are:

• resistance due to lack or reduction of infection;
• resistance due to lack or reduction of subsequent growth or spread after initial infection.

By far the most numerous examples of inhibition of infection in crop plants are related to hypersensitivity. Infection of the host plant causes a rapid localized reaction at the infection site. Host plant cells surrounding the infection point die, and hence the pathogen is effectively isolated from the live plant tissue and cannot spread further into the host plant. Hypersensitivity is usually associated with a necrotic flecking at the infection site, and the host plant is totally immune to the pathogen as a result. Plant resistance through hypersensitivity is controlled by single genes and hence can usually be easily incorporated into breeding lines. In cases of high levels of disease infection, cell death in the host plant can cause a significant reduction in the plant's photosynthetic area and, in extreme cases, plant death through lethal necrosis.

Other examples of disease infection inhibitors are less numerous and are usually associated with physical or morphological barriers. For example, the resistance to cabbage seedpod weevil found in yellow mustard (Sinapis alba) has been attributed to the very hairy surface of its pods and other parts, a feature not appreciated by the weevils, which are deterred from laying their eggs. Similarly, leaf wax mutants of cabbage can deter insect feeding, and tightly wrapped corn husks can prevent insect pests from feeding on the developing seed.

Growth inhibition after infection is caused by the host plant restricting the development of a pathogen after initial infection. The pathogen is not able to reproduce in a resistant host plant as rapidly after infecting compared with a susceptible host. For example, Russian wheat aphids feeding on susceptible wheat plants inject toxins into leaves, causing the leaves to fold. Adult Russian wheat aphids lay eggs in the folded leaves and the developing larvae gain protection from within the folds. Resistance genes have been identified that do not deter the adult Russian wheat aphids from feeding or injecting toxins into the leaves. However, the toxins do not cause the leaves of resistant wheat to fold, and hence there is greater mortality of developing Russian wheat aphid larvae, and reduced populations of the pest. Resistance to lack of spread of disease after infection can result from antibiosis, where the resistance reduces survival, growth, development or reproduction of the pathogens or insects feeding on the plant, or by antixenosis, where the resistant host plant has reduced preference or acceptance to the pest, usually insects. Resistance due to growth inhibition can be controlled by either qualitative or quantitative genes.

A complication in screening and determining plant disease resistance is related to tolerance. Tolerance is the ability of a genotype to be infected by a disease and yet not have a marked reduction in productivity as a result. Therefore, despite plants showing disease symptoms (e.g. fungal lesions or insect damage), the plant compensates for the infection or damage. Tolerance to disease has been related to plant vigour, which may be associated with other physiological stresses. For example, genotypic tolerance in potato to infection by potato cyst nematode, late blight, early blight (Alternaria) and wilt (Verticillium) are all highly correlated to drought stress or salinity tolerance.

One other factor needs to be considered in relation to disease resistance, and that is escape. This is where a genotype (although not having any resistance genes) is not affected by a disease because the infective agent of the disease is not present during the growth period of the genotype. Disease escape is most often related to maturity or other growth parameters of the plant and phenology of the pest. For example, potato cultivars that initiate tubers and mature early are unlikely to be affected by potato late blight (Phytophthora infestans) as the plants are mature before the disease normally reaches epidemic levels. The scope to use escape as a disease tolerance approach is rather limited because the life cycle of a crop is often constrained by the environment it is produced under, and also because of the strong association existing between early maturity and diminished yields, as the period of time to build up dry matter into the harvestable organ is reduced.

3.8 Testing plant resistance

In order to select for plant resistance to disease and pests, it is necessary to have a well-established testing scheme, one that truly mimics the disease or pest effects as they exist in an agricultural crop. If a plant's resistance to a pest or pathogen cannot be reliably measured, it will not be possible to screen germplasm for differential resistance levels; nor will it be possible to select resistant lines from amongst segregating populations.

Methods used for assessing disease and pest resistance in plant breeding are extremely varied but may be conveniently grouped into three categories.

• Plants can be artificially infected in a greenhouse or laboratory. This can be especially effective in screening for vertical resistance (single gene resistance) where an all-or-nothing reaction is expected. For example, a simple resistance or susceptible rating to pathogens of the air-borne fungi is commonly recorded on seedlings in the greenhouse or on detached leaves in the laboratory. Resistance screening to viruses is often carried out under greenhouse conditions where plants are ‘hand-infected’ with virus and the plant response noted. Similarly, resistance to potato cyst nematode (both qualitative and quantitative resistance) can be effectively screened in a greenhouse by growing test plants in soil with high cyst counts. These methods in general demand rather precise pathological control but are usually quick, accurate and give clear results. If greenhouse or laboratory testing is to be used, it is essential that the test results relate to actual resistance under field conditions. For example, seedling resistance to powdery mildew in barley is not always correlated with adult plant resistance observed under field conditions. The simplest method to authenticate small-scale testing is to carry out direct comparisons with field trials as an initial part of establishing the testing regime.
• In vitro testing and screening has been used, where the diseases that infect plant tissue are a result of toxins produced by the pathogens. These toxins can be extracted and in vitro plantlets, or plant tissue cultures, can be subjected to the toxin. As with testing in a greenhouse (above) it must be clearly shown that the in vitro plant tissue reaction to disease toxin is indeed related to whole plant resistance. It is never sufficient to observe phenotypic variation of in vitro material and to assume that this variation is useful in vivo. In vitro evaluation can be particularly effective if there are other reasons to propagate genotypes in vitro, for example, if embryo rescue is necessary (as in some interspecific crosses), if whole plants are being regenerated from single cells (protoplast fusion or transformation), or if initial plant propagation is carried out in vitro to avoid disease (e.g. with potato).
• Field testing, using natural infection, artificial infection, or commonly a combination of natural and artificial infection, is widely carried out. The object is usually to ensure that the initial infection rates are not limiting so that those estimates of genotypic resistance levels are more reliable (rather than simply a result of being escapes due to lack of infection). In the field there can be no precise control of the pathogen in terms of race composition or level of infection. Artificial infection may be achieved by inoculating seed or planting infecting material before planting the test plants, by inter-planting ‘spreader rows’ of plants that are highly susceptible to the disease, by spraying or otherwise infecting the crop with the disease, or by artificial infection of the soil with nematode or fungi. Uneven inoculation or infection is almost always a problem, especially with some of the soil pathogens. It is essential, therefore, that these trials use adequate experimental designs and in many cases suitably high levels of replication.

In conclusion, breeding for disease or pest resistance is no different (in many ways) to breeding and selecting for other traits. The steps that must be taken in a breeding scheme include:

• Develop a means to evaluate germplasm and breeding lines. In many cases success will be directly related to how effective the screening methods are at detecting differences in resistance levels. If it is not possible to differentiate consistently and accurately the level of disease or pest present, it will not be possible to identify sources of plant resistance or to screen for resistance within segregating progeny.
• Evaluate germplasm and breeding lines to identify sources of plant resistance. In the first instance, evaluation of the most adapted lines should be carried out. If no resistance is identified, then more primitive or wild genotypes need to be screened.
• Examine, if possible, the mechanism of resistance to determine the mode of resistance being exploited (e.g. avoiding infection, limiting spread, non-preference and antibiosis).
• Determine the mode of inheritance (i.e. qualitative or quantitative) of any resistance detected. The mode of inheritance can have a large influence on the method of introducing the resistance into the commercially acceptable gene pool (e.g. a single gene would perhaps be best handled by a back-crossing method).
• Introgress source of resistance into a new cultivar. Despite the importance of disease and pest resistance in plant breeding, it should always be remembered that a new cultivar will be unlikely to succeed simply because of disease resistance – new cultivars will also need to have acceptable levels of expression for the other important traits.

3.9 Conclusions

A house builder would not build a house without an architect first providing a plan, nor would an automobile producer build an automobile without having some form of test model. So also a plant breeder will not produce a successful cultivar development programme without suitable breeding objectives. This will involve:

• Examining the whole production and use system from farmer, through processor, to final product user. Determine the demands or preferences of each group in the production chain and take these into account in the selection scheme. Remember that there may be conflicts in the preferred requirements from different parts of this chain.
• Examine what is currently known about the crop. How is this end product produced at present? What types of cultivars presently predominate? What are the advantageous characters of these cultivars, and what are their defects? Is there any alternative type of cultivar that might offer more advantages to farmers and/or end-users?
• Examine how the operation of correcting present deficiencies can most effectively be addressed while always remembering that it is necessary to maintain at least the same level of acceptability for most other traits.

In order to set appropriate breeding objectives, the breeder needs to consider incorporating: yield potential, disease and pest resistance, end-use quality, and even the influence of potential political factors/decisions. Having taken these into account, it will be possible to design a successful plant breeding programme.

Think questions

1. Explain the difference between vertical and horizontal disease resistance and outline the advantages or disadvantages of each form of resistance as it relates to cultivar development.
2. Outline the major features involved in selecting for end-use quality, and indicate any particular problems that breeding for improved quality might cause.
3. When breeding new cultivars it is often necessary to try to predict events that may occur in the future. Briefly outline four factors that may influence cultivar breeding and hence need to be considered in setting the breeding objectives of a cultivar development programme.
4. In plant breeding, two main disease resistance mechanisms exist, inhibition of infection and inhibition of growth after infection. Explain each of these mechanisms.
5. Choose any agricultural/horticultural crop (e.g. wheat, barley, potato, apple, hops, etc.) and outline a set of breeding objectives to be used to develop new cultivars. Indicate potential markets for the new cultivars.
6. Explain, using examples as necessary, the meaning of the terms plant tolerance and plant escape in relation to pest and disease resistance and plant breeding.
7. Four loci affecting powdery mildew disease have been identified, at which single, dominant, disease-resistance alleles (coded, A, B, C and D) each offer complete immunity to a specific race of powdery mildew (with alleles a, b, c and d each showing susceptibility). Virulence genes have also been identified in the pest (A′, a′, B′, b′, C′, c′, and D′, d′). Given the information below, indicate whether each genotype would be resistant or susceptible to the disease.

   Plant genotype	Mildew genotype	Plant response
   AAbbCCdd	A′a′B′B′c′C′d′d′
   AaBbCcDd	A′a′B′b′C′c′D′d′
   aaBBccDD	A′A′b′b′C′c′d′d′
   Aabbccdd	A′A′B′B′C′C′D′D′

8. You have been offered a job as Senior Plant Breeder with the ‘Dryeye Onion Company’ in southern Idaho, United States. Your first task in this new position is to set breeding objectives for onion cultivar development over the next 12 years. Outline the main points to be considered when setting your breeding objectives; indicate what questions you would like answered to enhance the breeding objectives you will set. What might be the main sources of information that you would use to arrive at your response?