Module 3: Overview & Historical Perspective of Plant Breeding PDF

DAVAO ORIENTAL STATE UNIVERSITY INSTRUCTIONAL MATERIAL In AGRI 12 (Plant and Animal Improvement) Prepared by: RENEE ROSE Y. SAYLAN Agriculture Department ...

DAVAO ORIENTAL STATE UNIVERSITY INSTRUCTIONAL MATERIAL In AGRI 12 (Plant and Animal Improvement) Prepared by: RENEE ROSE Y. SAYLAN Agriculture Department  MODULE 3 Lesson 1 OVERVIEW & HISTORICAL PERSPECTIVE OF PLANT BREEDING The origin of cultivated plants is basically a process of displacement of wild characteristics and an enrichment of suitable traits—a process that began before thousands of years, for example, for wheat, barley, or millet. Nevertheless, plant breeding as an artificial version of natural evolution, involving artificial selection of desired plant characteristics and artificial generation of genetic variation. It complements other farming innovations (such as introduction of new crops, grafting, changed crop rotations and tillage practices, irrigation, and integrated pest management) for improving crop productivity and land stewardship. During the period from 1930 onward, crop breeding, in concert with these other innovations, has led to spectacular increases in crop yields especially of cereal grains. Plant breeding is now practiced worldwide by both government institutions and commercial enterprises. International development agencies believe that breeding new crops is important for ensuring food security and developing practices of sustainable agriculture through the development of crops suitable for minimizing agriculture’s impact on the environment. Plant breeding - is a branch of agriculture that focuses on manipulating plant heredity to develop new and improved plant types for use by society. - a deliberate effort by humans to nudge nature, with respect to the heredity of plants, to an advantage - is often used synonymously with “plant improvement” in modern society Plant breeders - the professionals who conduct plant breeding - specializes in breeding different groups of plants. Some focus on field crops (e.g., soybean, cotton), horticultural food crops (e.g., vegetables), ornamentals (e.g., roses, pine trees), fruit trees (e.g., citrus, apple), forage crops (e.g., alfalfa, grasses), or turf species. (e.g., Bluegrass, fescue) - uses various technologies and methodologies to achieve targeted and directional changes in the nature of plants. - aim to make the crop producer’s job easier and more effective in various ways. They may modify plant structure, so it will resist lodging and thereby facilitate mechanical harvesting. They may develop plants that resist pests, so that the farmer does not have to apply pesticides, or applies smaller amounts of these chemicals. - develop high yielding varieties (or cultivars), so the farmer can produce more for the market to meet consumer demands while improving his or her income As science and technology advance, new tools are developed while old ones are refined for use by breeders. Before initiating a breeding project, clear breeding objectives are defined based on factors such as producer needs, consumer preferences and needs, and environmental impact. Not applying pesticides in crop production means less environmental pollution from agricultural sources. When breeders think of consumers, they may, for example, develop foods with higher nutritional value and that are more flavorful. Higher nutritional value means reduced illnesses in society (e.g., nutritionally related ones such as blindness, rickettsia) caused by the consumption of nutrient- deficient foods, as pertains in many developing regions where staple foods (e.g., rice, cassava) often lack certain essential amino acids or nutrients. Plant breeders may also target traits of industrial value. For example, fiber characteristics (e.g., strength) of fiber crops such as cotton can be improved, while oil crops can be improved to yield high amounts of specific fatty acids (e.g., high oleic content sunflower seed). The latest advances in technology, specifically genetic engineering technologies, are being applied to enable plants to be used as bio reactors to produce certain pharmaceuticals (called biopharming or simply pharming). The technological capabilities and needs of societies in the past restricted plant breeders to achieving modest objectives (e.g., product appeal, adaptation to production environment). It should be pointed out that these “older” breeding objectives are still important today. However, with the availability of sophisticated tools, plant breeders are now able to accomplish these genetic alterations in novel ways that are sometimes the only option, or are more precise and more effective. Furthermore, as previously indicated, plant breeders are able to undertake more dramatic alterations that were impossible to attain in the past (e.g., transferring a desirable gene from a bacterium to a plant!). History of Plant Breeding Origins of Agriculture and Plant Breeding In its primitive form, plant breeding started after the invention of agriculture, when people of primitive cultures switched from a lifestyle of hunter–gatherers to sedentary producers of selected plants and animals. The Fertile Crescent in the Middle East is believed to be the cradle of agriculture, where deliberate tilling of the soil, seeding and harvesting occurred over 10 000 years ago. Agriculture is generally viewed as an invention and discovery. During this period humans also discovered the time-honored and most basic plant breeding technique – selection, the art of discriminating among biological variation in a population to identify and pick desirable variants. Selection implies the existence of variability. In the beginnings of plant breeding, the variability exploited was the naturally occurring variants and wild relatives of crop species. Furthermore, selection was based solely on the intuition, skill, and judgment of the operator. Needless to say that this form of selection is practiced to date by farmers in poorer economies, where they save seed from the best-looking plants or the most desirable fruit for planting the next season. These days, scientific techniques are used in addition to the aforementioned qualities to make the selection process more precise and efficient. Plant Manipulation Efforts by Early Civilizations Archaeological findings occasionally reveal some ancient practices which indicate that plant manipulation beyond phenotypic selection among natural variability occurred. Babylonians are said to have perceived the role of pollen in successful fruit production and applied it to the pistils of female date palms to produce fruit. The Assyrians did likewise in about 870 BC, artificially pollinating date palms. Early Pioneers of the Theories and Practices of Modern Plant Breeding Plant breeding as we know it today began in earnest in the nineteenth century. Prior to this era, a number of ground-breaking discoveries and innovations paved the way for scientific plant manipulation. Some of the early pioneers of plant breeding include the following:  Rudolph Camerarius (1665–1721)  a professor of philosophy at the University of Tubingen in Germany  conducted research that contributed to establishing sexual differentiation, defining the male and female reproductive parts of the plant and described its functions in fertilization and showed that pollen is required for this key process in heredity.  His seminal work, De sexu plantarum (On the sex of plants), was published in 1694 in a letter to a colleague  Joseph Gottlieb Koelreuter (1733–1806).  German botanist, became professor of natural history and director of the botanical gardens in Karlsruhe in 1764  a pioneer in the application of the discovery of sex in plants as a vehicle for their genetic manipulation  conducted the first systematic experiments in plant hybridization, using the tobacco plant  recognized the role of insects and wind in pollination of flowers, and also conducted experiments to study artificial fertilization and development in tobacco plants  the golden rain tree genus (Koelreuteria) is named in his honor.  Louis de Vilmorin (1902–1969)  a noted French seedsman  conducted studies in plant improvement in vegetables using a method called genealogical selection, which is the modern breeding equivalent of progeny testing  recognized that new varieties of plants could be developed by selecting certain characteristics, which would then be transmitted through genealogy to the progeny  published his “Note on the Creation of a New Race of Beetroot and Considerations on Heredity in Plants”, which laid the theoretical groundwork for the modern seed breeding industry in 1856  modern day company Vilmorin is a major player in the global seed industry; along with its international subsidiaries it is ranked among the top five largest seed companies in the world. The company is also credited with producing the first seed catalogue for farmers and academics, among other significant publications  Thomas Andrew Knight (1759–1838)  British horticulturalist and botanist credited with pioneering work in the science of fruit breeding  conducted basic research in plant physiology that led to the discovery of the phenomenon of geotropism, the effects of gravity on seedlings  conducted research in the breeding of horticultural plants, including strawberries, cabbages, peas, apples and pears  he developed the “Downton” strawberry that is noted in the pedigree of most of the important modern strawberries.  published a Treatise on the culture of apple and pear in 1797  Carl Linnaeus (1707–1778)  Swedish botanist, physician, and zoologist  noted for his work in plant taxonomy, which led to the development of his enduring conventions for naming living organisms, the universally accepted binomial  nomenclature, also called Linnaean taxonomy or the scientific classification of organisms.  binomial nomenclature classifies nature within a hierarchy, assigning a two-part name to an individual, a genus and a species (specific epithet)  His work was published in his most noted publication Species Plantarum  Charles Robert Darwin (1809–1882).  English naturalist  most recognizable names of all times, because of his work that led to one of the most enduring theories ever, the theory of evolution  proposed what is sometimes called the unifying theory of life sciences that all species of life have evolved over time from a common ancestor  published his seminal work in his 1859 book, On the origin of species.  Gregor Mendel (1822–1844)  Augustinian monk  known for his scientific research that led to the foundations of modern transmission genetics  was credited with being first to provide empirical evidence about the nature of heredity, the underpinnings of traits and how genes that condition them are transmitted from parents to off spring.  also made two other significant contributions to the field of genetics – the development of pure lines, and good record keeping for use in statistical analysis that led to his discoveries (he counted plant variants).  his paper Experiments with hybrid plants was published in 1866 to reveal what became known as the laws of Mendel – the laws of dominance, segregation, and independent assortment, which are the foundations of modern genetics  Luther Burbank (1849–1926)  American botanist and horticulturalist,  known to have developed numerous varieties of fruits, flowers, grains, grasses and vegetables  his most remarkable creations is the Russet Burbank potato, which has a russet-colored skin and which is used worldwide today Later pioneers and trailblazers Since the beginning of the nineteenth century, there has been an explosion of knowledge in plant breeding and its allied disciplines.  M.M Rhoades and D.N. Duvick  Discovered Cytoplasmic male sterility(CMS)  Marcus Rhoades in discovered CMS as a breeding technique 1933  Duvick was a major player in the discovery of various aspects of this technology and 1965, he published a summary of their work done  Nikolai I. Vavilov  designated the Centers of Diversity of Crop Species or centers of origin of crops which identified eight areas of the world  also established the Law of Homologous Series in heritable variation, showing the existence of parallelism in variability among related species which allows plant explorers to predict, within limits, forms that are yet to be described.  E.R. Sears and C.M. Ricks  first to apply their knowledge of cytogenetics to plant breeding of wheat and tomato, respectively   they showed how researchers could transfer genes and chromosomes from alien species to cultivated crop species  H.J. Muller  demonstrated that the physiology and genetics of an organism could be altered upon exposure to radiation  Mutagenesis or mutation breeding became possible because of this discovery  described the mutagenic effects of X-rays on barley in 1928  Wilhelm Johannsen  pioneered the single plant selection method  first to distinguish between genotype and phenotype  published the Pure Line Theory in 1903  H.H. Hardy and W. Weinberg  Hardy, an Englishman, and Weinberg, a German, laid the foundation for modern day breeding of cross-pollinated species in 1908  demonstrated Hardy–Weinberg Equilibrium or law which became the foundation to the breeding strategies employed for breeding cross-pollinated species.  Nilsson-Ehle  credited with being the leader of the first scientific wheat breeding program  developed the method of plant breeding called bulk breeding to cope with the large number of crosses, generations, and plants involved is his breeding program in1912  H.V Harlan and M.N. Pope  first applied the backcross breeding scheme to plants in 1922, after observing its success with animal breeding  C.H. Goulden  developed the single seed decent (rapid generation advance) selection scheme in 1941 as a means of speeding up the attainment of homozygosity  E.M. East and D.F. Jones  independently proposed the concept of recurrent selection in 1920  F.H. Hull  coined the term recurrent selection in 1945.  his work included recurrent selection for combining ability.  F.E Comstock, H.F. Robinson, and P.H. Harvey  proposed the method of reciprocal recurrent selection in 1949  C.M. Donald  Australian biologist, proposed the ideotype breeding concept as a way of managing plant breeding programs by modeling plant architecture  H.H. Flor  proposed the gene-for-gene hypothesis in 1956 to postulate that both host and parasite genetics were significant in determining whether or not a disease resistance reaction would be observed. . George Shull  coined the term “heterosis” for the phenomenon of hybrid vigor  research on crossing corn, an open pollinated species, led to the observation of hybrid vigor  gave the correct interpretation of heterosis in 1908   W.J. Beal  one of the pioneers in the development of hybrid corn  His noted publications include the The New Botany, Grasses of North America, and History of Michigan Agricultural College  Ronald Fisher  introduced the concept of randomization and the analysis of variance procedure that are indispensable to plant breeding research and evaluation  His contributions to quantitative genetics aided breeders in the understanding and manipulation of quantitative traits  C.C. Cockerham  connected statistics to genetics by shedding light on sources of variation and variance components, and covariance among relatives in genetic analysis.  Murashige and Skoog  develop the Murashige–Skoog media (MS media) in 1962  Watson and Crick  discover the double helical structure of the DNA molecule that laid the foundation for the understanding of the chemical basis of heredity.  Norman Borlaug  dubbed the “Borlaug Hypothesis” by some economists, proposes to increase the productivity of agriculture on the best farmland to help curb deforestation by reducing demand for new farmland  received the prestigious Nobel Prize (for Peace) in 1970 – the first agriculturalist to be so recognized – was the Green Revolution  continued his advocacy for the poor and those plagued by perpetual hunger, working hard until his death in 2009 to alleviate world hunger  Herb Boyer, Stanley Cohen, and Paul Berg  Proposed the recombinant DNA technology, genetic manipulation in which DNA from one organism could be transferred into another, by achieving the feat with bacteria  they began the era of genetic engineering - the major technologies in modern plant breeding, albeit controversial Importance of Plant Breeding The reasons for manipulating plant attributes or performance change according to the needs of society. Plants provide food, feed, fiber, pharmaceuticals, and shelter for humans. Furthermore, plants are used for aesthetic and other functional purposes in the landscape and indoors 1. Addressing world food and feed quality needs Food is the most basic of human needs. Plants are the primary producers in the ecosystem (a community of living organisms including all the nonliving factors in the environment). Without them, life on earth for higher organisms would be impossible. Most of the crops that feed the world are cereals. Twenty five major food crops of the world. Wheat Sweet potato Sorghum Sugar beet Yam Rice Cassava Sugarcane Oranges Peanut Corn Grapes Millets Coconut Watermelon Potato Soybean Banana Cottonseed oil Cabbage Barley Oats Tomato Apples Rye  Plant breeding is needed to enhance the value of food crops, by improving their yield and the nutritional quality of their products, for healthy living of humans. Certain plant foods are deficient in certain essential nutrients to the extent that where these foods constitute the bulk of a staple diet, diseases associated with nutritional deficiency are often common. The Golden Rice project currently underway at the International Rice Research Institute (IRRI) in the Philippines and other parts of the world, is geared towards developing, for the first time ever, a rice cultivar with the capacity to produce pro-vitamin A (Golden rice 2, with a 20-fold increase in pro-vitamin A, has been developed by Syngenta’s Jealott’s Hill International Research Centre in Berkshire, UK). Breeding is also needed to make some plant products more digestible and safer to eat, by reducing their toxic components and improving their texture and other qualities. A high lignin content of the plant material reduces its value for animal feed. Toxic substances occur in major food crops, such as alkaloids in yam, cynogenic glucosides in cassava, trypsin inhibitors in pulses, and steroidal alkaloids in potatoes. Forage breeders are interested, amongst other things, in improving feed quality (high digestibility, high nutritional profile) for livestock. 2. Addressing food supply needs for a growing world population As the world population increases, there would be a need for an agricultural production system that is aligned with population growth. Unfortunately, land for farming is scarce. Farmers have expanded their enterprise onto new lands. Further expansion is a challenge because land that can be used for farming is now being used for commercial and residential purposes to meet the demands of a growing population. Consequently, more food will have to be produced on less land. This calls for improved and high yielding cultivars to be developed by plant breeders. With the aid of plant breeding, the yields of major crops have dramatically changed over the years. 3. Need to adapt plants to environmental stresses The phenomenon of global climatic change that is occurring is partly responsible for modifying the crop production environment (e.g., some regions of the world are getting drier and others saltier). This means that new cultivars of crops need to be bred for new production environments. Whereas developed economies may be able to counter the effects of unseasonable weather by supplementing the production environment (e.g., by irrigating crops), poorer countries are easily devastated by even brief episodes of adverse weather conditions. Breeders also need to develop new plant types that can resist various biotic (diseases and insect pests) and other abiotic (e.g., salt, drought, heat, cold) stresses in the production environment. Crop distribution can be expanded by adapting crops to new production environments (e.g., adapting tropical plants to temperate regions). Development of photoperiod insensitive crop cultivars would allow an expansion in production of previously photoperiod sensitive species. 4. Need to adapt crops to specific production systems Breeders need to produce plant cultivars for different production systems to facilitate crop production and optimize crop productivity. For example, crop cultivars must be developed for rain- fed or irrigated production, and for mechanized or non-mechanized production. In the case of rice, separate sets of cultivars are needed for upland production and for paddy production. In organic production systems where pesticide use is highly restricted, producers need insect and disease resistant cultivars in crop production.  5. Developing new horticultural plant varieties The ornamental horticultural production industry thrives on the development of new varieties through plant breeding. Aesthetics is of major importance to horticulture. Periodically, ornamental plant breeders release new varieties that exhibit new colors and other morphological features (e.g., height, size, shape). Also, breeders develop new varieties of vegetables and fruits with superior yield, nutritional qualities, adaptation, and general appeal. 6. Satisfying industrial and other end-use requirements Processed foods are a major item in the world food supply system. Quality requirements for fresh produce meant for the table are different from those for the food processing industry. One of the reasons why the first genetically modified (GM) crop (produced by using genetic engineering tools to incorporate foreign DNA) approved for food, the “FlavrSavrTM” tomato, did not succeed was because the product was marketed as table or fresh tomato, when in fact the gene of interest was placed in a genetic background for developing a processing tomato variety. Different markets have different needs that plant breeders can address in their undertakings. For example, potato is a versatile crop used for food and industrial products. Different varieties are being developed by breeders for baking, cooking, fries (frozen), chipping, and starch. These cultivars differ in size, specific gravity, and sugar content, among other properties. High sugar content is undesirable for frying or chipping because the sugar caramelizes under high heat to produce undesirable browning of fries and chips. Breeding Objectives A successful plant breeding program depends on clearly defined breeding objectives. Some objectives (e.g., yield) are broad and generally part of most breeding programs. All new cultivars should yield highly and resist major disease in the production area. However, there are objectives that are specialized and may be designed for specialized markets or consumers. Increase Yield and morphological traits Yield is a generic term used by crop producers to describe the amount of the part of a crop plant of interest that is harvested from a given area at the end of the cropping season or within a given period. Plant breeders seldom select solely on yield basis without some attention to other morphological features of the plants. Yield is the best measure of the integrated performance of a plant. Over the years, various researchers have attempted to improve biological yield by (a) increasing the photosynthetic capacity of the individual leaf, (b) improving light interception characteristics of plants, and (c) reducing wasteful respiration. In addition to increasing plant biomass, the goal of breeding for physiological and morphological traits include redistribution of assimilates to the economic products within the plant as well as alleviating or avoiding the effects of adverse environmental conditions. Yield may be divided into two types – biological and economic. Biological yield may be defined as the total dry matter produced per plant or per unit area (i.e., biomass). Researchers use this measurement of yield in agronomic, physiological, and plant breeding research to indicate dry matter accumulation by plants. All yield is firstly biological yield. The economic yield represents the total weight per unit area of a specified plant product that is of marketable value or other use to the producer. The producer determines the product of economic. Yield depends on biomass and how it is partitioned. To increase yield, the breeder may breed for increased biomass and efficient partitioning of assimilates. The potential biomass of a crop is determined by factors including genotype, local environment (soil, weather), and the agronomic practices used to grow it. N.W Simmonds identified three strategies for enhancing biomass: (i) Seasonal adaptation. The objective of this strategy is to optimally exploit the growing season by sowing early and harvesting late to maximize biomass accumulation. Of course, this will have to be done within reasonable agricultural limits, as dictated by weather and crop ping sequence. Genotypes can be adapted to new growing conditions (e.g., cold tolerance to allow the farmer to plant earlier than normal). (ii) Tolerance of adverse environmental factors. Because of the vagaries of the weather and the presence of other inconsistencies or variation in the production environment (climate, prod uct management, etc.), biomass can be enhanced by breeding for tolerance to these factors. Such breeding efforts may be directed at developing tolerance to abiotic stresses (e.g., drought, heat, cold). This would allow the cultivar to produce acceptable yields in the face of moderate to severe adverse environ mental conditions. (iii) Pest and disease resistance. Diseases and pests can reduce biomass by killing plant tissue (or even an entire plant in extreme cases) and stunt ing or reducing the photosynthetic surface of the plant. Disease and pest resistance breeding will enhance the biomass potential of the crop. Breeding to control pests is one of the major undertakings in plant breeding. Plant Morphological Traits Improved to Increase Yield  Lodging resistance Lodging resistance may be defined as the leaning, bending, or breaking of the plant prior to harvesting. There are two basic types of lodging that may be caused by biotic or abiotic factors. Lodging may originate at the root level (root lodging) or at the stem or stalk level (stalk lodging). Soil-borne disease and insect pests may destroy plant roots, causing the plant to lean over starting at the root level. Disease and insect attack can also cause the stem or stalk to lodge. Breeding for lodging resistance is important because lodging results in yield reduction. Lodging prior to pod filling results in partial fruit or seed development. Lodging at maturity may also make pods or cobs inaccessible to mechanized harvesters (combines) and, hence, are left unharvested. Lodged plants are exposed to disease infestation.  Shattering resistance Dry fruits that split open upon maturity to discharge their seeds are called dehiscent fruits. Whereas shattering is advantageous in the wild, it is undesirable in modern crop production. Some fruits split along only one side (called a follicle), while others split along two sides (called a legume), or multiple sides (called a capsule). This natural mechanism of seed dispersal has adaptive value to plants in the wild. In crop production, the splitting of dry fruits to release their seeds prior to harvesting is called grain shattering. In serious cases, some  cultivars can lose over 90% of their seed to shattering, if harvesting is delayed by just a few days. Whereas shattering is often identified with pod-bearing species (e.g., soybean, peas), it also occurs in cereal crops such as wheat and rice. Shatter-sensitive cultivars are susceptible to high loses during harvesting. The physical contact of the harvesting equipment with the plant may be enough pressure to trigger shattering. However, most susceptible cultivars spontaneously shatter their seeds when the environmental condition is right (dry, sunny, and windy). Shattered seeds are not only lost but also become a nuisance when they germinate as volunteer plants in the next year’s crop. Being weeds, the volunteer crops are controlled at additional production cost  Reduced plant height Modern production of certain cereal crops is dominated by semi-dwarf or dwarf cultivars (e.g., rice, wheat, sorghum). These cultivars have advantages in mechanized agriculture and high input production systems. Reduced plant height is associated with, or promotes, lodging resistance. Similarly, early maturity also reduces plant internode length. Producers desire crop cultivars with reduced plant stature because they are easier to harvest mechanically. They produce less straw after the economic product has been harvested. However, in certain cultures, the straw is used for crafts or firewood, and hence tall cultivars are preferred. Reduced stature also increases the harvest index. Dwarf cultivars can be more closely spaced in the field for increased crop yield. These cultivars are also environmentally more responsive, responding to agronomic inputs, especially fertilizers, for increased productivity.  Photoperiod response Plants exhibit environmentally determined developmental switches from the initiation of leaves (vegetative phase) to flowering (reproductive phase). The two developmental switches that plant breeders pay attention to are photoperiod and vernalization. The key environmental factors are temperature and day length. In some plants, flowering is not promoted by temperature and day length but occurs regardless of the conditions (called facultative plants), whereas in others, flowering will not occur without the appropriate temperature–day length combination (called obligate plants). Photoperiodism is a photomorphogenic responsive to day length (actually, plants track or measure the duration of dark period rather than duration of daylight). Three categories of responses are known: (i) Long-day (short-night) plants. These plants require a light period longer than a certain critical length in order to flower. They will flower under continuous light. Cool season species (e.g., wheat, barley, alfalfa, sugar beet) are examples of long-day plants. (ii) Short-day (long-night) plants. These plants will not flower under continuous light, requiring a photoperiod of less than a certain critical value in a 24-hour daily cycle. Examples include corn, rice, soybean, peanut, and sugarcane. (iii) Day-neutral (photoperiod insensitive). Photoperiod insensitive plants will flower regardless of duration of day length. This trait is very desirable, enabling producers to grow the crops in a broad range of latitudes. Examples include tomato, cucumber, cotton, and sunflower. Plant breeders need plants to flower at the appropriate time for hybridization in a breeding program and also to influence the cultivars they develop for different growing  areas. Photoperiod influences the duration of the vegetative phase versus reproductive phase, and hence crop yield at different latitudes. Day length increases as one goes north in summer in the northern hemi sphere. Consequently, a cultivar developed for the southern latitudes may not be as productive in the northern latitudes where reproductive growth is not initiated until the fall (autumn) season when day length is short. Vernalization is the process by which floral induction in some plants is promoted by exposing plants to chilling temperatures for a certain period. Plant breeders of crops such as wheat either sow in the fall so the plant goes through a natural vernalization in the winter, or they place trays of seedlings in a cold chamber for the same purpose, prior to transplanting. Photoperiod and temperature are two major environmental factors that influence crop adaptation through their effect on days to flowering. Photo period is also known to affect photosynthate partitioning in some species, such as peanuts, in which researchers found a reduction in the partitioning of dry matter to pods in certain genotypes under long photoperiods. Decreasing partitioning to grain favors partitioning to vegetative parts of the plant, resulting in increased leaf area and dry matter production. Crop cultivars that are developed for high altitudes should mature before the arrival of winter as well as be less sensitive to a long photoperiod so that seed yield would be high.  Early maturity Crop maturity in general is affected by a variety of factors in the production environment, including photoperiod, temperature, altitude, moisture, soil fertility, and plant genotype. Early maturity could be used to address some environmental stresses in crop production, such as drought and temperature. Maturity impacts both crop yield and product quality. Sometimes, the producer desires the crop to grow to attain its maximum dry matter possible under the production conditions before harvesting is done. In some crops, premature harvesting produces the product quality for premium prices. There are two basic types of maturity – physiological and harvest (market) maturity. Physiological maturity is that stage at which the plant cannot benefit from additional production inputs (i.e., inputs such as fertilizer and irrigation will not translate into additional dry matter or gain in economic product) because it has attained its maximum dry matter. In certain crops, the product is harvested before physiological maturity to meet market demands. This stage of maturity is called harvest maturity. For example, green beans are harvested before physiological maturity to avoid the product becoming “stringy” or fibrous. It is desirable for a producer to grow a cultivar that fully exploits the growing season for optimal productivity. However, under certain production conditions, it is advantageous for the cultivar to mature early (i.e., exploit only part of the growing season). Early maturity may allow a cultivar to escape environ mental stresses (e.g., disease, insects, early frost, early fall rain storms, drought) that may occur later in the season. Also, early maturing cultivars are suitable for use in multiple cropping systems, allowing more than one crop to be grown in a production season. Early maturity has made it possible to extend the production of some crops to regions in higher altitudes and with shorter summers, as well as low rainfall. Early maturity has its disadvantages. Because the plant only partially exploits the growing season, economic yield may be significantly reduced in species including corn,  soybean, wheat, and rice. In cotton, earliness is negatively correlated with traits such as fiber length. Improve Quality traits The market value and utilization of a plant product is affected by a variety of factors. For example, for grain crops, the factors that affect grain quality and form the basis of crop quality improvement programs include market quality, milling quality, cooking and processing qualities, and nutritional quality. The specific breeding goals with respect to each of these factors differ among crop species and agricultural production regions. For example, for the same crop, the quality aspect of importance in developed economies may be very different and even opposite to that of developing economies. Some cultures prefer white, non-scented, or non-sticky rice, whereas other cultures prefer colored, scented, or sticky rice. Quality means different things to different people. The terms used to describe quality vary from crop production to food consumption, and include terms for appearance, storage quality, processing quality, and nutritional worth or quality. Plant breeders should be very familiar with the market quality standards for their crops. These standards are based on complex interaction of social, economic, and biological factors, and are highly crop specific. Plant qualities that are subject to improvements are the following:  Protein Content Nutritional quality augmentation through addition of new quality traits, removing or reducing undesirable traits, or other manipulations, is an important goal in bioengineering of food crops. Crops that feed the world are primarily cereals, roots and tubers, and legumes. Unfortunately, they are nutritionally inadequate in providing certain amino acids required for proper growth and development of humans and monogastric animals. Molecular genetic approaches are being adopted for genetically engineering seed protein. They may be categorized as follows: (i) Altering amino acid profile of the seed. (ii) Selective enhancement of expression of existing genes. (iii) Designing and producing biomolecules for nutritional quality  Oil Quality Oil quality improvement is a major breeding objective for major oil crops such as soybean and rape. Soybean oil accounts for about 22% of the world’s total edible oil production. Conventional breeding approaches have been success fully applied to improve seed quality of various oil crops. Soybean lines with reduced palmitic acid content have been developed using traditional approaches of hybridization, recurrent selection, and chemical mutagenesis. Research has shown that seed protein and oil con tent are negatively correlated. Consequently, developing high protein and high oil seed has limited success. Alternatively, breeders have devoted efforts to breeding cultivars with high protein and low oil, and those with high oil but low protein.   Shelf Life Plant products that are harvested and used fresh (e.g., fruits, vegetables) are perishable and highly susceptible to spoilage soon after harvesting. Plant products that are harvested and used fresh (e.g., fruits, vegetables) are perishable and highly susceptible to spoilage soon after harvesting. Extended shelf life is hence an important plant trait from the point of view of producers, wholesalers, and consumers. Delayed ripening is desired in crops such as tomato and banana. Biotechnology has been successfully used to develop this quality in some crops. Ripening is a complex process that includes fruit color change and softening. Ripening in tomato has received great attention because it is one of the most widely grown and eaten fruits in the world. Ethylene plays a key role in tomato ripening. When biosynthesis of ethylene is inhibited, fruits fail to ripen, indicating that ethylene regulates fruit ripening in tomato. Knowing the pathway of ethylene biosynthesis, scientists may manipulate the ripening process by either reducing the synthesis of ethylene or reducing the effects of ethylene (i.e., plant response).  Seedlessness Fresh fruits without seeds are more convenient to eat, because there are no seeds to spit out. Common fresh fruits in which seedless cultivars exist include water melon, grape, orange, and strawberry. The conventional way of producing seedless fruits is the use of triploid hybrids.  Industrial uses Some crops have multiple uses – food, feed, and industrial. Corn, for example, may be milled for flour, extraction of oil, starch production, or sugar production. Breeders have developed special-purpose hybrids for these uses. For example, by inserting the endosperm gene, sugary (su), and another mutant gene, shrunken (sh2), in the same genotype, the resulting hybrid has increased sugar content (called supersweet or extra sweet corn). Similarly, waxy corn is developed for use in the production of adhesives, gums, and pudding, because of its high amylopectin content.  Novel Traits An application of genetic engineering to breed novel traits is the use of organisms as bioreactors to produce pharmaceuticals. One of the earliest applications of this technology was the commercial production of human insulin in microbial systems. Plant-made vaccines are currently under development for protection against cholera, diarrhea (Norwalk virus), and hepatitis B. The most common plants that are being used in plant-made pharmaceuticals are corn, tobacco, and rice. Other crops being investigated include alfalfa, potato, safflower, soybean, sugarcane, and tomato. To be usable, the plant should be readily amenable to genetic engineering and capable of producing high levels of protein. Breeding for resistance to diseases and insect pests Plants are plagued by a host of pathogens and pests that often must be controlled or managed in crop production. To control these organisms that “consume plants” effectively requires an understanding of their biology, epidemics, spread, and damage they cause. A variety of methods are used in pathogen and pest control, each with advantages and disadvantages. These methods are chemical, biological, cultural, legislative, and physical controls. A specific tactic in the method of biological pest control is the use of disease-resistant cultivars in crop production. Breeding for disease and insect resistance is one of the primary objectives in plant breeding programs.  Pest is an organism that is damaging to a crop. Broadly defined, a pest may include plant pathogenic fungi, bacteria, viruses, insects, and mammals  Parasite is an organism that feeds, grows, and is sheltered on or in a different organism while contributing nothing to the survival or well-being of the host.  Disease is any condition caused by the presence of an invading organism or a toxic component that damages the host.  Pathogenecity is the ability of an organism to enter a host and cause disease  Virulence is the degree of pathogenecity (the comparative ability to cause disease)  Infection is the invasion by and multiplication of a pathogenic mircrooganism in a bodily part or tissue; may lead to tissue injury and disease.  Resistance is a response to a cause (such as an attempted infection).  Immunity is a genotype is said to be immune to a pathogen if it is completely or totally resistant to it, not showing any sign of infection.  Host resistance is the ability of specific plant species to resist specific insects and pathogens because of a certain genetic architecture in the plant.  Non-host resistance is the phenomenon of immunity against the majority of pathogens. Plant diseases and pests are caused by organisms that vary in nature and may be microscopic or readily visible (e.g., virus versus insect pests like beetles). These pathogens may be airborne or soil borne. Important groups of causal agents of diseases are microbes – air borne fungi, soil- borne fungi, oomycetes, bacteria, viruses, viroids, phytoplasmas, parasitic plants, nematodes, and insects. Through an understanding of the biology, epidemics, spread, and damage caused by these organisms in each category, breeders have developed certain strategies and methods for breeding cultivars to resist certain types of biotic stress in plant production. Plant breeders devote varying amounts of resources to breeding for resistance in these categories with varying degrees of success. Plant species vary in their susceptibility to diseases caused by pathogens or pests in each group. Some crop production pathogens and pests are conspicuously absent from the list because they are relatively unimportant (e.g., mites), relatively more easily controlled by application of pesticides, or are not practical to breed against (e.g., birds). Disease breeding is a major objective for plant breeders all over the world. Breeders may use conventional or genetic modification strategies for breeding resistance. A combination of traits rather than just one trait makes a cultivar desirable. Yield, quality and resistance to diseases are top considerations in breeding programs, the first trait being usually the most important breeding objective. The first step in breeding for resistance to pathogens or insect pests is to assemble and maintain sources of resistance genes. The sources of resistance genes include commercial cultivars, landraces, wild progenitors, related species and genera, mutagenesis, and biotechnology. Once a desirable source has been found, the backcross method of breeding is commonly used to transfer resistance genes into adapted cultivars. There should be an effective and efficient screening technique for disease resistance breeding. For cross-pollinated species and also in autogamous crops, recurrent selection is effective for increasing the level of resistance in a population of genetically heterogeneous population.  One of the successful applications of agricultural biotechnology is in pest resistance breeding. The first disease resistance gene, Pto (binds with products of the pathogen to give resistance), was cloned in 1993 by Greg Martin and co-workers. Since then hundreds of R-genes have been cloned in many more crops to many more pathogen and pest species. Breeding for resistance to abiotic stresses Crop production is subject to the vagaries of the weather. Unpredictable weather can drastically reduce crop yield. Crop varieties used in regions that are prone to adverse weather during production need to have the capacity to resist or tolerate environmental stresses to an extent that they produce acceptable economic yield. Only about 30% of the earth is land. Of this, about 50% is not suitable for economic crop production mainly because of constraints of temperature, moisture and topography. Of the remaining portion of arable land, optimum production is further limited by a variety of environmental stresses, requiring mineral and moisture supplementation for economic crop production. As the world population increases more food will have to be produced by increasing the productivity of existing farm lands as well as bringing new lands into production. This means marginal lands will have to be considered. Plants breeders will have to develop cultivars that are adapted to specific environ mental stresses. It is estimated that abiotic environ mental stresses are responsible for about 70% of yield reduction of crops in production. Each species has natural limits of adaptability. There are tropical plants and temperate plants. Breeders are able, within limits, to adapt certain tropical plants to temperate production, and vice versa. To achieve this, plant breeders use various strategies and techniques (e.g., genetic modification, introgression of traits from adapted relatives) to develop new cultivars that are able to resist environmental stresses in their new environment. The common stresses that plants may be exposed to in agro-ecological systems include the following:  Drought. This is the stress perceived by a plant as a consequence of water deficit.  Heat. Heat stress occurs when temperatures are high enough to cause irreversible damage to plant function.  Cold. Cold stress manifests itself when plants are exposed to low temperatures that cause physiological disruptions that may be irreversible.  Salinity. Stress from salinity occurs when the dis solved salts accumulate in the soil solution to an extent that plant growth is inhibited.  Mineral toxicity. Mineral toxicity occurs when an element in the soil solution is present at a concentration such that plants are physiologically impaired.  Oxidative. Secondary stress (induced by other stresses) caused by oxygen free radicals (or activated oxygen) that are known to induce damage in plant cells.  Water-logging. Excessive soil moisture as a result of prolonged rainfall can cause anoxic soil conditions, leading to roots suffering from lack of oxygen.  Mineral deficiency. Inadequate amounts of essential soil minerals available for plant growth causes growth inhibition and crop injury. The terms “tolerance” and “resistance” are used in the literature to describe the mechanisms by which a plant responds to stress. Often, they are used as though they were interchangeable. According to J. Lewitt, from a physiological standpoint, a plant’s response to stress may be characterized as “avoidance” (i.e., the environmental factor is excluded from the plant tissue), or “tolerance” (i.e., the factor penetrates the tissue but the tissue survives). The term resistance, from a physiological standpoint, is mechanism-neutral (implying neither tolerance nor exclusion). When the term is applied to bacteria, the development of resistance to an antibiotic has evolutionary stages. Full antibiotic resistance is not necessarily conferred by an immediate change in the bacterial genome. It is preceded by tolerance. Because bacteria can survive in the presence of an antibiotic, they have the opportunity to develop resistance. Researchers who use resistance to describe the plant response to a stress (cause) appear to view resistance as a generic term for describing a number of mechanisms of which tolerance is one. In breeding for response to a stress, the ultimate goal of the breeder is to transfer genes to the cultivar that would enable it to perform to a desirable degree in spite of the stress.  Application A. Essay 1. How does breeding address the following importance? a. world food and feed quality needs _______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ b. food supply needs for a growing world population _______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ c. adaption of plants to environmental stresses _______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ 2. How does plant breeding help/promote resistance to diseases and insect pests? _______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ 3. Discuss briefly the objectives of plant breeding. _______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ ______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ _______________________________________________________________________________ ______________________________________________________________________________ Congratulations! You can now proceed to the next lesson.  Lesson 2 SELECTION AND BREEDING METHODS Plant breeders depend on variability for success in their breeding programs. Once assembled or created, breeders used selection strategies or methods to discriminate among the variability to identify those with the desired genotypes that can be developed into cultivars. Selection strategies used depend on the modes of reproduction of the species being genetically improved. Breeding self-pollinated species Self-pollinated species have a genetic structure that has implication in the choice of methods for their improvement. They are naturally inbred and hence inbreeding to fix genes is one of the goals of a breeding program for self-pollinated species in which variability is generated by crossing. However, crossing does not precede some breeding methods for self-pollinated species. Types of cultivars There are six basic types of cultivars that plant breeders develop. These cultivars derive from four basic populations used in plant breeding – inbred pure lines, open-pollinated populations, hybrids, and clones. Plant breeders use a variety of methods and techniques to develop these cultivars. 1. Pure-line cultivars  developed for species that are highly self-pollinated  are homogeneous and homozygous in genetic structure, a condition attained through a series of self-pollination.  are often used as parents in the production of other kinds of cultivars and have a narrow genetic base  are desired in regions where uniformity of a product has a high premium 2. Open-pollinated cultivars  developed for species that are naturally cross-pollinated.  are genetically heterogeneous and heterozygous  two basic types of open-pollinated cultivars are developed - recurrent (or repeated) selection or bulking and increasing material from selected superior inbred lines and a synthetic cultivar derived from planned matings involving selected genotypes.  have a broad genetic base 3. Hybrid cultivars  are produced by crossing inbred lines that have been evaluated for their ability to produce hybrids with superior vigor over and above those of the parents used in the cross  exploits the phenomenon of hybrid vigor (or heterosis) to produce superior yields  are homogeneous but highly heterozygous  Pollination is highly controlled and restricted in hybrid breeding to only the designated pollen source  Is more widespread in cross-pollinated species (e.g., corn, sorghum), because the natural reproductive mechanisms (e.g., cross fertilization, cytoplasmic male sterility) are more readily economically exploitable than in self-pollinated species  4. Clonal cultivars  Seeds are used to produce most commercial crop plants. However, a significant number of species are propagated by using plant parts other than seed (vegetative parts such as stems and roots)  using vegetative parts, the cultivar produced consists of plants with identical genotypes and is homogeneous.  is genetically highly heterozygous  Some plant species are sexually reproducing but are propagated clonally (vegetatively) by choice. Such species are improved through hybridization, so that when hybrid vigor exists it can be fixed (i.e., the vigor is retained from one generation to another) and then the improved cultivar propagated asexually.  In seed propagated hybrids, hybrid vigor is highest in the F1, but is reduced by 50% in each subsequent generation  clonally propagated hybrid cultivars may be harvested and used for planting the next season’s crop without adverse effects, producers of sexually reproducing species using hybrid seed must obtain a new supply of seed, as previously indicated 5. Apomictic cultivars  Apomixis is the phenomenon of production of seed without the benefit of the union of sperm and egg cells (i.e., without fertilization)  have the same benefits of clonally propagated ones  have the convenience of vegetative propagation through seed (versus propagation through cuttings or vegetative plant parts)  is common in perennial forage grasses. 6. Multilines  are developed for self-pollinating species  consist of a mixture of specially developed genotypes called isolines (or near isogenic lines) because they differ only in a single gene (or a defined set of genes)  Isolines are developed primarily for disease control, even though these cultivars, potentially, could be developed to address other environmental stresses and are developed by using the techniques of backcrossing in which the F1 is repeatedly crossed to one of the parents (recurrent parent) that lacked the gene of interest (e.g., disease resistance). Types of self-pollinated cultivars In terms of genetic structure, there are two types of self-pollinated cultivars: (i) Those derived from a single plant. (ii) Those derived from a mixture of plants Single plant selection may or may not be preceded by a planned cross but often it is the case. Cultivars derived from single plants are homozygous and homogeneous. However, cultivars derived from plant mixtures may appear homogeneous but, because the individual plants have different genotypes, and because some outcrossing (albeit small) occurs in most selfing species, heterozygosity would arise later in the population. The methods of breeding self-pollinated species may be divided into two broad groups – those preceded by hybridization and those not proceeded by hybridization. Breeding & Selection Methods Mass selection  an example of selection from a biologically variable population in which differences are genetic in origin   developed by Danish biologist, W. Johansen in 1903  described as the oldest method of breeding self-pollinated plant species  applicable to both self- and cross-pollinated species, provided there is genetic variation  the purpose is population improvement by increasing the gene frequencies of desirable genes  goal in cultivar development by mass selection is to improve the average performance of the base population  The improvement is limited to the genetic variability that existed in the original populations (i.e., new variability is not generated during the breeding process)  As a modern method of plant breeding, mass selection has several applications:  used to maintain the purity of an existing cultivar that has become contaminated, or is segregating. The off-types are simply rogued out of the population and the rest of the material bulked.  can also be used to develop a cultivar from a base population created by hybridization  used to preserve the identity of an established cultivar or soon to be released new cultivar  When a new crop is introduced into a new production region, the breeder may adapt it to the new region by selecting for key factors needed for successful production (e.g., maturity). This, hence, becomes a way of improving the new cultivar for the new production region  can be used to breed horizontal (durable) disease resistance into a cultivar  use to rogue out undesirable plants, thereby reducing the materials advanced and saving time and reducing cost of breeding  Advantages includes:  It is rapid, simple, and straightforward. Large populations can be handled and one generation per cycle can be used  It is inexpensive to conduct  The cultivar is phenotypically fairly uniform even though it is a mixture of pure lines  Disadvantages includes:  To be most effective, the traits of interest should have high heritability  Because selection is based on phenotypic values, optimal selection is achieved if it is conducted in a uniform environment  Phenotypic uniformity is less than in cultivars produced by pure line selection  With dominance, heterozygotes are indistinguishable from homozygous dominant genotypes. Without progeny testing, the selected heterozygotes will segregate in the next generation Pure-line selection  was developed in 1903 by the Danish botanist Johannsen  Lines that are genetically different may be success fully isolated from within a population of mixed genetic types.  Any variation that occurs within a pure line is not heritable but due to environmental factors only. Consequently, as Johansen’s bean study showed, further selection within the line is not effective  plant breeders call pure-line cultivars are best aptly called “near” pure-line cultivars because, as researchers such as K.J. Frey observed, high mutation rates occur in such genotypes  Line cultivars have a very narrow genetic base and tend to be uniform in traits of interest (e.g., height, maturity). In case of pro prietary dispute, lines are easy to clearly identify.  Pure-line breeding is desirable for developing cultivars for certain uses:   Cultivars for mechanized production that must meet a certain specification for uniform operation by farm machines (e.g., uniform maturity, uniform height for uniform location of economic part).  Cultivars developed for a discriminating market that puts a premium on eye-appeal (e.g., uniform shape, size).  Cultivars for the processing market (e.g., with demand for certain canning qualities, texture).  Cultivars for the processing market (e.g., with demand for certain canning qualities, texture).  The pure-line selection method is also an integral part of other breeding methods such as the pedigree selection and bulk population selection.  Advantages includes:  It is a rapid breeding method  is inexpensive to conduct. The base population can be a landrace. The population size selected is variable and can be small or large, depending on the objective.  The cultivar developed by this method has great “eye appeal” (because of the high uniformity of, e.g., harvesting time, height, etc.).  It is applicable to improving traits of low heritability, because selection is based on progeny performance  Mass selection may include some inferior pure lines. In pure line selection, only the best pure line is selected for maximum genetic advance  Disadvantages includes:  The purity of the cultivar may be altered through admixture, natural crossing with other cultivars, and mutations.  The purity of the cultivar may be altered through admixture, natural crossing with other cultivars, and mutations.  A new genotype is not created. Rather, improvement is limited to the isolation of the most desirable or best genotype from a mixed population  A new genotype is not created. Rather, improvement is limited to the isolation of the most desirable or best genotype from a mixed population  Progeny rows takes up more resources (time, space, funds). Pedigree selection  widely used method of breeding self-pollinated species (and even cross-pollinated species such as corn and other crops produced as hybrids)  A key difference between pedigree selection and mass selection or pure-line selection is that hybridization is used to generate variability (for the base population), unlike the other methods in which production of genetic variation is not a feature.  was first described by H.H. Lowe in 1927  a breeding method in which the breeder keeps records of the ancestry of the cultivar  To be successful, the breeder should be able to distinguish between desirable and undesirable plants on the basis of a single plant phenotype in a segregating population  Pedigree selection is applicable to breeding species that allow individual plants to be observed, described, and harvested separately. It has been used to breed species including peanuts, tobacco, tomato, and some cereals, especially where readily identifiable qualitative traits are targeted for improvement.  Advantages:  Record keeping provides a catalog of genetic information of the cultivar unavailable from other methods.   Selection is based not only on phenotype but also on genotype (progeny row) making it an effective method for selecting superior lines from among segregating.  Using the records, the breeder is able to advance only the progeny lines in which plants that carry the genes for the target traits occur.  A high degree of genetic purity is produced in the cultivar, an advantage where such property is desirable (e.g., certification of products for certain markets).  Disadvantages:  Record keeping is slow, tedious, time consuming, and expensive. It places pressure on resources  not suitable for species in which individual plants are difficult to isolate and characterize.  Pedigree selection is a long procedure, requiring about 10–12 years or more to complete, if only one growing season is possible  The method is more suited for qualitative than for quantitative disease resistance breeding. It is not effective for accumulating the number of minor genes needed to provide horizontal resistance.  Selecting in the F2 (early generation testing) on the basis of quantitative traits such as yield may not be effective. It is more efficient to select among F3 lines planted in rows than selecting based on individual plants in the F2. Bulk population breeding  is a strategy of crop improvement in which natural selection effect is solicited more directly in the early generations of the procedure by delaying stringent artificial selection until later generations.  The Swede, H. Nilsson-Ehle, developed the procedure. H.V. Harlan and colleagues provided additional theoretical foundation for this method through their work in barley breeding in 1940s  entails yield testing of the F2 bulk progenies from crosses and discarding whole crosses based on yield performance  the primary objective is to stratify crosses for selection of parents based on yield values  applies pure line theory to segregating populations to develop pure line cultivars.  used primarily for breeding self-pollinated species, but can be adapted to produce inbred populations for cross-pollinated species. It is most suitable for breeding species that are normally closely spaced in production (e.g., small grains – wheat, barley). It is used for field beans and soybeans. However, it is not suitable for improving fruit crops and many vegetables in which competitive ability is not desirable.  Advantages:  It is simple and convenient to conduct.  It is less labor intensive and less expensive in early generations.  Natural selection may increase frequency of desirable genotypes by the end of the bulking period.  It is compatible with mass selection in self-pollinated species.  Bulk breeding allows large amounts of segregating materials to be handled. Consequently, the breeder can make and evaluate more crosses.  The cultivar developed would be adapted to the environment, having been derived from material that had gone through years of natural selection.  Single plant selections are made when plants are more homozygous, making it more effective to evaluate and compare plant performance.   Disadvantages:  Superior genotypes may be lost to natural selection, while undesirable ones are promoted during the early generations.  It is not suited to species that are widely spaced in normal production.  Genetic characteristics of the populations are difficult to ascertain from one generation to the next.  Genotypes are not equally represented in each generation because all plants in one generation are not advanced to the next generation. Improper sampling may lead to genetic drift.  Selecting in off-season nurseries and the greenhouse may favor genotypes that are undesirable in the production region where the breeding is conducted, and hence is not a recommended practice.  The procedure is lengthy, but cannot take advantage of off-season planting. Single seed descent  was born out of a need to speed up the breeding program by rapidly inbreeding a population prior to beginning individual plant selection and evaluation, while reducing a loss of genotypes during the segregating generations.  was first proposed by C.H. Goulden in 1941 when he attained the F6 generation in two years by reducing the number of generations grown from a plant to one or two, while conducting multiple plantings per year, using the greenhouse and the off sea son  H.W. Johnson and R.L. Bernard described the procedure of harvesting a single seed per plant for soybean in 1962  C.A. Brim who, in 1966, provided a formal description of the procedure of single seed descent, calling it a modified pedigree method.  allows the breeder to advance the maxi mum number of F2 plants through the F5 generation  achieved by advancing one randomly selected seed per plant through the early segregating stages  Applications- Growing plants in the greenhouse under artificial conditions tends to reduce flower size and increase cleistogamy. Consequently, single seed descent is best for self- pollinated species. It is effective for breeding small grains as well as legumes, especially those that can tolerate close planting and still produce at least one seed per plant. Species that can be forced to mature rapidly are suitable for breeding by this method. It is widely used in soybean breeding to advance the early generation.  Advantages:  It is an easy and rapid way to attain homozygosity (2–3 generations per year).  Small spaces are required in early generations (e.g., can be conducted in a greenhouse) to grow the selections.  Natural selection has no effect (hence it can’t impose adverse impact).  The duration of the breeding program can be reduced by several years by using single seed descent.  Every plant originates from a different F2 plant, resulting in greater genetic diversity in each generation.  It is suited to environments that do not represent those in which the ultimate cultivar will be commercially produced (no natural selection imposed).  Disadvantages:  Natural selection has no effect (hence no benefit from its possible positive impact).  Plants are selected based on individual phenotype not progeny performance.   Inability of seed to germinate or plant to set seed may prohibit every F2 plant from being represented in the subsequent population.  The number of plants in the F2 is equal to the number of plants in the F4. Selecting a single seed per plant runs the risks of losing desirable genes. The assumption is that the single seed rep resents the genetic base of each F2. This may not be true. Backcross breeding  was first proposed by H.V. Harlan and M.N. Pope in 1922  to replace a specific undesirable gene with a desirable alternative, while preserving all other qualities (adaptation, productivity, etc.) of an adapted cultivar (or breeding line).  Instead of inbreeding the F1 as normally done, it is repeatedly crossed with the desirable parent to retrieve (by “modified inbreeding”) the desirable genotype.  The adapted and highly desirable parent is called the recurrent parent in the crossing program, while the source of the desirable gene missing in the adapted parent is called the donor parent  best suited to improving established cultivars that are later found to be deficient in one or two specific traits  most effective and easy to conduct when the missing trait is qualitatively (simply) inherited, dominant, and produces a phenotype that is readily observed in a hybrid plant.  used to transfer entire sets of chromosomes in the foreign cytoplasm to create a cytoplasmic male sterile (CMS) genotype that is used to facilitate hybrid production in species  also used for the introgression of genes via wide crosses  can also be used to develop isogenic lines (genotypes that differ only in alleles at specific a locus) for traits (e.g., disease resistance, plant height) in which phenotypes contrast.  effective for breeding when the expression of a trait depends mainly on one pair of genes, the heterozygote is readily identified, and the species is self-fertilizing  applicable in the development of multilines  Advantages:  reduces the amount of field testing needed, as the new cultivar will be adapted to the same area as the original cultivar (especially true when both parents are adapted).  Backcross breeding is repeatable. If the same parents are used, the same backcrossed cultivar can be recovered.  It is a conservative method, not permitting new recombination to occur.  It is useful for introgressing specific genes from wide crosses.  It is applicable to breeding both self-pollinated and cross-pollinated species.  Disadvantages:  is not effective for transferring quantitative traits  The presence of undesirable linkages may prevent the cultivar being improved from attaining the performance of the original recurrent parent.  Recessive traits are more time consuming to transfer. Multiline breeding and cultivar blends  N.F. Jensen is credited with first using this breeding method in oat breeding in 1952 to achieve a more lasting form of disease resistance.  generally more expensive to produce than developing a synthetic cultivar, because each component line must be developed by a separate backcross.  the key feature of a multiline cultivar is disease protection  a multiline or blend is a planned seed mixture of cultivars or lines (multiple pure lines) such that each component constitutes at least 5% of the whole mixture   One of the earliest applications of multilines was for breeding “variable cultivars” to reduce the risk of loss to pests that have multiple races and whose incidence is erratic from season to season  Advantages:  A multiline would provide protection to a broad spectrum of races of a disease- producing pathogen.  The cultivar is phenotypically uniform.  Multilines provide greater yield stability.  A multiline can be readily modified (reconstituted) by replacing a component line that becomes susceptible to the pathogen, with new disease resistant line.  Disadvantages:  It takes a long time to develop all the isolines to be used in a multiline, making it laborious and expensive to produce.  Multilines are most effective in areas where there is a specialized disease pathogen that causes frequent severe damage to plants.  Maintaining the isolines is labor intensive. Recurrent selection  is a cyclical improvement technique aimed at gradually concentrating desirable alleles in a population  one of the oldest techniques of plant breeding  was coined by F.H. Hull in 1945  was first developed for improving cross-pollinated species (maize) and has been a major breeding method for this group of plants  effective for improving quantitative traits.  Advantages:  Opportunities to break linkage blocks exist because of repeated intercrossing exists.  It is applicable to both autogamous grasses (monocots) and legumes (dicots).  Disadvantages:  Extensive crossing is required, something that is a challenge in autogamous species. Male sterility system may be used to facilitate this process.  Sufficient seed may not be available after intercrossing. This also may be resolved by including male sterility in the breeding program.  More intermatings may prolong the duration of the breeding program.  There is also the possibility of breaking desirable linkages. Breeding cross-pollinated species Breeding cross-pollinated species tends to focus on population improvement rather than the improvement of individual plants, as is the focus in breeding self-pollinated species. In addition to methods such as mass selection that are applicable to both self-pollinated and cross-pollinated species, there are specific methods that are suited to population improvement. Some methods are used less frequently in breeding. Further, certain methods are more effective and readily applied for breeding certain species than others. The methods of improving cross-fertilized species tend to focus on improving a population of plants. A population is a large group of interbreeding individuals. The application of the principles and concepts of population genetics are made to effect changes in the genetic structure of a population of plants. Overall, breeders seek to change the gene frequency such that desirable genotypes predominate in the population. Also, in the process of changing gene frequencies, new genotypes (that did not exist in the initial population) will arise. It is important for breeders to maintain genetic variability in these populations, so that further improvements of the population may be achieved in the future. To improve the population, breeders generally assemble germplasm, evaluate, self-selected plants, cross the progenies of the selected selfed plants in all possible combinations, bulk, and develop inbred lines from the populations. In cross-pollinated species, a cyclical selection approach, called recurrent selection, is often used for intermating. The cyclical selection was developed to increase the frequency of favorable genes for quantitative traits. The procedures for population improvement may be classified in several ways, such as according to the unit of selection – either individual plants or family of plants. Also, the method may be grouped according to the populations undergoing selection as either intrapopulation or interpopulation. Intrapopulation improvement Selection is practiced within a specific population for its improvement for specific purposes. Intrapopulation improvement is suitable for improving populations for:  Which the end product will be a population or synthetic cultivar.  Developing elite pure lines for hybrid production.  Developing mixed genotype cultivars (in self-fertilized species) Interpopulation improvement Methods of interpopulation improvement entail selection on the basis of the performance of a cross between two populations. This approach is suitable for use when the final product will be a hybrid cultivar. Interpopulation heterosis is exploited Selection & Breeding Methods Recurrent selection  the purpose of a recurrent selection in a plant breeding program is to improve the performance of a population with respect to one or more traits of interest, such that the new population is superior to the original population in mean performance and in the performance of the best individuals within it  used to establish a broad genetic base in a breeding program. Because of multiple opportunities for intermating, the breeder may add new germplasm during the procedure when the genetic base of the population rap idly narrows after selection cycles  There are four basic recurrent selection schemes, based on how plants with the desired traits are identified: (i) Simple recurrent selection. This is similar to mass selection with one or two years per cycle. The procedure does not involve the use of a tester. Selection is based on phenotypic scores. This procedure is also called phenotypic recurrent selection. (ii) Recurrent selection for general combining ability. This is a half-sib progeny test procedure in which a wide genetic based genotype (e.g., a cultivar) is used as a tester. The test cross performance is evaluated in replicated trials prior to selection. (iii) Recurrent selection for specific combining ability. This scheme uses an inbred line (narrow genetic base) for a tester. The test cross performance is evaluated in replicated trails before selection. (iv) Reciprocal recurrent selection. This scheme is capable of exploiting both general and specific combining ability. It entails two heterozygous populations, each serving as a tester for the other. Two genetically different populations are altered to improve their cross bred mean. To achieve this, individual plants from two populations (A and B) are selfed and also crossed with plants from the reciprocal female tester population (B and A, respectively).  Intrapopulation improvement methods 1. Individual plant selection methods  selection units are individual plants  Seed from selected plants (pollinated by the population at large) are bulked to start the next generation  No crosses are made, but progeny test is conducted  The process is repeated until a desirable level of improvement is observed  effectiveness of the method depends on the heritability of the trait since selection is solely on the phenotype  Disadvantages:  selection of superior plant often difficult  Lack of pollen control means both desirable and undesirable pollen will be involved in pollination of the selected plants.  If selection intensity is high (small population size advanced) the possibility of inbreeding depression is increased, as well as the probability of losing individuals with desirable combinations 2. Family selection methods  Family selection methods are characterized by three general steps: (i) Creation of a family structure. (ii) Evaluation of families and selection of superior ones by progeny testing. (iii) Recombination of selected families or plants within families to create a new base population for the next cycle of selection.  the duration of each step is one generation, but variations exist. 3. Family selection based on test cross  The key feature of this approach to selection is that it is designed to improve both the population per se as well as its combining ability  plants are selected from the source population and selfed in year 1. Prior to intermating, the selected plants are crossed as females to a tester in year 2. Intermating of selected plants occur in year 3. Backcross breeding  The key concern in the application of the backcross technique to cross-pollinated species is the issue of inbreeding.  The use of a recurrent parent in a backcross with cross pollinated species is tantamount to inbreeding  To minimize the loss of vigor, large populations should be used to enable the breeder sample and maintain the diversity of the cultivar and to insure against the harmful effects of inbreeding. Breeding hybrid cultivars A hybrid cultivar, by definition, is the F1 offspring of a planned cross between inbred lines, cultivars, clones, or populations. Depending on the breeding approach, the hybrid may comprise two or more par ents. A critical requirement of hybrid production is that the parents are not identical. As will be discussed next, it is this divergence that gives hybrids their superior performance. The outstanding yields of certain modern crops, notably corn, owe their success to the exploitation of the phenomenon of heterosis (hybrid vigor), which is high when parents are divergent. Much of what we know about hybrid breeding came from the discoveries and experiences of scientists engaged in corn hybrid cultivar development. However, commercial hybrids are now available for many crops, including self-pollinating species. Brief historical perspective  the earliest records on hybridization dates back to 1716 when American Cotton Mather observed the effects of cross fertilization in maize, attributing the multicolored kernels to wind-borne inter- mixture of different colored cultivars  the German T.G. Koelreuter conducted the first systematic studies on plant hybridization in 1766  G.H. Shull who, in 1909, first made clear scientific based proposals for exploiting heterosis to produce uniform and high yielding cultivars  In 1918, D.F. Jones proposed a more practical and cost-effective approach to producing hybrid cultivars by the method of the double-cross which produced significantly more economic yield than the single-cross hybrids originally proposed by Shull  corn production industry was transformed by hybrids, starting in the 1930s  M.I. Jenkins in 1934 who devised a method (topcross performance) to evaluate the effectiveness of parents in a cross (i.e., combining ability). Through this screening process, breeders were able to select a few lines that were good combiners (productive in a cross) for use in a hybrid breeding  The discovery and application of cytoplasmic male sterility (CMS) to corn hybrid programs eliminated the need for emasculation by the late 1960s  Breeders were able to develop outstanding inbred lines to make single-cross hybrids economical enough to replace double-cross hybrids by the 1970s  The idea of commercializing hybrid seed production is traced to Henry A. Wallace, an Iowa farmer, who studied self-pollination and selfing of corn in 1913. His industry led to the founding of Pioneer Hi-Bred Corn Company in Iowa, in 1925. Hybrid Vigor and Inbreeding depression Hybrid vigor may be defined as the increase in size, vigor, fertility, and overall productivity of a hybrid plant over the mid-parent value (average performance of the two parents). The synonymous term, heterosis, was coined by G.H. Shull. It should be pointed out immediately that, as it stands, heterosis is of no value to the breeder (and hence farmer), if a hybrid will only exceed the mid-parent in performance. Such advantageous hybrid vigor is observed more fre quently when breeders cross parents that are geneti cally diverse. The practical definition of heterosis is hybrid vigor that greatly exceeds the better or higher parent in a cross. Heterosis occurs when two inbred lines of outbred species are crossed, as much as when crosses are made between pure lines of inbreeders. Heterosis, though widespread in the plant kingdom, is not uniformly manifested in all species and for all traits. It is manifested at a higher intensity in traits that have fitness value, and also more frequently among cross-pollinated species than self-pollinated species. All breeding methods that are preceded by crossing make use of heterosis to some extent. However, it is only in hybrid cultivar breeding and the breeding of clones in which the breeder has opportunity to exploit the phenomenon to full advantage. Heterosis is opposite to inbreeding depression (reduction in fitness as a direct result of inbreeding). In theory, the heterosis observed on crossing is expected to be equal to the depression upon inbreed ing, considering a large number of crosses between lines derived from a single base population. In practice, plant breeders are interested in heterosis expressed by specific crosses between selected parents, or between populations that have no known common origin. Reduction in fitness is usually manifested as a reduction in vigor, fertility, and productivity. The effect of inbreeding is more severe in the early generations (5–8). Just like heterosis, inbreeding depression is not uniformly manifested in plants. Plants including onions, sunflower, cucurbits, and rye are more tolerant of inbreeding with minimal consequences of inbreeding depression. Selection of parents (inbred lines) The choice of parents to be used in a cross is the most critical step in a plant breeding program for the development of hybrids. The choice of parents depends on the specific objectives of the breeding program and what germplasm is available. Once the inbred lines have been developed, the breeder has the task of identifying a few lines with potential for use as parents in hybrid production. Certain inbreds have high general combining ability, being able to produce high performing hybrids with a series of other inbreds. On the other hand, certain inbreds are able to “nick” with only a few in the set of inbreds tested. The key decision in combining ability testing is the type of tester to use. A tester can have broad genetic base (e.g., open pollinated cultivars) or a narrow genetic base (e.g., elite inbreds, related inbred lines). Where a hybrid breeding program already exists, breeders may want to develop one or two new inbreds to replace those in the program that have been shown to have weaknesses. To replace an inbred in an established single cross, for example, the opposite inbred should be used as tester. Substitute inbred lines may be developed by backcross procedures (so the inbred is least genetically reorganized), or by isolating new inbreds from the same genetic source. New inbreds may also be developed from completely new sources. Development and Maintenance of Inbred Lines An inbred line is a breeding material that is homozygous. It is developed and maintained by repeated selfing of selected plants. In principle, developing inbred lines from cross-pollinated species is not different from developing pure lines in self-pollinated species. About 5–7 generations of selfing and pedigree selection are required for developing an inbred line. Inbreeders tolerate inbreeding, whereas outbreeders experience varying degrees of inbreeding depression. Consequently, the extent of inbreeding in developing inbred lines varies with the species. Hybrid breeding, as previously stated, exploits the phenomenon of heterosis. Heterosis will be highest when one allele is fixed in one parent to be used in a cross and the other allele fixed in the other parent. Inbred lines of inbreeding species Inbred lines in self-pollinated species have been discussed previously. They are relatively easy to maintain. The breeder should be familiar with the material to be able to spot off-types that may arise from admixtures or outcrossing in the field. Off-types should be rogued out and discarded, unless they are interesting and warrant additional observation and evaluation. Physical mixtures occur at harvesting (e.g., due to equipment not cleaned properly before switching to another line), threshing, processing and handling, storage, and at planting. When maintaining certain lines, especially those developed from wild species, it may be necessary to be more vigilant and harvest promptly, or bag the inflorescence before complete maturity occurs to avoid losing seed to shattering. Inbred lines of cross-pollinated species Because of the mode of reproduction, breeding lines from cross-pollinated species are more challenging to develop and maintain. Inbred lines may be developed from heterozygous  materials obtained from a natural population, or from F2 selected genotypes. Depend ing on the breeding procedure, parents for hybrid production may be developed in the conventional fashion, or non-conventional fashion. Conventional or normal inbreds. Normal inbreds are developed by repeatedly self-pollinating selected plants from S0–Sn (for materials drawn from natural populations) or from F1 to Fn (for materials obtained from crossing), the latter being akin to the pedigree breeding method previously described for self- pollinated species. The S1 or F2 populations are heterogeneous, as are results of segregation of traits. Superior plants are selected and progeny-rowed to expose inferior genotypes. Superior individuals are selected for the next cycle of selfing. By S3, the plant