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Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation R DePauw, Agriculture and AgriFood Canada, Swift Current, SK, Canada L O’Brien, The University of Sydney, Narrabri, NSW, Australia; Solheimar Pty Ltd, Narrabri, NSW, Australia ã 2016 Elsevier Ltd. All rights reserved.
Topic Highlights
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Common hexaploid wheat and durum wheat have evolved from diploid grasses. Several key mutations resulted in polyploid wheat evolving a genetic system conferring diploidization and domestication. The observed wheat plant is a phenotype that is determined by its genetic composition (genotype), environment, and interaction of genotype and environment. New wheat cultivars respond to the challenges and limitations of abiotic and biotic stresses of the target environment and specifications for end-use suitability. Development of a new wheat cultivar is based on assembling genetic variability to meet all of the objectives and use of breeding methods and selection strategies to identify that genotype that has the maximum concentration of desirable genes. Genetic gain for a trait per unit of time is governed by selection intensity, selection accuracy, genetic variance, and years per plant breeding cycle. Emerging and enabling technologies enable earlier and more accurate characterization of the genotype, and selection can be practiced on the individual seed or plant.
Learning Objective
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To achieve an understanding of the origin of wheat, genetic variation, and strategies to assemble genes to increase their value for cultivation and use as field-ready cultivars.
Origin of Wheat There are two known main species of wheat grown and consumed globally: common hexaploid wheat (Triticum aestivum L.) used for the production of breads, noodles, cakes, and pastries and durum wheat (Triticum turgidum L. subsp. turgidum conv. durum) used primarily for the production of pasta, couscous, and bulgur. Both occur as natural interspecific hybrids (https://www.ksu.edu/wgrc/Taxonomy/taxintro.html). The progenitors of wheat (e.g., Triticum monococcum L. with three subspecies (one wild and two cultivated), Aegilops speltoides Tausch, and Aegilops tauschii Cosson) are diploid grasses, having seven pairs of chromosomes (2n ¼ 14). The natural chromosome complement or genome of each grass is unique, which supplies the grass its species attributes. Through many natural hybridization events, possibly over thousands of years in the West Asian region, a range of natural
Reference Module in Food Sciences
polyploids developed. The best known of these are durum wheat and common hexaploid wheat. Durum wheat is a tetraploid (4n ¼ 28), which originated from the natural hybridization of several diploid grasses, Triticum monococcum L. and T. urartu Tumanian ex Gandilyan (A genome) with Aegilops speltoides and possibly other extinct or extant Sitopsis species (B genome), giving it a genomic constitution of AABB. Hexaploid wheat (6n ¼ 42), resulted from a natural hybridization event between Triticum turgidum ssp. dicoccoides (AABB) and Aegilops tauschii (DD). Hexaploid wheat has a genomic constitution of AABBDD. Wheat evolved a genetic system conferring diploidization based on genes known as ph (pairing homologous) mutants that facilitates pairing of the chromosomes at mitosis and meiosis in a homologous fashion, rather than across the genomes, thus preventing multivalent chromosome formation with deleterious intergenomic exchange. The recognition of a naturally occurring line deficient in the pairing homologous gene allows wheat chromosomes to pair across the genomes at both meiosis and mitosis. This means that genetic recombination can occur across the genomes, rather than between chromosomes within a genome. This ability to have wheat chromosomes pair either within or across its genomes facilitates the movement of genes between wheat and its near and distant relatives, making wheat relatives a very valuable source of genetic variation for pest and disease resistance, grain quality, and abiotic stress tolerances.
The Earliest Plant Breeders The earliest wheat breeders were undoubtedly man’s forebears, the hunter-gatherers. Most primitive wheats contain a gene for brittle rachis, where the main branch of the flower fragments at each spikelet when mature resulting in the spikelets falling to the ground. Thus, harvesting would entail picking up spikelets from the ground. A naturally occurring mutant variant for a nonbrittle rachis keeps the head intact. The ease with which this type could be harvested would have resulted in its selection as the preferred type by early hunter-gatherers. Major and minor mutations selected by humans were the free-threshing feature of the lemma, palea, and glumes separating easily from the seed or caryopsis. Prior to the free-threshing attribute, humans burned the chaff off of the grain or ground it off.
Working at the Phenotype Level Just like the hunter-gatherer, today’s wheat breeder has to work with the phenotype or what we see when we look at the plant.
http://dx.doi.org/10.1016/B978-0-08-100596-5.00216-X
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BREEDING OF GRAINS | Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
The phenotype is influenced by both the genetic constitution of the plant and the environment in which it is grown, plus the manifestation of the interaction between the genotype and its environment or the genotype environment (G E) interaction. This can be expressed as follows: Phenotype ¼ Genotype þ Environment þ G E As long as the breeder has to work with the phenotype, the design and implementation of all plant breeding is based around this simple but fundamental equation. It is clear from this statement that all three factors can influence the phenotype. Critically, for breeding to be effective, an understanding of how all components interact on the phenotype is fundamental to success. Phenotypes in which the environmental and G E components prevail will, by definition, alter in their expression when the environment changes. This will result in differing performance of a genotype from location to location and from year to year, resulting in the absence of genetic progress. On the other hand, phenotypes where the genotype component prevails and where the influence of the environment and G E components are minimized will result in a consistent performance across locations and years. Under this scenario, genetic advance is made, resulting in the identification of the genetically superior wheat cultivars that get released as new cultivars.
Understanding the Environment and the Setting of Breeding Objectives A thorough knowledge of the target environment is fundamental, as it is the environment that determines breeding objectives. In its entirety, the environment consists of the soils, climate, and the biological environment in which the plant has to live. The breeder also has other environmental or managementrelated dimensions to consider such as the financial and physical resources available to the breeding program, access to supporting scientific disciplines and enabling technologies, and the grain quality demanded by the major markets to which grain may be sold.
The Environment
production environment can be managed using agronomic approaches and further ameliorated with genetic variability that exists for most of the aforementioned aspects.
Climate The amount of rainfall the wheat crop receives and the timing of the rainfall events over the growing season impact plant growth via the obvious extremes of waterlogging or drought. Rainfall and soil fertility are two of the major factors determining grain yield and quality. Even transient periods of either event can have dramatic impacts on plant growth and thus on grain yield and quality. Temperature has a regulating influence on plant growth. Extremes such as high temperatures cause heat stress and drought, with downsides on yield and quality. Cold temperatures during winter slow down growth or lead to soil freezing and the need for breeders to incorporate winter hardiness in most of the major winter wheat-growing areas of the world. Transient periods of low temperature to below 0 C during critical stages of plant growth, such as from terminal spikelet formation to flowering, can cause severe yield losses as a result of frost damage. In most areas of the world, the practice is to breed for frost avoidance, by delaying flowering to a time of more acceptable frost risk. This commonly means that flowering is delayed, so that grain filling has to take place under conditions of increasing temperature and decreasing availability of water. While at high-latitude wheat production areas, the ripening period occurs during decreasing temperature and reduced evapotranspiration. The occurrence of rainfall events prior to harvest determines that preharvest sprouting resistance based on seed dormancy is important to prevent the seeds from germinating prior to the grain being harvested so as to avoid downgrading in grain quality. Wind increases transpiration from plants, so in dry areas, this places crops under risk of increased moisture stress (drought at its severest). In combination with high temperatures during and after flowering, the grain-fill period experiences transient periods of moisture stresses. Breeders need to select and evaluate their materials under similar conditions to which they will be grown in order to produce varieties that can tolerate such conditions. Wind also demands that ripe crops can stand and ripen without lodging and/or shedding their grain prior to harvest.
Soils The soil provides the plant with its base for growing and its water and nutrients. Soil structure affects water penetration and holding ability. High-clay content soils generally have superior water-holding capacity compared with sandy-clay loams or deep sands. Factors such as pH, with its effect on plant growth and on nutrient availability, and factors toxic to plant growth such as free aluminum at low pH, high levels of available boron in ex-marine soils, unavailability of essential nutrients such as zinc at high pH, and unavailability of minor nutrients such as copper under waterlogging conditions all can have dramatic impacts on plant growth and, if not understood, can reduce genetic gain by appearing to be uncontrollable G E interactions. However, when properly understood, the
Biological Component The interaction between soils and climate provides the conditions for organisms, both favorable and destructive to plant growth, to prosper. Favorable soil conditions that include microorganisms such as vesicular arbuscular mycorrhizae are important for healthy plant growth. The availability of moisture and nutrients is affected by what happens in the rhizosphere. This can also result in conditions where fungi, bacteria, viruses, and nematodes pathogenic to wheat plants can flourish. A wide range of fungi can infect wheat roots and their crowns, causing major yield losses. These include a range of Fusarium species, common root rot, Rhizoctonia root rot, a
BREEDING OF GRAINS | Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
number of viruses, and plant nematodes. It is the environmental conditions in conjunction with a susceptible host plant that predisposes the plant to attack. An example is snow mold, where it is the amount and period of snow cover that determines the extent and severity of disease development. Above the ground, it is again the interaction of all the climatic components, in conjunction with susceptible host plants, that determines which plant diseases and pests will prosper, and the range is vast. The major foliar fungal pathogens are the rusts (stem rust caused by Puccinia graminis Pers.:Pers. f. sp. tritici Eriks. and E. Henn., leaf rust caused by Puccinia triticina Eriks., and stripe rust caused by Puccinia striiformis f. sp. tritici), the septorias (septoria tritici caused by Mycosphaerella graminicola (Fuckel) J. Schro¨t. in Cohn (anamorph Septoria tritici Roberge in Desmaz.)), and glume blotch caused by Phaeosphaeria nodorum (E. Mu¨ller) Hedjaroude (anamorph Stagonospora nodorum (Berk.) Castellani & E.G. Germano), powdery mildew caused by Blumeria graminis (DC.) E.O. Speer f.sp. tritici E´m. Marchal (syn. Erysiphe graminis DC. F.sp. tritici E´m. Marchal), and yellow (tan) spot caused by Pyrenophora tritici-repentis (Died.) Drechs (anamorph Drechslera tritici-repentis (Died.) Shoemaker). Each of these has unique sets of environmental conditions for development, mostly governed by the length of the dew period on the leaves for spores to germinate and then in the cases of the septorias and yellow spot rain drops for splash dispersal of spores to adjacent plants and new leaves of existing plants. Various pathogens infect the kernels and produce mycotoxins and cause yield loss such as Fusarium species, common bunt caused by Tilletia species results in yield loss and loss of market value due to offensive odors or primarily yield loss such as loose smut (Ustilago tritici (Pers.) Rostr.), and others such as pink smudge caused by Pyrenophora tritici-repentis (Died.) Drechs. and anamorph Drechslera tritici-repentis (Died.) Shoemaker result in discolored kernels that discolor flour or semolina. A range of viruses can also cause yield loss. Some require vectors for transfer between plants, such as barley yellow dwarf virus that is dispersed by aphids and wheat streak mosaic virus that is spread by the wheat curl mite.
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A variety of insect pests attack wheat plants causing yield and quality losses. Examples are wheat stem sawfly (Cephus cinctus Norton), which lays its larvae into wheat stems; the larvae feed on the parenchyma tissue of the stem and girdling of the stem above ground level prior to maturity, weakening the stem and leading to straw breakage and lodging. Orange wheat blossom midge (Sitodiplosis mosellana (Ge´hin)) feeds on the developing seed resulting in loss of grain yield and grain functionality. Cereal leaf beetle eats the epidermal tissues from leaves, thereby reducing photosynthetic area and causing yield loss. The cinch bug and some aphids feed on developing grains, releasing proteolytic enzymes into the grain and causing deterioration of the gluten proteins responsible for dough quality. Sunn pest (Eurygaster integriceps Puton) damages wheat by feeding on leaves, stems, and grains. During feeding, they
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inject enzymes that cause a breakdown of gluten manifested in physical dough properties and baking performance. Sunn pest occurs in parts of North Africa, Central Asia, and West Asia. This brief overview of the major pests and diseases of wheat is intended to highlight that they are many and varied and they cause major losses in both yield and quality. As a result, most wheat breeding programs direct a major share of their resources to breeding for resistance. In order to effectively prioritize which resistances should be addressed by a breeding solution, breeders must have a comprehensive understanding of the environment of their target breeding area. For the full range of pests and diseases of wheat, biological variability exists. For the breeder, this means that one source of germplasm is rarely effective against all races, strains, or pathotypes of the pest or disease. Thus, effective breeding requires ongoing access to resistant germplasm, reliable screening tests, and molecular technologies linked to the resistant genes.
Grain Quality Major areas of world wheat production, especially those with production that is exported, are often located at considerable distances from where the grain will be consumed, resulting in the development of sophisticated grain handling and transport systems as part of grain trading. Increasingly, grain is traded on the basis of rigid quality specifications of dryness, cleanliness, protein content, and enzymes, for example, alpha-amylase. More discriminating markets have even tighter specifications relating to dough properties and end-product quality. It is this diversity of requirements that breeders must satisfy when setting quality objectives for their breeding programs. The environment of the target breeding and production region influences the quality of wheat that can be grown in any area. The production environment has a major impact on grain protein content, one of the major specifications upon which grain is traded internationally. For example, dryer regions tend to be lower yielding and favor the production of higher-protein, stronger, more extensible gluten wheat. To set effective market-based quality objectives, the breeder needs a reliable supply of market intelligence that has been interpreted into what is achievable by breeding. In most of the large wheat-producing and wheat-exporting countries, breeding programs obtain this information from grain traders, processors such as millers and bakers, and/or grower-supported marketing and research agencies.
Assembling and Creating Genetic Variability Genetic variability is the cornerstone of wheat breeding. Variability can be sourced from hexaploid wheat or its near and distant relatives. Traits can be introgressed into hexaploid wheat from these sources using conventional hybridization techniques. For interspecific or intergeneric hybridizations, the use of chromosome doubling may be required to get a balanced chromosome complement for successful cell division of the embryo and the resultant plant.
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BREEDING OF GRAINS | Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
With the advent of molecular biology, traditional interspecific, intergeneric, and plant-type barriers to gene transfer have been removed. By isolating the gene for a particular trait and inserting it into a new host by a range of techniques (e.g., biolistic bombardment or Agrobacterium transfer), the gene becomes part of the host DNA, replicating itself at cell division and expressing itself in plant development. The development of such genetic engineering techniques considerably enhances the range of genes available to the modern plant breeder. But to date, there have been no commercial deployments of cultivars that have genes inserted into wheat from outside of the grass tribe. Gene-editing technologies are developing to alter a gene and thereby express new forms of the trait such as resistance to a pathogen or seed storage proteins. Traditionally, breeders have gone to other breeding programs or to major germplasm collections to source their genetic variability. Utilizing genetic variability is always done in a targeted manner, with the breeder seeking new genes for an agronomic, disease resistance, quality, or yield-related trait. Transfer of the new gene is usually performed by conventional hybridization, followed by cycles of selection until the new gene is fixed in its new background. To facilitate transfer of new genes, knowledge of the inheritance of the trait and the ability to select for it in its new background are essential.
Role of Germplasm Collections for New Trait Discovery Large collections of wheat are kept in international collections (USDA-ARS Beltsville http://www.ars-grin.gov/, Vavilov Collection http://www.vir.nw.ru/, CIMMYT http://www.cimmyt.org, Svalbard Global Seed Vault http://www.regjeringen.no/en/dep/ lmd/campain/svalbard-global-seed-vault.html?id¼462220, etc.) and are major sources of variability utilized by breeders. In some instances, passbook data are held on entries in these collections. However, often when a new disease or pest problem arises, the breeder has to systematically screen the collection for sources of resistance. As this is done, data are fed back to the collections, thereby creating some passbook data for future use. However, in the case of a new disease or change in an existing disease, the breeder usually has to go back to the collection and commence the screening process all over again, as it is only with virulence in a pathogen that new resistance in a host plant can be identified. Until we understand the genetic basis of what actually confers resistance at the DNA level, this cyclic process of screening germplasm collections will continue as new problems emerge. The Seeds of Discovery (http://seedsofdiscovery.org/seed/about/) project strives to generate knowledge of the phenotype and genotype of germplasm accessions and enhance their utility to breeders by developing bridging germplasm that carries exotic gene variants in elite adapted backgrounds.
Hybridization Systems Wheat is a self-pollinating crop and so lends itself to hybridization by a range of methods. Breeders design their crossing programs so that the resulting populations produced will segregate for all the traits desired in the new varieties. Breeders
choose one of the parents to become the female of the cross and affect this by removing the anthers from all florets of the ear. Hybridization is completed a few hours to a few days later by transferring pollen from the plant designated as the male. This is done using a range of methods, with the transfer being completed using tweezers to shake the pollen from individual anthers onto the receptive stigma or by cutting back florets of the designated male plant so that anthers are exposed. The dry air causes them to dehisce, and the male plant is then shaken or twirled over the stigma, thereby effecting pollination. Other means for hybridizing wheat include the use of cytoplasmic male sterility–nuclear fertility restoration mechanisms or the use of chemical hybridization agents. Both of these systems still rely on making one of the parents the nominal female, while pollen is transferred from another parent chosen as the male of the cross. Both of these mechanisms, while useful for crossing, are better deployed for making hybrid wheat where the advantages of heterosis (hybrid vigor) can be captured.
Crossing Strategies Choice of crossing strategy depends on the range of traits available in the parents and those desired in the progeny of a cross. If all the desired attributes can be obtained from just using two parents, A and B, then the straight cross A/B strategy can be deployed. If one of the parents (A) has more desirable traits than the other, then to increase the frequency of the desired genes from A, a further cross to that parent can be made, making for an A/B//A crossing strategy. When all the desired traits cannot be assembled from a straight crossing strategy and three parents are needed (A, B, and C) to get all of them in the progeny, then a three-way crossing system can be used, such as A/B//C. When a variety has most of the traits desired but has had a resistance breakdown or can be enhanced by the addition of a new resistance or trait, then the new gene(s) can be rapidly introgressed using the backcross crossing strategy. If the new resistance gene is dominantly inherited and all that is wanted from this donor parent is that gene, the original variety becomes the recurrent parent and repeated cycles of crossing between the recurrent parent and the F1 generation can be made until the desired percentage of the recurrent parent is recovered. The gene frequency of the recurrent parent increases according to the formula (1 (1/2)n) where n is the number of crosses to the recurrent parent. The straight cross F1 contains 50% of genes from each parent. The first backcross to the recurrent parent increases the frequency of recurrent parent genes to 75%. Subsequent backcrosses increase the gene frequency to 87, 93, 96, and 98% for the second to fifth backcrosses, respectively, and so on. When deploying the backcross breeding strategy for recessively inherited genes, it is necessary to allow the first cross to go to the F2 generation and then screen for the presence of the new gene or trait, prior to making the next backcross. At each backcross cycle, it is necessary to go to the F2 and conduct screening for the new trait prior to crossing to the recurrent parent.
BREEDING OF GRAINS | Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
Selection and Evaluation Systems and Breeding Methods Factors Influencing the Sequence of Trait Selection and Choice of Breeding Method Modern wheat breeding programs have an extensive array of breeding objectives that must be addressed. Many are simply inherited, but many of the economically important traits like yield and quality are complexly inherited and subject to the influence of G E interaction, meaning that selection and evaluation need to occur over locations and years. This dictates that modern programs need to be large in scale handling thousands of different genotypes in each breeding cycle. This demands significant investment in high-quality land for field evaluations for yield experiments, disease resistances, etc. (see Figure 1 of contra season generation) and the mechanization needed at each phase of the breeding process, namely, seed preparation, field testing (Figure 2), and laboratory- and glasshouse-based screening tests (Figure 3). The number of gene-pair differences and inbreeding has a geometric impact on the frequency of desirable alleles, which in turn impacts the size of population required to have a
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chance occurrence of the desirable type and the optimum generation to initiate selection. The geometric changes that occur with increasing number of loci and decreasing frequency of genotypes with the desirable alleles upon inbreeding provide a rationale for early generation selection. There are many different ways in which breeders can manage material flow in breeding programs each with pros and cons. Choice of method depends on many factors, including cost of variety development, which makes the shortening of the breeding cycle a high priority, resources available to the breeding program, and the availability of effective selection methodologies for the target traits. Genetic gain for any individual trait is governed by the equation Rt ¼ irVa =y where Rt is genetic gain over time; i is the selection intensity and can be increased to a limit; r is the selection accuracy and can be improved by more precise measurements, replication in space and time, reduction of errors, correction for environmental factors, and genomic tools such as perfect molecular markers for traits; Va is the genetic variance and can be increased by incorporation of beneficial alleles and minimal introduction of undesirable alleles; and y is the years per plant breeding cycle and can be reduced by growing more than one generation per year and use of doubled haploid technology.
Pedigree method This is the method of choice where disease resistances are the priority traits that must be incorporated into new varieties. The pedigree method allows for simply inherited, often single-gene traits to be selected and fixed through repeated cycles (2–4) of selection until homozygosity is achieved. To shorten varietal development, this method is often combined with the use of two or more field-grown generations per year.
Modified pedigree Figure 1 Aerial view of a contra season nursery in New Zealand used by SPARC, AAFC Canada.
Figure 2 Fleet of combines to harvest early generation yield trials. (courtesy SPARC, AAFC; photograph taken by D. Schott).
In this process, the basic pedigree cycle is followed, but with the addition of a round of yield evaluation and/or quality testing as early as possible, F3 or F4, in order to remove lowyielding and poor-quality families from the breeding program and use multiple generations per year (Figure 4).
Figure 3 Sampling plant tissue to collect DNA to perform marker assisted breeding (courtesy SPARC, AAFC; photograph taken by C. Barlow).
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BREEDING OF GRAINS | Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
Cross: Choose parents which combine all the traits Single seed descent
Pedigree with two generations per year Winter cycle F1, F3, F5 inbred, select, multiply contra season
Summer cycle
F1 self to F2 grow out in selection nursery
F2
Single seed decent F2 selections to F3 and F4 in greenhouse
F4 , F6 diseases, agronomics, quality
F4 plant to F5 head row diseases F7 and F8 diseases, agronomics, quality
Doubled haploid DH1 confined DH2 unconfined diseases DH3 select multiply contra season DH4 and DH5 diseases, agronomics quality
F6 multiplication contra season F7 and F8 diseases, agronomics, quality
Registration trials and breeder seed production F9 or DH 1 year
1st year initiate Pre-breeder seed
F10 or DH 2 years
2nd year Pre-breeder seed
F11 or DH 3 years
3rd year Breeder seed
6 to 7 years
6 to 7 years
6 to 7 years
Figure 4 Schematic steps to develop and produce breeder seed of a new cultivar with a comparison of pedigree, single seed descent, and doubled haploid breeding methods.
Single-seed descent This method allows for up to four generations per year using growth chambers and glasshouse conditions (Figure 4). A population of 200 or more seeds is planted, and only single tiller plants are produced by manipulating the watering and nutrition regime to speed up the growth of plants. At harvest, one seed from each plant is taken and planted again for the next generation. This process is repeated until plants are advanced to between the F4 and F6 generations. Seed is then increased and planted in the field in observation rows or yield plots. The advantages of single-seed descent are speed combined with cycles of recombination, giving the possibility of desirable recombinants being produced.
Doubled haploid or dihaploid development In this method, F1 seeds are produced by conventional crossing techniques using the two parents that between them have all the traits desired in the new variety (Figure 4). Doubled haploids can be produced from microspore culture, but the wheat–maize method is the most widely used system. In the wheat–maize system, F1 seed is made by hybridization, the seeds are planted, and their flowers are emasculated and pollinated with maize pollen. A haploid (a plant with single chromosome of each of the 21 hexaploid wheat pairs) starts to develop. This haploid embryo is rescued and allowed to grow into a haploid plantlet, which is then treated with a chromosome-doubling agent such as colchicine, nitrous oxide, or caffeine to produce a diploid plant. Seeds from these plants are instantly homozygous for all genes, thus imparting the major advantage of this breeding system, that
is, it takes material to true breeding status in less than 1 year, thus considerably shortening the breeding cycle.
Early-, Mid-, and Late-Generation Selection In the early generations, the focus is on selection of traits of highest heritability. These are usually agronomic attributes and disease resistances. In the mid and later generations, irrespective of what breeding method a breeder chooses to use, selection is about validating performance of breeding lines, demonstrating their merit for potential release as new varieties. However, some breeding programs select simultaneously for qualitatively and quantitatively inherited traits simultaneously starting in the F4 generation. This usually involves the use of replicated, multisite, multiyear yield and quality evaluations to gather the data needed to support the decision to bulk up seed for release. Most breeding programs consider that 3 years of such evaluations are needed to demonstrate the reliability of any potential variety.
Emerging and Enabling Technologies Marker-assisted breeding (MAB) is being used as a tool with markers linked to genes controlling high-value traits. Preferably, the marker resides within the target gene but closely linked markers on each side of the target gene are almost as effective. MAB has been applied to a range of fungal pathogens and two insect pests, end-use suitability traits, and phenological and morphological traits. MAB can be used to target individual traits as they are introgressed by backcrossing or straight
BREEDING OF GRAINS | Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
crossing into adapted backgrounds and/or used to retain a high proportion of the adapted parent background when adequate marker coverage across the genome is available to the breeder. One of the greatest impacts of applying markers is in the earliest stages of segregation, for example, top cross F1 or F2 to shift gene frequencies. MAB is being effectively combined with doubled haploid technology where haploids are screened and only those having the desired marker profile are doubled. Randhawa et al. provided a short list of some of the traits that breeders can target using MAB, but as the technology continues to develop, this list continually expands. Exciting technologies have emerged that characterize germplasm at the DNA sequence level. Exome sequencing of diverse collections of hexaploid and tetraploid wheat coupled with transcriptome profiling of well-characterized genetic stocks is being used to identify genes controlling traits. There has been a massive number of single-nucleotide polymorphism (SNP) markers discovered, which enables high-density genetic maps to be constructed for gene cloning and opportunities for whole-genome selection strategies to be formulated. Chip technology is developing rapidly, and SNP chips are available that generate genome-wide data and information on target traits that are outpacing data handling capability to analyze the information being generated. Genomic selection (GS) is a tool to enable selection on a single plant or seed, selection in unobserved environments, maintenance of genetic diversity, and evaluation of larger populations. The value of GS is that it shifts the basis of selection from the phenotype level to the gene level. Hence, it is extremely attractive to breeders for traits that are difficult and time-consuming to screen for and are highly modulated in their expression by the environment. Furthermore, it allows for selection to be practiced in unobserved environments. Gene editing has the potential to alter an existing gene to express a different biochemical compound that makes it resistant to a fungal pathogen. Another example of gene editing would be to alter a gene encoding a protein subunit to alter its rheological properties. Use of the genetically modified organism (GMO) approach is in its infancy in wheat breeding. These technologies remove species and genus barriers to gene transfer, so they considerably expand the range of genes available to the wheat breeder. Currently, the processes of inserting a gene into wheat breeding material means that the position the gene inserts itself into the host DNA is random, so success rate of gene expression is low. As gene-splicing techniques improve, the success rate can be expected to improve. Backcrossing is the preferred method for rapidly transferring GMO traits into adapted wheat backgrounds. Varietal fingerprinting is another useful breeding aid where both the DNA complement of a recurrent parent and a DNAbased marker for the gene to be introgressed in a backcross breeding program can be tracked at the DNA level. The use of these combined strategies will shorten the breeding cycle by earlier recovery of sufficient contribution of the recurrent parent DNA at an earlier stage in the backcross process. This technology will also be increasingly used to identify breeding programs for varietal identification at the point of sale for integrity of marketing and trading grain and for intellectual property issues associated with the protection of plant breeders’ rights.
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Wheat Breeding as Part of Supply Chain Management Modern wheat breeding is just one part of a sophisticated supply chain, whereby all parts of the chain are important in adding value to a major food source. All members in the supply chain can have a major impact on the overall product as it moves through the chain, so the more these components can be integrated, the more efficient the process and the less downside on the quality of the end product. This demands good information flow up and down the supply chain. With the wheat breeder sitting at the end of the supply chain most distant from the consumer, the effectiveness of information flow and the quality of that information are critical for effective wheat breeding.
Exercises for Revision
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What is the meaning of a phenotype and a genotype? For a wheat cultivar to have value for cultivation in a specific region, what are some of the agronomic traits and response to diseases and insects it should have? How can genetic variation be generated in a plant breeding program upon which selection can be practiced? What are the similarities and differences among the breeding methods: pedigree, single-seed descent, and doubled haploidy? What is genetic gain for a trait and what factors determine genetic gain? What is marker-assisted breeding?
Exercises for Readers to Explore the Topic Further
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What is the evolutionary origin of hexaploid and durum wheat? What are some of the health benefits of consuming whole wheat products? For a cultivar to have value for use to make a specific consumer product, what are some of the specifications for milling, protein quantity and quality, and enzymes such as alpha-amylase? What are three diseases of wheat and how can they be controlled? What is genomic selection and how could it be applied to cultivar development?
See also: Agronomy of Grain Growing: Wheat, Agronomy (00200); The Cereal Species; Grain Nutrition; Wheat-based foods; Wheat and Barley Processing; Marketing and grading; Harvest, Storage & Transport; WHEAT|Genetics.
Further Reading Allard RW (1999) Principles of Plant Breeding, 2nd edn. New York: Wiley. Baenziger PS and DePauw RM (2009) Cultivar development in wheat – Procedures and strategies. In: Carver B (ed.) Wheat: Science and Trade, pp. 273–308. Ames, IA: Wiley-Blackwell Publishing.
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BREEDING OF GRAINS | Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
Bonjean AP and Angus WJ (eds.) (2001) The World Wheat Book: A History of Wheat Breeding Paris: Lavoisier. Carver B (ed.) (2009) Wheat: Science and Trade. Ames, IA: Wiley-Blackwell Publishing. Heffner EL, Sorrells ME, and Jannink JL (2009) Genomic selection for crop improvement. Crop. Sci. 49: 1–12. http://dx.doi.org/10.2135/ cropsci2008.08.0512. Heyne EG (ed.) (1997) Wheat and Wheat Improvement, 2nd edn. Madison, WI: American Society of Agronomy. Lupton FGH (ed.) (1996) Wheat Breeding. London: Chapman and Hall. O’Brien L and Blakeney AB (eds.) (1998) An Introduction to the Australian Grains Industry. North Melbourne, Australia: Royal Australian Chemical Institute. Randhawa HS, Asif M, Pozniak C, et al. (2013) Application of molecular markers to wheat breeding in Canada. Plant Breed. 132: 458–471. Sears ER (1977) An induced mutant with homoeologous pairing in common wheat. Can. J. Genet. Cytol. 19: 585–593.
Relevant Websites http://www.agronomycanada.com – Canadian Society of Agronomy. http://www.ahdb.org.uk/ – Agriculture and Horticulture Development Board UK. http://www.ars-grin.gov – National Plant Germplasm System, USDA – ARS. http://www.ars.usda.gov/main/site_main.htm?modecode¼36-40-05-00 – Cereal Disease Lab (Rust Lab – USDA – ARS). http://www.cimmyt.org – CIMMYT. http://www.cgiar.org – Consultative Group on International Agricultural Research.
http://www.fao.org – Food and Agriculture Organization of the United Nations. http://www.fao.org/statistics/en/ – Food and Agriculture Organization of the United Nations. http://www.fera.defra.gov.uk/ – The Food and Environment Research Agency. http://www.grainscanada.gc.ca – Canadian Grain Commission. http://www.grdc.com.au – Grain Research and Development Corporation, Australia. http://www.icarda.cgiar.org/ – ICARDA. http://www.inspection.gc.ca – Canadian Food Inspection Agency for plant products for variety registration and PBR. https://www.ksu.edu/wgrc/Taxonomy/taxintro.html – Wheat Classification Tables Site. http://meteo.gc.ca/ – Environment Canada weather forecast by location worldwide. http://pgrc3.agr.gc.ca – Plant Gene Resources Canada. http://phytopath.ca/index.shtml – The Canadian Phytopathological Society. http://www.sas.com – Statistical Analysis Systems. http://www.scabusa.org – US Wheat and Barley Scab Initiative. http://seedsofdiscovery.org/seed/about/ – Seeds of Discovery. http://www.regjeringen.no/en/dep/lmd/campain/svalbard-global-seed-vault.html? id¼462220 – Svalbard Global Seed Vault. http://www.ars.usda.gov/main/site_main.htm?modecode¼36-40-05-00 – UK Cereal Disease Lab. http://www.usda.gov – US Dept of Agriculture. http://www.uswheat.org – US Wheat Associates. http://www.vir.nw.ru/ – Vavilov Research Institute of Plant Industry. http://westerngrains.com/ – Western Grains Research Foundation, Canada. http://wheat.pw.usda.gov – Graingenes.
Topic Highlights
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Common hexaploid wheat and durum wheat have evolved from diploid grasses. Several key mutations resulted in polyploid wheat evolving a genetic system conferring diploidization and domestication. The observed wheat plant is a phenotype that is determined by its genetic composition (genotype), environment, and interaction of genotype and environment. New wheat cultivars respond to the challenges and limitations of abiotic and biotic stresses of the target environment and specifications for end-use suitability. Development of a new wheat cultivar is based on assembling genetic variability to meet all of the objectives and use of breeding methods and selection strategies to identify that genotype that has the maximum concentration of desirable genes. Genetic gain for a trait per unit of time is governed by selection intensity, selection accuracy, genetic variance, and years per plant breeding cycle. Emerging and enabling technologies enable earlier and more accurate characterization of the genotype, and selection can be practiced on the individual seed or plant.
Learning Objective
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To achieve an understanding of the origin of wheat, genetic variation, and strategies to assemble genes to increase their value for cultivation and use as field-ready cultivars.
Origin of Wheat There are two known main species of wheat grown and consumed globally: common hexaploid wheat (Triticum aestivum L.) used for the production of breads, noodles, cakes, and pastries and durum wheat (Triticum turgidum L. subsp. turgidum conv. durum) used primarily for the production of pasta, couscous, and bulgur. Both occur as natural interspecific hybrids (https://www.ksu.edu/wgrc/Taxonomy/taxintro.html). The progenitors of wheat (e.g., Triticum monococcum L. with three subspecies (one wild and two cultivated), Aegilops speltoides Tausch, and Aegilops tauschii Cosson) are diploid grasses, having seven pairs of chromosomes (2n ¼ 14). The natural chromosome complement or genome of each grass is unique, which supplies the grass its species attributes. Through many natural hybridization events, possibly over thousands of years in the West Asian region, a range of natural
Reference Module in Food Sciences
polyploids developed. The best known of these are durum wheat and common hexaploid wheat. Durum wheat is a tetraploid (4n ¼ 28), which originated from the natural hybridization of several diploid grasses, Triticum monococcum L. and T. urartu Tumanian ex Gandilyan (A genome) with Aegilops speltoides and possibly other extinct or extant Sitopsis species (B genome), giving it a genomic constitution of AABB. Hexaploid wheat (6n ¼ 42), resulted from a natural hybridization event between Triticum turgidum ssp. dicoccoides (AABB) and Aegilops tauschii (DD). Hexaploid wheat has a genomic constitution of AABBDD. Wheat evolved a genetic system conferring diploidization based on genes known as ph (pairing homologous) mutants that facilitates pairing of the chromosomes at mitosis and meiosis in a homologous fashion, rather than across the genomes, thus preventing multivalent chromosome formation with deleterious intergenomic exchange. The recognition of a naturally occurring line deficient in the pairing homologous gene allows wheat chromosomes to pair across the genomes at both meiosis and mitosis. This means that genetic recombination can occur across the genomes, rather than between chromosomes within a genome. This ability to have wheat chromosomes pair either within or across its genomes facilitates the movement of genes between wheat and its near and distant relatives, making wheat relatives a very valuable source of genetic variation for pest and disease resistance, grain quality, and abiotic stress tolerances.
The Earliest Plant Breeders The earliest wheat breeders were undoubtedly man’s forebears, the hunter-gatherers. Most primitive wheats contain a gene for brittle rachis, where the main branch of the flower fragments at each spikelet when mature resulting in the spikelets falling to the ground. Thus, harvesting would entail picking up spikelets from the ground. A naturally occurring mutant variant for a nonbrittle rachis keeps the head intact. The ease with which this type could be harvested would have resulted in its selection as the preferred type by early hunter-gatherers. Major and minor mutations selected by humans were the free-threshing feature of the lemma, palea, and glumes separating easily from the seed or caryopsis. Prior to the free-threshing attribute, humans burned the chaff off of the grain or ground it off.
Working at the Phenotype Level Just like the hunter-gatherer, today’s wheat breeder has to work with the phenotype or what we see when we look at the plant.
http://dx.doi.org/10.1016/B978-0-08-100596-5.00216-X
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BREEDING OF GRAINS | Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
The phenotype is influenced by both the genetic constitution of the plant and the environment in which it is grown, plus the manifestation of the interaction between the genotype and its environment or the genotype environment (G E) interaction. This can be expressed as follows: Phenotype ¼ Genotype þ Environment þ G E As long as the breeder has to work with the phenotype, the design and implementation of all plant breeding is based around this simple but fundamental equation. It is clear from this statement that all three factors can influence the phenotype. Critically, for breeding to be effective, an understanding of how all components interact on the phenotype is fundamental to success. Phenotypes in which the environmental and G E components prevail will, by definition, alter in their expression when the environment changes. This will result in differing performance of a genotype from location to location and from year to year, resulting in the absence of genetic progress. On the other hand, phenotypes where the genotype component prevails and where the influence of the environment and G E components are minimized will result in a consistent performance across locations and years. Under this scenario, genetic advance is made, resulting in the identification of the genetically superior wheat cultivars that get released as new cultivars.
Understanding the Environment and the Setting of Breeding Objectives A thorough knowledge of the target environment is fundamental, as it is the environment that determines breeding objectives. In its entirety, the environment consists of the soils, climate, and the biological environment in which the plant has to live. The breeder also has other environmental or managementrelated dimensions to consider such as the financial and physical resources available to the breeding program, access to supporting scientific disciplines and enabling technologies, and the grain quality demanded by the major markets to which grain may be sold.
The Environment
production environment can be managed using agronomic approaches and further ameliorated with genetic variability that exists for most of the aforementioned aspects.
Climate The amount of rainfall the wheat crop receives and the timing of the rainfall events over the growing season impact plant growth via the obvious extremes of waterlogging or drought. Rainfall and soil fertility are two of the major factors determining grain yield and quality. Even transient periods of either event can have dramatic impacts on plant growth and thus on grain yield and quality. Temperature has a regulating influence on plant growth. Extremes such as high temperatures cause heat stress and drought, with downsides on yield and quality. Cold temperatures during winter slow down growth or lead to soil freezing and the need for breeders to incorporate winter hardiness in most of the major winter wheat-growing areas of the world. Transient periods of low temperature to below 0 C during critical stages of plant growth, such as from terminal spikelet formation to flowering, can cause severe yield losses as a result of frost damage. In most areas of the world, the practice is to breed for frost avoidance, by delaying flowering to a time of more acceptable frost risk. This commonly means that flowering is delayed, so that grain filling has to take place under conditions of increasing temperature and decreasing availability of water. While at high-latitude wheat production areas, the ripening period occurs during decreasing temperature and reduced evapotranspiration. The occurrence of rainfall events prior to harvest determines that preharvest sprouting resistance based on seed dormancy is important to prevent the seeds from germinating prior to the grain being harvested so as to avoid downgrading in grain quality. Wind increases transpiration from plants, so in dry areas, this places crops under risk of increased moisture stress (drought at its severest). In combination with high temperatures during and after flowering, the grain-fill period experiences transient periods of moisture stresses. Breeders need to select and evaluate their materials under similar conditions to which they will be grown in order to produce varieties that can tolerate such conditions. Wind also demands that ripe crops can stand and ripen without lodging and/or shedding their grain prior to harvest.
Soils The soil provides the plant with its base for growing and its water and nutrients. Soil structure affects water penetration and holding ability. High-clay content soils generally have superior water-holding capacity compared with sandy-clay loams or deep sands. Factors such as pH, with its effect on plant growth and on nutrient availability, and factors toxic to plant growth such as free aluminum at low pH, high levels of available boron in ex-marine soils, unavailability of essential nutrients such as zinc at high pH, and unavailability of minor nutrients such as copper under waterlogging conditions all can have dramatic impacts on plant growth and, if not understood, can reduce genetic gain by appearing to be uncontrollable G E interactions. However, when properly understood, the
Biological Component The interaction between soils and climate provides the conditions for organisms, both favorable and destructive to plant growth, to prosper. Favorable soil conditions that include microorganisms such as vesicular arbuscular mycorrhizae are important for healthy plant growth. The availability of moisture and nutrients is affected by what happens in the rhizosphere. This can also result in conditions where fungi, bacteria, viruses, and nematodes pathogenic to wheat plants can flourish. A wide range of fungi can infect wheat roots and their crowns, causing major yield losses. These include a range of Fusarium species, common root rot, Rhizoctonia root rot, a
BREEDING OF GRAINS | Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
number of viruses, and plant nematodes. It is the environmental conditions in conjunction with a susceptible host plant that predisposes the plant to attack. An example is snow mold, where it is the amount and period of snow cover that determines the extent and severity of disease development. Above the ground, it is again the interaction of all the climatic components, in conjunction with susceptible host plants, that determines which plant diseases and pests will prosper, and the range is vast. The major foliar fungal pathogens are the rusts (stem rust caused by Puccinia graminis Pers.:Pers. f. sp. tritici Eriks. and E. Henn., leaf rust caused by Puccinia triticina Eriks., and stripe rust caused by Puccinia striiformis f. sp. tritici), the septorias (septoria tritici caused by Mycosphaerella graminicola (Fuckel) J. Schro¨t. in Cohn (anamorph Septoria tritici Roberge in Desmaz.)), and glume blotch caused by Phaeosphaeria nodorum (E. Mu¨ller) Hedjaroude (anamorph Stagonospora nodorum (Berk.) Castellani & E.G. Germano), powdery mildew caused by Blumeria graminis (DC.) E.O. Speer f.sp. tritici E´m. Marchal (syn. Erysiphe graminis DC. F.sp. tritici E´m. Marchal), and yellow (tan) spot caused by Pyrenophora tritici-repentis (Died.) Drechs (anamorph Drechslera tritici-repentis (Died.) Shoemaker). Each of these has unique sets of environmental conditions for development, mostly governed by the length of the dew period on the leaves for spores to germinate and then in the cases of the septorias and yellow spot rain drops for splash dispersal of spores to adjacent plants and new leaves of existing plants. Various pathogens infect the kernels and produce mycotoxins and cause yield loss such as Fusarium species, common bunt caused by Tilletia species results in yield loss and loss of market value due to offensive odors or primarily yield loss such as loose smut (Ustilago tritici (Pers.) Rostr.), and others such as pink smudge caused by Pyrenophora tritici-repentis (Died.) Drechs. and anamorph Drechslera tritici-repentis (Died.) Shoemaker result in discolored kernels that discolor flour or semolina. A range of viruses can also cause yield loss. Some require vectors for transfer between plants, such as barley yellow dwarf virus that is dispersed by aphids and wheat streak mosaic virus that is spread by the wheat curl mite.
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A variety of insect pests attack wheat plants causing yield and quality losses. Examples are wheat stem sawfly (Cephus cinctus Norton), which lays its larvae into wheat stems; the larvae feed on the parenchyma tissue of the stem and girdling of the stem above ground level prior to maturity, weakening the stem and leading to straw breakage and lodging. Orange wheat blossom midge (Sitodiplosis mosellana (Ge´hin)) feeds on the developing seed resulting in loss of grain yield and grain functionality. Cereal leaf beetle eats the epidermal tissues from leaves, thereby reducing photosynthetic area and causing yield loss. The cinch bug and some aphids feed on developing grains, releasing proteolytic enzymes into the grain and causing deterioration of the gluten proteins responsible for dough quality. Sunn pest (Eurygaster integriceps Puton) damages wheat by feeding on leaves, stems, and grains. During feeding, they
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inject enzymes that cause a breakdown of gluten manifested in physical dough properties and baking performance. Sunn pest occurs in parts of North Africa, Central Asia, and West Asia. This brief overview of the major pests and diseases of wheat is intended to highlight that they are many and varied and they cause major losses in both yield and quality. As a result, most wheat breeding programs direct a major share of their resources to breeding for resistance. In order to effectively prioritize which resistances should be addressed by a breeding solution, breeders must have a comprehensive understanding of the environment of their target breeding area. For the full range of pests and diseases of wheat, biological variability exists. For the breeder, this means that one source of germplasm is rarely effective against all races, strains, or pathotypes of the pest or disease. Thus, effective breeding requires ongoing access to resistant germplasm, reliable screening tests, and molecular technologies linked to the resistant genes.
Grain Quality Major areas of world wheat production, especially those with production that is exported, are often located at considerable distances from where the grain will be consumed, resulting in the development of sophisticated grain handling and transport systems as part of grain trading. Increasingly, grain is traded on the basis of rigid quality specifications of dryness, cleanliness, protein content, and enzymes, for example, alpha-amylase. More discriminating markets have even tighter specifications relating to dough properties and end-product quality. It is this diversity of requirements that breeders must satisfy when setting quality objectives for their breeding programs. The environment of the target breeding and production region influences the quality of wheat that can be grown in any area. The production environment has a major impact on grain protein content, one of the major specifications upon which grain is traded internationally. For example, dryer regions tend to be lower yielding and favor the production of higher-protein, stronger, more extensible gluten wheat. To set effective market-based quality objectives, the breeder needs a reliable supply of market intelligence that has been interpreted into what is achievable by breeding. In most of the large wheat-producing and wheat-exporting countries, breeding programs obtain this information from grain traders, processors such as millers and bakers, and/or grower-supported marketing and research agencies.
Assembling and Creating Genetic Variability Genetic variability is the cornerstone of wheat breeding. Variability can be sourced from hexaploid wheat or its near and distant relatives. Traits can be introgressed into hexaploid wheat from these sources using conventional hybridization techniques. For interspecific or intergeneric hybridizations, the use of chromosome doubling may be required to get a balanced chromosome complement for successful cell division of the embryo and the resultant plant.
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BREEDING OF GRAINS | Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
With the advent of molecular biology, traditional interspecific, intergeneric, and plant-type barriers to gene transfer have been removed. By isolating the gene for a particular trait and inserting it into a new host by a range of techniques (e.g., biolistic bombardment or Agrobacterium transfer), the gene becomes part of the host DNA, replicating itself at cell division and expressing itself in plant development. The development of such genetic engineering techniques considerably enhances the range of genes available to the modern plant breeder. But to date, there have been no commercial deployments of cultivars that have genes inserted into wheat from outside of the grass tribe. Gene-editing technologies are developing to alter a gene and thereby express new forms of the trait such as resistance to a pathogen or seed storage proteins. Traditionally, breeders have gone to other breeding programs or to major germplasm collections to source their genetic variability. Utilizing genetic variability is always done in a targeted manner, with the breeder seeking new genes for an agronomic, disease resistance, quality, or yield-related trait. Transfer of the new gene is usually performed by conventional hybridization, followed by cycles of selection until the new gene is fixed in its new background. To facilitate transfer of new genes, knowledge of the inheritance of the trait and the ability to select for it in its new background are essential.
Role of Germplasm Collections for New Trait Discovery Large collections of wheat are kept in international collections (USDA-ARS Beltsville http://www.ars-grin.gov/, Vavilov Collection http://www.vir.nw.ru/, CIMMYT http://www.cimmyt.org, Svalbard Global Seed Vault http://www.regjeringen.no/en/dep/ lmd/campain/svalbard-global-seed-vault.html?id¼462220, etc.) and are major sources of variability utilized by breeders. In some instances, passbook data are held on entries in these collections. However, often when a new disease or pest problem arises, the breeder has to systematically screen the collection for sources of resistance. As this is done, data are fed back to the collections, thereby creating some passbook data for future use. However, in the case of a new disease or change in an existing disease, the breeder usually has to go back to the collection and commence the screening process all over again, as it is only with virulence in a pathogen that new resistance in a host plant can be identified. Until we understand the genetic basis of what actually confers resistance at the DNA level, this cyclic process of screening germplasm collections will continue as new problems emerge. The Seeds of Discovery (http://seedsofdiscovery.org/seed/about/) project strives to generate knowledge of the phenotype and genotype of germplasm accessions and enhance their utility to breeders by developing bridging germplasm that carries exotic gene variants in elite adapted backgrounds.
Hybridization Systems Wheat is a self-pollinating crop and so lends itself to hybridization by a range of methods. Breeders design their crossing programs so that the resulting populations produced will segregate for all the traits desired in the new varieties. Breeders
choose one of the parents to become the female of the cross and affect this by removing the anthers from all florets of the ear. Hybridization is completed a few hours to a few days later by transferring pollen from the plant designated as the male. This is done using a range of methods, with the transfer being completed using tweezers to shake the pollen from individual anthers onto the receptive stigma or by cutting back florets of the designated male plant so that anthers are exposed. The dry air causes them to dehisce, and the male plant is then shaken or twirled over the stigma, thereby effecting pollination. Other means for hybridizing wheat include the use of cytoplasmic male sterility–nuclear fertility restoration mechanisms or the use of chemical hybridization agents. Both of these systems still rely on making one of the parents the nominal female, while pollen is transferred from another parent chosen as the male of the cross. Both of these mechanisms, while useful for crossing, are better deployed for making hybrid wheat where the advantages of heterosis (hybrid vigor) can be captured.
Crossing Strategies Choice of crossing strategy depends on the range of traits available in the parents and those desired in the progeny of a cross. If all the desired attributes can be obtained from just using two parents, A and B, then the straight cross A/B strategy can be deployed. If one of the parents (A) has more desirable traits than the other, then to increase the frequency of the desired genes from A, a further cross to that parent can be made, making for an A/B//A crossing strategy. When all the desired traits cannot be assembled from a straight crossing strategy and three parents are needed (A, B, and C) to get all of them in the progeny, then a three-way crossing system can be used, such as A/B//C. When a variety has most of the traits desired but has had a resistance breakdown or can be enhanced by the addition of a new resistance or trait, then the new gene(s) can be rapidly introgressed using the backcross crossing strategy. If the new resistance gene is dominantly inherited and all that is wanted from this donor parent is that gene, the original variety becomes the recurrent parent and repeated cycles of crossing between the recurrent parent and the F1 generation can be made until the desired percentage of the recurrent parent is recovered. The gene frequency of the recurrent parent increases according to the formula (1 (1/2)n) where n is the number of crosses to the recurrent parent. The straight cross F1 contains 50% of genes from each parent. The first backcross to the recurrent parent increases the frequency of recurrent parent genes to 75%. Subsequent backcrosses increase the gene frequency to 87, 93, 96, and 98% for the second to fifth backcrosses, respectively, and so on. When deploying the backcross breeding strategy for recessively inherited genes, it is necessary to allow the first cross to go to the F2 generation and then screen for the presence of the new gene or trait, prior to making the next backcross. At each backcross cycle, it is necessary to go to the F2 and conduct screening for the new trait prior to crossing to the recurrent parent.
BREEDING OF GRAINS | Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
Selection and Evaluation Systems and Breeding Methods Factors Influencing the Sequence of Trait Selection and Choice of Breeding Method Modern wheat breeding programs have an extensive array of breeding objectives that must be addressed. Many are simply inherited, but many of the economically important traits like yield and quality are complexly inherited and subject to the influence of G E interaction, meaning that selection and evaluation need to occur over locations and years. This dictates that modern programs need to be large in scale handling thousands of different genotypes in each breeding cycle. This demands significant investment in high-quality land for field evaluations for yield experiments, disease resistances, etc. (see Figure 1 of contra season generation) and the mechanization needed at each phase of the breeding process, namely, seed preparation, field testing (Figure 2), and laboratory- and glasshouse-based screening tests (Figure 3). The number of gene-pair differences and inbreeding has a geometric impact on the frequency of desirable alleles, which in turn impacts the size of population required to have a
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chance occurrence of the desirable type and the optimum generation to initiate selection. The geometric changes that occur with increasing number of loci and decreasing frequency of genotypes with the desirable alleles upon inbreeding provide a rationale for early generation selection. There are many different ways in which breeders can manage material flow in breeding programs each with pros and cons. Choice of method depends on many factors, including cost of variety development, which makes the shortening of the breeding cycle a high priority, resources available to the breeding program, and the availability of effective selection methodologies for the target traits. Genetic gain for any individual trait is governed by the equation Rt ¼ irVa =y where Rt is genetic gain over time; i is the selection intensity and can be increased to a limit; r is the selection accuracy and can be improved by more precise measurements, replication in space and time, reduction of errors, correction for environmental factors, and genomic tools such as perfect molecular markers for traits; Va is the genetic variance and can be increased by incorporation of beneficial alleles and minimal introduction of undesirable alleles; and y is the years per plant breeding cycle and can be reduced by growing more than one generation per year and use of doubled haploid technology.
Pedigree method This is the method of choice where disease resistances are the priority traits that must be incorporated into new varieties. The pedigree method allows for simply inherited, often single-gene traits to be selected and fixed through repeated cycles (2–4) of selection until homozygosity is achieved. To shorten varietal development, this method is often combined with the use of two or more field-grown generations per year.
Modified pedigree Figure 1 Aerial view of a contra season nursery in New Zealand used by SPARC, AAFC Canada.
Figure 2 Fleet of combines to harvest early generation yield trials. (courtesy SPARC, AAFC; photograph taken by D. Schott).
In this process, the basic pedigree cycle is followed, but with the addition of a round of yield evaluation and/or quality testing as early as possible, F3 or F4, in order to remove lowyielding and poor-quality families from the breeding program and use multiple generations per year (Figure 4).
Figure 3 Sampling plant tissue to collect DNA to perform marker assisted breeding (courtesy SPARC, AAFC; photograph taken by C. Barlow).
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BREEDING OF GRAINS | Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
Cross: Choose parents which combine all the traits Single seed descent
Pedigree with two generations per year Winter cycle F1, F3, F5 inbred, select, multiply contra season
Summer cycle
F1 self to F2 grow out in selection nursery
F2
Single seed decent F2 selections to F3 and F4 in greenhouse
F4 , F6 diseases, agronomics, quality
F4 plant to F5 head row diseases F7 and F8 diseases, agronomics, quality
Doubled haploid DH1 confined DH2 unconfined diseases DH3 select multiply contra season DH4 and DH5 diseases, agronomics quality
F6 multiplication contra season F7 and F8 diseases, agronomics, quality
Registration trials and breeder seed production F9 or DH 1 year
1st year initiate Pre-breeder seed
F10 or DH 2 years
2nd year Pre-breeder seed
F11 or DH 3 years
3rd year Breeder seed
6 to 7 years
6 to 7 years
6 to 7 years
Figure 4 Schematic steps to develop and produce breeder seed of a new cultivar with a comparison of pedigree, single seed descent, and doubled haploid breeding methods.
Single-seed descent This method allows for up to four generations per year using growth chambers and glasshouse conditions (Figure 4). A population of 200 or more seeds is planted, and only single tiller plants are produced by manipulating the watering and nutrition regime to speed up the growth of plants. At harvest, one seed from each plant is taken and planted again for the next generation. This process is repeated until plants are advanced to between the F4 and F6 generations. Seed is then increased and planted in the field in observation rows or yield plots. The advantages of single-seed descent are speed combined with cycles of recombination, giving the possibility of desirable recombinants being produced.
Doubled haploid or dihaploid development In this method, F1 seeds are produced by conventional crossing techniques using the two parents that between them have all the traits desired in the new variety (Figure 4). Doubled haploids can be produced from microspore culture, but the wheat–maize method is the most widely used system. In the wheat–maize system, F1 seed is made by hybridization, the seeds are planted, and their flowers are emasculated and pollinated with maize pollen. A haploid (a plant with single chromosome of each of the 21 hexaploid wheat pairs) starts to develop. This haploid embryo is rescued and allowed to grow into a haploid plantlet, which is then treated with a chromosome-doubling agent such as colchicine, nitrous oxide, or caffeine to produce a diploid plant. Seeds from these plants are instantly homozygous for all genes, thus imparting the major advantage of this breeding system, that
is, it takes material to true breeding status in less than 1 year, thus considerably shortening the breeding cycle.
Early-, Mid-, and Late-Generation Selection In the early generations, the focus is on selection of traits of highest heritability. These are usually agronomic attributes and disease resistances. In the mid and later generations, irrespective of what breeding method a breeder chooses to use, selection is about validating performance of breeding lines, demonstrating their merit for potential release as new varieties. However, some breeding programs select simultaneously for qualitatively and quantitatively inherited traits simultaneously starting in the F4 generation. This usually involves the use of replicated, multisite, multiyear yield and quality evaluations to gather the data needed to support the decision to bulk up seed for release. Most breeding programs consider that 3 years of such evaluations are needed to demonstrate the reliability of any potential variety.
Emerging and Enabling Technologies Marker-assisted breeding (MAB) is being used as a tool with markers linked to genes controlling high-value traits. Preferably, the marker resides within the target gene but closely linked markers on each side of the target gene are almost as effective. MAB has been applied to a range of fungal pathogens and two insect pests, end-use suitability traits, and phenological and morphological traits. MAB can be used to target individual traits as they are introgressed by backcrossing or straight
BREEDING OF GRAINS | Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
crossing into adapted backgrounds and/or used to retain a high proportion of the adapted parent background when adequate marker coverage across the genome is available to the breeder. One of the greatest impacts of applying markers is in the earliest stages of segregation, for example, top cross F1 or F2 to shift gene frequencies. MAB is being effectively combined with doubled haploid technology where haploids are screened and only those having the desired marker profile are doubled. Randhawa et al. provided a short list of some of the traits that breeders can target using MAB, but as the technology continues to develop, this list continually expands. Exciting technologies have emerged that characterize germplasm at the DNA sequence level. Exome sequencing of diverse collections of hexaploid and tetraploid wheat coupled with transcriptome profiling of well-characterized genetic stocks is being used to identify genes controlling traits. There has been a massive number of single-nucleotide polymorphism (SNP) markers discovered, which enables high-density genetic maps to be constructed for gene cloning and opportunities for whole-genome selection strategies to be formulated. Chip technology is developing rapidly, and SNP chips are available that generate genome-wide data and information on target traits that are outpacing data handling capability to analyze the information being generated. Genomic selection (GS) is a tool to enable selection on a single plant or seed, selection in unobserved environments, maintenance of genetic diversity, and evaluation of larger populations. The value of GS is that it shifts the basis of selection from the phenotype level to the gene level. Hence, it is extremely attractive to breeders for traits that are difficult and time-consuming to screen for and are highly modulated in their expression by the environment. Furthermore, it allows for selection to be practiced in unobserved environments. Gene editing has the potential to alter an existing gene to express a different biochemical compound that makes it resistant to a fungal pathogen. Another example of gene editing would be to alter a gene encoding a protein subunit to alter its rheological properties. Use of the genetically modified organism (GMO) approach is in its infancy in wheat breeding. These technologies remove species and genus barriers to gene transfer, so they considerably expand the range of genes available to the wheat breeder. Currently, the processes of inserting a gene into wheat breeding material means that the position the gene inserts itself into the host DNA is random, so success rate of gene expression is low. As gene-splicing techniques improve, the success rate can be expected to improve. Backcrossing is the preferred method for rapidly transferring GMO traits into adapted wheat backgrounds. Varietal fingerprinting is another useful breeding aid where both the DNA complement of a recurrent parent and a DNAbased marker for the gene to be introgressed in a backcross breeding program can be tracked at the DNA level. The use of these combined strategies will shorten the breeding cycle by earlier recovery of sufficient contribution of the recurrent parent DNA at an earlier stage in the backcross process. This technology will also be increasingly used to identify breeding programs for varietal identification at the point of sale for integrity of marketing and trading grain and for intellectual property issues associated with the protection of plant breeders’ rights.
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Wheat Breeding as Part of Supply Chain Management Modern wheat breeding is just one part of a sophisticated supply chain, whereby all parts of the chain are important in adding value to a major food source. All members in the supply chain can have a major impact on the overall product as it moves through the chain, so the more these components can be integrated, the more efficient the process and the less downside on the quality of the end product. This demands good information flow up and down the supply chain. With the wheat breeder sitting at the end of the supply chain most distant from the consumer, the effectiveness of information flow and the quality of that information are critical for effective wheat breeding.
Exercises for Revision
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What is the meaning of a phenotype and a genotype? For a wheat cultivar to have value for cultivation in a specific region, what are some of the agronomic traits and response to diseases and insects it should have? How can genetic variation be generated in a plant breeding program upon which selection can be practiced? What are the similarities and differences among the breeding methods: pedigree, single-seed descent, and doubled haploidy? What is genetic gain for a trait and what factors determine genetic gain? What is marker-assisted breeding?
Exercises for Readers to Explore the Topic Further
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What is the evolutionary origin of hexaploid and durum wheat? What are some of the health benefits of consuming whole wheat products? For a cultivar to have value for use to make a specific consumer product, what are some of the specifications for milling, protein quantity and quality, and enzymes such as alpha-amylase? What are three diseases of wheat and how can they be controlled? What is genomic selection and how could it be applied to cultivar development?
See also: Agronomy of Grain Growing: Wheat, Agronomy (00200); The Cereal Species; Grain Nutrition; Wheat-based foods; Wheat and Barley Processing; Marketing and grading; Harvest, Storage & Transport; WHEAT|Genetics.
Further Reading Allard RW (1999) Principles of Plant Breeding, 2nd edn. New York: Wiley. Baenziger PS and DePauw RM (2009) Cultivar development in wheat – Procedures and strategies. In: Carver B (ed.) Wheat: Science and Trade, pp. 273–308. Ames, IA: Wiley-Blackwell Publishing.
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BREEDING OF GRAINS | Wheat Breeding: Exploiting and Fixing Genetic Variation by Selection and Evaluation
Bonjean AP and Angus WJ (eds.) (2001) The World Wheat Book: A History of Wheat Breeding Paris: Lavoisier. Carver B (ed.) (2009) Wheat: Science and Trade. Ames, IA: Wiley-Blackwell Publishing. Heffner EL, Sorrells ME, and Jannink JL (2009) Genomic selection for crop improvement. Crop. Sci. 49: 1–12. http://dx.doi.org/10.2135/ cropsci2008.08.0512. Heyne EG (ed.) (1997) Wheat and Wheat Improvement, 2nd edn. Madison, WI: American Society of Agronomy. Lupton FGH (ed.) (1996) Wheat Breeding. London: Chapman and Hall. O’Brien L and Blakeney AB (eds.) (1998) An Introduction to the Australian Grains Industry. North Melbourne, Australia: Royal Australian Chemical Institute. Randhawa HS, Asif M, Pozniak C, et al. (2013) Application of molecular markers to wheat breeding in Canada. Plant Breed. 132: 458–471. Sears ER (1977) An induced mutant with homoeologous pairing in common wheat. Can. J. Genet. Cytol. 19: 585–593.
Relevant Websites http://www.agronomycanada.com – Canadian Society of Agronomy. http://www.ahdb.org.uk/ – Agriculture and Horticulture Development Board UK. http://www.ars-grin.gov – National Plant Germplasm System, USDA – ARS. http://www.ars.usda.gov/main/site_main.htm?modecode¼36-40-05-00 – Cereal Disease Lab (Rust Lab – USDA – ARS). http://www.cimmyt.org – CIMMYT. http://www.cgiar.org – Consultative Group on International Agricultural Research.
http://www.fao.org – Food and Agriculture Organization of the United Nations. http://www.fao.org/statistics/en/ – Food and Agriculture Organization of the United Nations. http://www.fera.defra.gov.uk/ – The Food and Environment Research Agency. http://www.grainscanada.gc.ca – Canadian Grain Commission. http://www.grdc.com.au – Grain Research and Development Corporation, Australia. http://www.icarda.cgiar.org/ – ICARDA. http://www.inspection.gc.ca – Canadian Food Inspection Agency for plant products for variety registration and PBR. https://www.ksu.edu/wgrc/Taxonomy/taxintro.html – Wheat Classification Tables Site. http://meteo.gc.ca/ – Environment Canada weather forecast by location worldwide. http://pgrc3.agr.gc.ca – Plant Gene Resources Canada. http://phytopath.ca/index.shtml – The Canadian Phytopathological Society. http://www.sas.com – Statistical Analysis Systems. http://www.scabusa.org – US Wheat and Barley Scab Initiative. http://seedsofdiscovery.org/seed/about/ – Seeds of Discovery. http://www.regjeringen.no/en/dep/lmd/campain/svalbard-global-seed-vault.html? id¼462220 – Svalbard Global Seed Vault. http://www.ars.usda.gov/main/site_main.htm?modecode¼36-40-05-00 – UK Cereal Disease Lab. http://www.usda.gov – US Dept of Agriculture. http://www.uswheat.org – US Wheat Associates. http://www.vir.nw.ru/ – Vavilov Research Institute of Plant Industry. http://westerngrains.com/ – Western Grains Research Foundation, Canada. http://wheat.pw.usda.gov – Graingenes.