Ebook Principles of plant genetics and breeding: Part 2

Continued part 1, part 2 of ebook Principles of plant genetics and breeding provide readers with content about: classic methods of plant breeding; selected breeding objectives; cultivar release and commercial seed production; breeding selected crops;... Please refer to the part 2 of ebook for details!

Section Classic methods of plant breeding Chapter 16 Breeding self-pollinated species Chapter 17 Breeding cross-pollinated species Chapter 18 Breeding hybrid cultivars Methods of breeding (or precisely, methods of selection) crops vary according to the natural method of reproduction of the species Generally, there are two categories of breeding methods: those for self-pollinated species and those for cross-pollinated species In practice, there is no hard distinction between the two; breeders crossover and use methods as they find useful Furthermore, plant breeders may use a combination of several methods in one breeding program, using one procedure at the beginning and switching to another along the way It should be mentioned also that the steps described in the various chapters for each selection method are only suggested guidelines Breeders may modify the steps, regarding the number of plants to select, the number of generations to use, and other aspects of breeding, to suit factors such as budget and the nature of the trait being improved 16 Breeding self-pollinated species Purpose and expected outcomes As previously discussed, 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 The purpose of this chapter is to discuss specific methods of selection for improving self-pollinated species After studying this chapter, the student should be able to discuss the characteristics, application, genetics, advantages, and disadvantages of the following methods of selection: Mass selection Pure-line selection Pedigree selection Bulk population Single-seed descent And to: Describe the technique/method of backcrossing Discuss the method of multiline breeding Discuss the method of breeding composites Discuss the method of recurrent selection Types of cultivars At the beginning of each project, the breeder should decide on the type of cultivar to breed for release to producers The breeding method used depends on the type of cultivar to be produced 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 Pure-line cultivars Pure-line cultivars are developed for species that are highly self-pollinated These cultivars are homogeneous and homozygous in genetic structure, a condition attained through a series of self-pollinations These cultivars are often used as parents in the production of other kinds of cultivars Pure-line cultivars have a narrow genetic base They are desired in regions where uniformity of a product has a high premium BREEDING SELF-POLLINATED SPECIES Open-pollinated cultivars Contrary to pure lines, open-pollinated cultivars are developed for species that are naturally cross-pollinated The cultivars are genetically heterogeneous and heterozygous Two basic types of open-pollinated cultivars are developed One type is developed by improving the general population by recurrent (or repeated) selection or bulking and increasing material from selected superior inbred lines The other type, called a synthetic cultivar, is derived from planned matings involving selected genotypes Open-pollinated cultivars have a broad genetic base Hybrid cultivars 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 Hybrid production exploits the phenomenon of hybrid vigor (or heterosis) to produce superior yields Heterosis is usually less important in crosses involving self-pollinated species than in those involving cross-pollinated species Hybrid cultivars are homogeneous but highly heterozygous Pollination is highly controlled and restricted in hybrid breeding to only the designated pollen source In the past, physical human intervention was required to enforce this strict pollination requirement, making hybrid seed expensive However, with time, various techniques have been developed to capitalize on natural reproductive control systems (e.g., male sterility) to facilitate hybrid production Hybrid production is more widespread in crosspollinated 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 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) By using vegetative parts, the cultivar produced consists of plants with identical genotypes and is homogeneous However, the cultivar is genetically highly heterozygous Some plant species sexually reproduce 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 283 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 In other words, whereas 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 Apomictic cultivars Apomixis is the phenomenon of the production of seed without the benefit of the union of sperm and egg cells (i.e., without fertilization) The seed harvested is hence genetically identical to the mother plant (in much the same way as clonal cultivars) Hence, apomictic cultivars have the same benefits of clonally propagated ones, as previously discussed In addition, they have the convenience of vegetative propagation through seed (versus propagation through cuttings or vegetative plant parts) Apomixis is common in perennial forage grasses Multilines Multilines are developed for self-pollinating species These cultivars 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 could, potentially, be developed to address other environmental stresses Isolines 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) Genetic structure of cultivars and its implications The products of plant breeding that are released to farmers for use in production vary in genetic structure and consequently the phenotypic uniformity of the product Furthermore, the nature of the product has implications in how it is maintained by the producers, regarding the next season’s planting Homozygous and homogeneous cultivars A cultivar may be genetically homozygous and hence produce a homogeneous phenotype or product 284 CHAPTER 16 Self-pollinated species are naturally inbred and tend to be homozygous Breeding strategies in these species are geared toward producing cultivars that are homozygous The products of economic importance are uniform Furthermore, the farmer may save seed from the current season’s crop (where legal and applicable) for planting the next season’s crop, without loss of cultivar performance, regarding yield and product quality This attribute is especially desirable to producers in many developing countries where the general tradition is to save seed from the current season for planting the next season However, in developed economies with well-established commercial seed production systems, intellectual property rights prohibit the reuse of commercial seed for planting the next season’s crop, thus requiring seasonal purchase of seed by the farmer from seed companies Heterozygous and homogeneous cultivars The method of breeding of certain crops leaves the cultivar genetically heterozygous yet phenotypically homogeneous One such method is hybrid cultivar production, a method widely used for the production of especially outcrossing species such as corn The heterozygous genetic structure stems from the fact that a hybrid cultivar is the F1 product of a cross of highly inbred (repeatedly selfed, homozygous) parents Crossing such pure lines produces highly heterozygous F1 plants Because the F1 is the final product released as a cultivar, all plants are uniformly heterozygous and hence homogeneous in appearance However, the seed harvested from the F1 cultivar is F2 seed, consequently producing maximum heterozygosity and heterogeneity upon planting The implication for the farmer is that the current season’s seed cannot be saved for planting the next season’s crop for obvious reasons The farmer who grows hybrid cultivars must purchase fresh seed from the seed company for planting each season Whereas this works well in developed economies, hybrids generally not fit well into the farming systems of developing countries where farmers save seed from the current season for planting the next season’s crop Nonetheless, the use of hybrid seed is gradually infiltrating crop production in developing countries Heterozygous and heterogeneous cultivars Other approaches of breeding produce heterozygous and homogeneous (relatively) cultivars, for example, synthetic and composite breeding These approaches will allow the farmer to save seed for planting Composite cultivars are suited to production in developing countries, while synthetic cultivars are common in forage production all over the world Homozygous and heterogeneous cultivars Examples of such a breeding product are the mixed landrace types that are developed by producers The component genotypes are homozygous, but there is such a large amount of diverse genotypes included that the overall cultivar is not uniform Clonal cultivar Clones, by definition, produce offspring that are not only identical to each other but also to the parent Clones may be very heterozygous but whatever advantage heterozygosity confers is locked in for as long as propagation is clonally conducted The offspring of a clonal population are homogeneous Once the genotype has been manipulated and altered in a desirable way, for example through sexual means (since some species are flowering, but are vegetatively propagated and not through seed), the changes are fixed for as long as clones are used for propagation Flowering species such as cassava and sugarcane may be genetically improved through sex-based methods, and thereafter commercially clonally propagated Types of self-pollinated cultivars In terms of genetic structure, there are two types of selfpollinated cultivars: Those derived from a single plant 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 preceded by hybridization BREEDING SELF-POLLINATED SPECIES Common plant breeding notations Plant breeders use shorthand to facilitate the documentation of their breeding programs Some symbols are standard genetic notations, while others were developed by breeders Unfortunately there is no one comprehensive and universal system in use, making it necessary, especially with the breeding symbols, for the breeder to always provide some definitions to describe the specific steps in a breeding method employed in the breeding program Symbols for basic crosses F The symbol F (for filial) denotes the progeny of a cross between two parents The subscript (x) represents the specific generation (Fx) If the parents are homozygous, the F1 generation will be homogeneous Crossing of two F1 plants (or selfing an F1) yields an F2 plant (F1 × F1 = F2) Planting seed from the F2 plants will yield an F2 population, the most diverse generation following a cross, in which plant breeders often begin selection Selfing F2 plants produces F3 plants, and so on It should be noted that the seed is one generation ahead of the plant, that is, an F2 plant bears F3 seed ⊗ The symbol ⊗ is the notation for selfing S The S notation is also used with numeric subscripts In one usage S0 = F1; another system indicates S0 = F2 Symbols for inbred lines Inbred lines are described by two systems System I describes an inbred line based on the generation of plants that are being currently grown System II describes both the generation of the plant from which the line originated as well as the generation of plants being currently grown Cases will be used to distinguish between the two systems Case The base population is F2 The breeder selects an F2 plant from the population and plants the F3 seeds in the next season System I: the planted seed produces an F3 line System II: the planted seed produces an F2 derived line in F3 or an F2:3 line If seed from the F3 plants is harvested and bulked, and the breeder samples the F4 seed in 285 the next season, the symbolism will be as follows: System I: the planted seed produces an F4 line System II: the planted seed produces an F2 derived line in F4 or an F2:4 line Case The breeder harvests a single F4 and plants F5 seed in a row System I: the planted row produces an F5 line System II: the planted row constitutes an F4 derived line in F5 or an F4:5 line Similarly the S notation may be treated likewise Taking case for example: System I: S1 line System II: S0 derived line in S1 or an S0:1 line Notation for pedigrees Knowing the pedigree or ancestry of a cultivar enables the plant breeder to retrace the steps in a breeding program to reconstitute a cultivar Plant breeders follow a short-hand system of notations to write plant pedigrees Some pedigrees are simple, others are complex Some of the common notations are as follows: A slash, /, indicates a cross A figure between slashes, /2/, indicates the sequence or order of crossing A /2/ is equivalent to // and indicates the second cross Similarly, / is the first cross, and /// the third cross A backcross is indicated by *; *3 indicates the genotype was backcrossed three times to another genotype The following examples will be used to illustrate the concept Pedigree 1: MSU48-10/3/Pontiac/Laker/2/MS-64 Interpretation: (a) The first cross was Pontiac (as female) × Laker (as male) (b) The second cross was [Pontiac/Laker (as female)] × MS-64 (as male) (c) The third cross was MSU48-10 (as female) × [Pontiac/Laker//MS-64 (as male)] 286 CHAPTER 16 Pedigree 2: MK2-57*3/SV-2 Equivalent formula: MK2-57/3/MK2-57/2/MK257/SV-2 Interpretation: the genotype MK2-57 was backcrossed three times to genotype SV-2 Mass selection Mass selection is an example of selection from a biologically variable population in which differences are genetic in origin The Danish biologist, W Johansen, is credited with developing the basis for mass selection in 1903 Mass selection is often described as the oldest method of breeding self-pollinated plant species However, this by no means makes the procedure outdated As an ancient art, farmers saved seed from desirable plants for planting the next season’s crop, a practice that is still common in the agriculture of many developing countries This method of selection is applicable to both self- and crosspollinated species Key features The purpose of mass selection is population improvement through increasing the gene frequencies of desirable genes Selection is based on plant phenotype and one generation per cycle is needed Mass selection is imposed once or multiple times (recurrent mass selection) 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) The goal in cultivar development by mass selection is to improve the average performance of the base population Applications As a modern method of plant breeding, mass selection has several applications: It may be 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 Existing cultivars become contaminated over the years by natural processes (e.g., outcrossing, mutation) or by human error (e.g., inadvertent seed mixture during harvesting or processing stages of crop production) It can also be used to develop a cultivar from a base population created by hybridization, using the procedure described next It may be used to preserve the identity of an established cultivar or soon-to-be-released new cultivar The breeder selects several hundreds (200–300) of plants (or heads) and plants them in individual rows for comparison Rows showing significant phenotypic differences from the other rows are discarded, while the remainder is bulked as breeder seed Prior to bulking, sample plants or heads are taken from each row and kept for future use in reproducing the original 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 Mass selection can be used to breed horizontal (durable) disease resistance into a cultivar The breeder applies low densities of disease inoculum (to stimulate moderate disease development) so that quantitative (minor gene effects) genetic effects (instead of major gene effects) can be assessed This way, the cultivar is race-non-specific and moderately tolerant of disease Further, crop yield is stable and the disease resistance is durable Some breeders use mass selection as part of their breeding program to rogue out undesirable plants, thereby reducing the materials advanced and saving time and reducing costs of breeding Procedure Overview The general procedure in mass selection is to rogue out off-types or plants with undesirable traits This is called by some researchers, negative mass selection The specific strategies for retaining representative individuals for the population vary according to species, traits of interest, or creativity of the breeder to find ways to facilitate the breeding program Whereas rouging out and bulking appears to be the basic strategy of mass selection, some breeders may rather select and advance a large number of plants that are desirable and uniform for the trait(s) of interest (positive mass selection) Where applicable, single pods from each plant may be picked and bulked for planting For cereal species, the heads may be picked and bulked Steps The breeder plants the heterogeneous population in the field, and looks for off-types to remove and discard BREEDING SELF-POLLINATED SPECIES Source population Select and bulk seed of desired plants or Rogue out undesired plants and bulk Plant replicated trials (a) Release best performer Year Source population Plant source population consisting of about 500–1,000 desirable plants Year Grow about 200 plants or heads in progeny rows; rogue out off-types Year Bulk harvest (b) Figure 16.1 Generalized steps in breeding by mass selection for (a) cultivar development, and (b) purification of an existing cultivar (Figure 16.1) This way, the original genetic structure is retained as much as possible A mechanical device (e.g., using a sieve to determine which size of grain would be advanced) may be used, or selection may be purely on visual basis according to the breeder’s visual evaluation Further, selection may be based on targeted traits (direct selection) or indirectly by selecting a trait correlated with the trait to be improved 287 Genetic issues Contamination from outcrossing may produce heterozygotes in the population Unfortunately, where a dominance effect is involved in the expression of the trait, heterozygotes are indistinguishable from homozygous dominant individuals Including heterozygotes in a naturally selfing population will provide material for future segregations to produce new off-types Mass selection is most effective if the expression of the trait of interest is conditioned by additive gene action Mass selection may be conducted in self-pollinated populations as well as cross-pollinated populations, but with different genetic consequences In self-pollinated populations, the persistence of inbreeding will alter population gene frequencies by reducing heterozygosity from one generation to the next However, in crosspollinated populations, gene frequencies are expected to remain unchanged unless the selection of plants was biased enough to change the frequency of alleles that control the trait of interest Mass selection is based on plant phenotype Consequently, it is most effective if the trait of interest has high heritability Also, cultivars developed by mass selection tend to be phenotypically uniform for qualitative (simply inherited) traits that are readily selectable in a breeding program This uniformity not withstanding, the cultivar could retain significant variability for quantitative traits It is helpful if the selection environment is uniform This will ensure that genetically superior plants are distinguishable from mediocre plants When selecting for disease resistance, the method is more effective if the pathogen is uniformly present throughout the field without “hot spots” Some studies have shown correlated response to selection in secondary traits as a result of mass selection Such a response may be attributed to linkage or pleiotropy Advantages and disadvantages Year If the objective is to purify an established cultivar, seed of selected plants may be progeny-rowed to confirm the purity of the selected plants prior to bulking This would make a cycle of mass selection have a 2-year duration instead of year The original cultivar needs to be planted alongside for comparison Year Evaluate composite seed in a replicated trial, using the original cultivar as a check This test may be conducted at different locations and over several years The seed is bulk harvested Some of the major advantages and disadvantages of mass selection for improving self-pollinated species are given here Advantages It is rapid, simple, and straightforward Large populations can be handled and one generation per cycle can be used It is inexpensive to conduct 288 CHAPTER 16 The cultivar is phenotypically fairly uniform even though it is a mixture of pure lines, hence making it genetically broad-based, adaptable, and stable Mixed seed source Disadvantages 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 Random size selection Pure line no 19 Pure line no 0.351 g 0.358 g Modifications Mass selection may be direct or indirect Indirect selection will have high success if two traits result from pleiotropy or if the selected trait is a component of the trait targeted for improvement For example, researchers improve seed protein or oil by selecting on the basis of density separation of the seed Pure-line selection The theory of the pure line was developed in 1903 by the Danish botanist Johannsen Studying seed weight of beans, he demonstrated that a mixed population of selfpollinated species could be sorted out into genetically pure lines However, these lines were subsequently nonresponsive to selection within each of them (Figure 16.2) Selection is a passive process since it eliminates variation but does not create it The pure-line theory may be summarized as follows: Lines that are genetically different may be successfully 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 Lines are important to many breeding efforts They are used as cultivars or as parents in hybrid production (inbred lines) Also, lines are used in the development of genetic stock (containing specific genes such as disease 0.348 g 0.6246 g 0.631 g 0.649 g Figure 16.2 The development of the pure-line theory by Johannsen resistance or nutritional quality) and synthetic and multiline cultivars Key features A line cultivar, by definition, is one that has a coefficient of parentage of at least 0.87 A pure line suggests that a cultivar has identical alleles at all loci Even though plant breeders may make this assumption, it is one that is not practical to achieve in a breeding program What plant breeders call pure-line cultivars are most 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 cases of proprietary dispute, lines are easy to unequivocally identify Applications 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 location of economic part) BREEDING SELF-POLLINATED SPECIES Cultivars developed for a discriminating market that puts a premium on visual appeal (e.g., uniform shape, size) Cultivars for the processing market (e.g., demand for certain canning qualities, texture) Advancing “sports” that appear in a population (e.g., a mutant flower for ornamental use) Improving newly domesticated crops that have some variability The pure-line selection method is also an integral part of other breeding methods such as pedigree selection and bulk population selection Steps The first step is to obtain a variable base population (e.g., introductions, segregating populations from crosses, landrace) and space plant it in the first year, select, and harvest desirable individuals (Figure 16.3) Year Grow progeny rows of selected plants Rogue out any variants Harvest selected progenies individually These are experimental strains Years 3–6 Conduct preliminary yield trials of the experimental strains including appropriate check cultivars Years 7–10 Conduct advanced yield trials at multiple locations Release highest yielding line as new cultivar Year Procedure Overview The pure-line selection in breeding entails repeated cycles of selfing, following the initial selection from a mixture of homozygous lines Natural populations of self-pollinated species consist of mixtures of homozygous lines with transient heterozygosity originating from mutations and outcrossing 289 Genetic issues Pure-line breeding produces cultivars with a narrow genetic base and hence less likely to produce stable Number of plants Action Year 1,000 Obtain variable population; space plant; select superior plants Year 200 Plant progeny rows of superior plants; compare Years 3–5 25–50 Select plants from superior rows to advance Year 15 Preliminary yield trials Years 7–10 10 Advanced yield trial Release Figure 16.3 Generalized steps in breeding by pure-line selection 290 CHAPTER 16 yields over a wider range of environments Such cultivars are more prone to being wiped out by pathogenic outbreaks Because outcrossing occurs to some extent within most self-pollinated cultivars, coupled with the possibility of spontaneous mutation, variants may arise in commercial cultivars over time It is tempting to select from established cultivars to develop new lines, an action that some view as unacceptable and unprofessional practice As previously discussed, pure-line cultivars depend primarily on phenotypic plasticity for production response and stability across environments Pedigree selection Pedigree selection is a 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 The method was first described by H H Lowe in 1927 Key features Advantages and disadvantages Some of the major advantages and disadvantages of the application of the pure-line method for improving selfpollinated species are given here Advantages It is a rapid breeding method The 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 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 The purity of the cultivar may be altered through admixture, natural crossing with other cultivars, and mutations Such off-type plants should be rouged out to maintain cultivar purity The cultivar has a narrow genetic base and hence is susceptible to devastation from adverse environmental factors, because of uniform response A new genotype is not created Rather, improvement is limited to the isolation of the most desirable or best genotype from a mixed population The method promotes genetic erosion because most superior pure lines are identified and multiplied to the exclusion of other genetic variants Progeny rows take up more resources (time, space, funds) Pedigree selection is a breeding method in which the breeder keeps records of the ancestry of the cultivar The base population, of necessity, is established by crossing selected parents, followed by handling an actively segregating population Documentation of the pedigree enables breeders to trace parent–progeny back to an individual F2 plant from any subsequent generation 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 It is a method of continuous individual selection after hybridization Once selected, plants are reselected in each subsequent generation This process is continued until a desirable level of homozygosity is attained At that stage, plants appear phenotypically homogeneous The breeder should develop an effective, easy to maintain system of record keeping The most basic form is based on numbering of plants as they are selected, and developing an extension to indicate subsequent selections For example, if five crosses are made and 750 plants are selected in the F2 (or list the first selection generation), a family could be designated 5-175 (meaning, it was derived from plant 175 selected from cross number 5) If selection is subsequently made from this family, it can be named, for example, 5-175-10 Some breeders include letters to indicate the parental sources or the kind of crop (e.g., NP-5-175-10), or some other useful information The key is to keep it simple, manageable, and informative Applications 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 peanut, tobacco, tomato, and some cereals, BREEDING COTTON Part B Please answer the following questions: Give the four species of cotton that produce economic seed fibers Distinguish between Old and New World cotton groups Discuss the importance of G hirsutum in cotton production Part C Please write a brief essay on each of the following topics: Discuss the American upland cotton types grown in the US Discuss pollination of cotton in breeding Discuss the key breeding objectives of cotton relating to lint yield and quality 555 Glossary of terms Accession: A distinct, uniquely identified sample of seeds, plants, or other germplasm materials that is maintained as an integral part of a germplasm collection Adapatedness: The degree or capacity of an individual to survive in a local environment and to transmit its genotype to the next generation Additive gene effect: The effect of an allele expected after it has replaced another allele at a locus Agrobacterium: A type of soil-inhabiting bacteria that is capable of introducing DNA from plasmids in the bacteria into the genome of plant cells Often used in the genetic transformation of plants Allele: One of several alternate forms (DNA sequences) that resides at the same locus on the chromosome and controls the same phenotype (although with potentially differing effects) Allogamy: Alternative term for cross-pollination Alloploid (or allopolyploid): An individual with somatic cells that contain more than two sets of chromosomes, each of which derives from a different species Amino acid: A building block of proteins Each protein consists of a specific sequence of amino acids (with the sequence of amino acids determined by the sequence of the underlying DNA) There are 20 types of amino acid molecules that make up proteins Amphidiploid (or amphiploid): An alloploid with the complete chromosome complements of two diploid species Aneuploid: An individual with a chromosome number that is not the exact multiple of the basic number for the species Antisense: The complementary strand of a coding sequence (gene); often an expressed copy of an antisense sequence is transformed into a cell or organism to shut off the expression of the corresponding gene Apomixis: Asexual reproduction in plants through the formation of seeds without fertilization (agamospermy) Asexual reproduction: The reproduction process that does not involve the union of gametes Autoploid (or autopolyploid): An individual with more than two complete sets of the basic number of chromosomes for the species Average effect of a gene: The change in mean value of the population produced by combining a gene with a random sample of gametes from the original population Backcross: A cross of an F1 to either parent used to generate it Base collection: A comprehensive collection of germplasm accessions held for the purpose of long-term conservation Base pair (bp): Two nitrogenous bases (adenine and thymine or guanine and cytosine) held together by weak bonds Two strands of DNA are held together in the shape of a double helix by the bonds between base pairs Bioinformatics: A broad term to describe applications of computer technology and information science to organize, interpret, and predict biological structure and function Bioinformatics is usually applied in the context of analyzing DNA sequence data Biopharming: The use of genetically transformed crop plants and livestock animals to produce valuable compounds, especially pharmaceuticals Also called pharming Bioremediation: The use of biological organisms to render hazardous wastes non-hazardous or less hazardous Biotechnology: A set of biological techniques developed through basic research and now applied to research and product development Breeding: The science and art of manipulating the heredity of an organism for a specific purpose Breeding line: A genetic group that has been selected and bred for its special combinations of traits Breeding value: The mean genotypic value or the progeny of an individual expressed as a deviation from the population mean Bt (Bacillus thuringiensis): A naturally occurring bacterium that produces a protein toxic to certain lepidopteran insects Callus: A cluster of undifferentiated plant cells that have the capacity to regenerate a whole plant in some species Cell: The fundamental level of structural organization in complex organisms Cells contain a nucleus (with chromosomes) and cytoplasm with the protein synthesis machinery, bounded by a membrane Cell culture: A technique for growing cells under laboratory conditions Cell fusion: The formation of a hybrid cell produced by fusing two different cells Centimorgan (cM): A unit of measure of recombination frequency One centimorgan is equal to a 1% chance that a marker at one genetic locus will be separated from a marker at a second locus due to crossing over in a single generation GLOSSARY OF TERMS Central dogma: The underlying model for describing gene structure and function It states that genes are transcribed in the nucleus into messenger RNA molecules, which are then translated into proteins on ribosomes Certified seed: The progeny or increase from a breeder or foundation seed and approved by a certifying agency Chimera: An individual consisting of cells of two or more types Chromosome: A condensed structure found in the cell nucleus that contains the genes of that cell Clonal propagation: The reproduction of plants through asexual means, such as cuttings, grafts, or tissue culture Cloning: Asexually producing multiple copies of genetically identical cells or organisms descended from a common ancestor Codon: A triplet of nucleotides in a DNA or RNA molecule that codes for one of the 20 amino acids in proteins, or for a signal to start or stop protein production Each gene that codes for protein is a series of codons that gives the instructions for building that protein Combining ability: The performance of a line with others in a cross Complementary: The opposite or “mirror” image of a DNA sequence A complementary DNA sequence has an A for every T, and a C for every G Two complementary strands of single-stranded DNA will join to form a double-stranded molecule Complementary DNA (cDNA): A single-stranded DNA molecule that is complementary to a specific RNA molecule and synthesized from it Complementary DNAs are important laboratory tools as DNA probes and for isolating and studying individual genes Conserved sequence: A base sequence in a DNA molecule (or an amino acid sequence in a protein) that has remained essentially unchanged throughout evolution Crossing over: The breaking during meiosis of one maternal and one paternal chromosome, the exchange of corresponding sections of DNA, and the rejoining of the chromosomes Cultivar: A product of plant breeding that is released for access to producers Deoxyribonucleic acid (DNA): The molecule that encodes genetic information DNA is a double-stranded molecule held together by weak bonds between base pairs of nucleotides The four nucleotides in DNA contain the bases: adenine (A), guanine (G), cytosine (C), and thymine (T) In nature, base pairs form only between A and T and between G and C; thus the base sequence of each single strand can be deduced from that of its partner Diploid: A full set of genetic material consisting of paired chromosomes, one chromosome from each parental set DNA chip: A high density array of short DNA molecules bound to a solid surface for use in probing a biological sample to determine gene expression, marker pattern, or nucleotide sequence of DNA/RNA See also Microarray 557 DNA probe: A single-stranded DNA molecule used in laboratory experiments to detect the presence of a complementary sequence among a mixture of other single-stranded DNA molecules Also called gene probe DNA profile: The distinctive pattern of DNA restriction fragments or PCR products that can be used to identify, with great certainty, any person, biological sample from a person, or organism from the environment DNA replication: The use of existing DNA as a template for the synthesis of new DNA strands In humans and other eukaryotes, replication occurs in the cell nucleus DNA sequencing: Determining the order of nucleotides in a specific DNA molecule Domestication: The process of bringing wild plants under cultivation to produce crops under the supervision of humans Dominant: A phenotype that is expressed in an organism whose genotype may be either homozygous or heterozygous for the corresponding allele Double helix: The shape that two linear strands of DNA assume when bonded together Doubled haploid: An individual that is produced by doubling its gametic (n) chromosome number into 2n Electrophoresis: A method of separating substances, such as DNA fragments, by using an electric field to make them move through a “gel” at rates that correspond to their electric charge and size Embryo rescue: The removal and culture of an immature embryo to produce a plant, often following a wide cross Enhancement: The process of improving a germplasm accession by breeding while retaining the important genetic contributions of the accession Enzyme: A protein that acts as a catalyst, speeding the rate at which a biochemical reaction proceeds but not altering the direction or nature of the reaction Epistasis: The interaction of genes at different loci; the situation in which one gene affects the expression of another Eukaryote: Cell or organism with a membrane-bound, structurally discrete nucleus and other well-developed subcellular compartments Functional genomics: The field of study that attempts to determine the function of all genes (and gene products), largely based on knowing the entire DNA sequence of an organism Gamete: Mature male or female reproductive cell (sperm or ovum) with a haploid set of chromosomes) Gene: The fundamental unit of heredity; a bundle of information for a specific biological structure or function Gene cloning: Isolating a gene and making many copies of it by inserting the DNA sequence into a vector, then into a cell, and allowing the cell to reproduce and make many copies of the gene Gene expression: The process in which a cell produces the protein, and thus the characteristic, that is specified by a gene’s nucleotide sequence 558 GLOSSARY OF TERMS Gene library: A collection of DNA fragments (carried on vector molecules) that, taken together, represents the total DNA of a certain cell type or organism Gene regulation: The process of controlling the synthesis or suppression of gene products in specific cells or tissues Gene splicing: Joining pieces of DNA from different sources using recombinant DNA technology Genetic code: The language in which DNA’s instructions are written The code consists of triplets of nucleotides (codons), with each triplet corresponding to one amino acid in a protein structure or to a signal to start or stop protein production Genetic engineering: The manipulation of genes, composed of DNA, to create heritable changes in biological organisms and products that are useful to people, living things, or the environment Genetic erosion: The loss of genetic diversity caused by either natural or manmade processes Genetic marker: A genetic factor that can be identified and thus acts to determine the presence of genes or traits linked with it but not easily identified Genetic stocks: Accessions that typically possess one or more special genetic traits that make them of interest for research Genetic vulnerability: The condition that results when a crop or a plant species is genetically and uniformly susceptible to a pest, pathogen, or environmental hazard Genetically modified (GM) organism: An organism whose genetic makeup has been changed by any method including natural processes, genetic engineering, cloning, mutagenesis, or others Genetics: Study of the patterns of inheritance of specific traits Genome: The complete set of chromosomes found in each cell nucleus of an individual Genomics: The field of study that seeks to understand the structure and function of all genes in an organism based on knowing the organism’s entire DNA sequence, with an extensive reliance on powerful computer technologies Genotype: The specific combination of alleles present at a single locus in the genome Germ cells: The sex cell(s) of an organism (sperm or egg, pollen or ovum) They differ from other cells (somatic) in that they contain only half the usual number of chromosomes Germ cells fuse during fertilization to begin the next generation Germplasm: The sum total of all hereditary material in a single (interbreeding) species Green Revolution: An aggressive effort between 1950 and 1975 where agricultural scientists applied modern principles of genetics and breeding to improve crops grown primarily in less developed countries Haploid: A cell or organism with a single genome Heterozygosity: The presence of different alleles at one or more loci on homologous chromosomes Heterozygous: Situation where the two alleles at a specific genetic locus are not the same Homologous: Stretches of DNA that are very similar in sequence, so similar that they tend to stick together in hybridization experiments Homologous can also be used to indicate related genes in separate organisms controlling similar phenotypes Homologous chromosomes: A pair of chromosomes containing the same linear gene sequences, each derived from one parent Homozygous: Situation where the two alleles at a specific genetic locus are identical to one another Hybrid: The progeny of a cross between two different species, races, cultivars, or breeding lines Hybridization (or crossing): The process of pollen transfer from the anther of the flower of one plant to the stigma of the flower of a different plant for the purpose of gene transfer to produce an offspring (hybrid) with a mixed parental genotype Hybridization: Bringing complementary single strands of nucleic acids together so that they stick and form a double strand Hybridization is used in conjunction with DNA and RNA probes to detect the presence or absence of specific complementary nucleic acid sequences In vitro: Performed in a test tube or other laboratory apparatus In vivo: In the living organism Inbreeding: The breeding of individuals that are related Isoenzyme (isozyme): Different chemical forms of the same enzyme that can generally be distinguished from one another by electrophoresis Landrace: A population of plants, typically genetically heterogeneous, commonly developed in traditional agriculture from many years of farmer-directed selection, and which is specifically adapted to local conditions Linkage: The proximity of two or more markers (e.g., genes, RFLP markers) on a chromosome Linkage map: A map of the relative positions of genetic loci on a chromosome, determined on the basis of how often the loci are inherited together Distance is measured in centimorgans (cM) Locus: The position on a chromosome where the gene for a particular trait resides; a locus may be occupied by any one of several alleles (variants) for a given gene Meiosis: The process of two consecutive cell divisions in the diploid progenitors of sex cells Meiosis results in four rather than two daughter cells, each with a haploid set of chromosomes Messenger RNA (mRNA): The ribonucleic acid molecule that transmits genetic information from the nucleus to the cytoplasm, where it directs protein synthesis Microarray: A large set of cloned DNA molecules spotted onto a solid matrix (such as a microscope slide) for use in probing a biological sample to determine the gene expression, marker pattern, or nucleotide sequence of DNA/RNA Microsatellite: A repeated motif of nucleotides, usually only two or three bases in length, where the number of repeats frequently differs between different members of a species GLOSSARY OF TERMS Mitosis: The process of nuclear division in cells which produces daughter cells that are genetically identical to each other and to the parent cell Molecular marker: An identifiable physical location on a chromosome (e.g., restriction enzyme cutting site, gene) whose inheritance can be monitored Multiline: A mixture of isolines, each of which is different for a single gene conditioning different forms of the same trait Mutagen: A substance that induces mutations Mutation: A permanent change in the genetic material involving either a physical alteration in the chromosome or a biochemical change in the underlying DNA molecule Nitrogenous base: A nitrogen-containing molecule having the chemical properties of a base Nucleic acid: A large molecule composed of nucleotide subunits Nucleotide: A subunit of DNA or RNA consisting of a nitrogenous base (adenine, guanine, thymine, or cytosine in DNA) Nucleus: Membrane-bound structure in the cell that contains the chromosomes (genetic material) The nucleus divides whenever the cell divides Pathogen: A specific biological causative agent of disease in plants or animals Pedigree: A record of the ancestry of an individual of family Phenotype: A biological characteristic or trait possessed by an organism that results from the expression of a specific gene Physical map: A map of the locations of identifiable landmarks on DNA (e.g., restriction enzyme cutting sites, genes), regardless of inheritance Distance is measured in base pairs Plasmid: A small, self-replicating molecule of DNA that is separate from the main chromosome Because plasmids are easily moved from cell to cell or to the test tube, scientists often cleave them with restriction enzymes and insert foreign DNA, and then transfer the recombinant DNA plasmid molecule (as a vector) into other cells Pollination: The transfer of pollen from the anthers to the stigma of a flower Polymerase chain reaction (PCR): A technique to amplify a specific DNA sequence in vitro using a DNA replicating enzyme, specific oligonucleotide primers, and repeated cycles of heating and cooling PCR often amplifies the starting material many thousands or millions of times Polymorphism: The simultaneous occurrence of two or more distinct forms in a population in a frequency that cannot be accounted for by the balance of mutation and selection Polyploidy: An individual with more than two sets of chromosomes characteristic of the species Primer: Short pre-existing polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase Probe: Single-stranded DNA or RNA molecules of a specific base sequence, labeled either radioactively or immunologically, that are used to detect the complementary base sequence by hybridization 559 Prokaryotes: Organisms whose genetic material is not enclosed by a nucleus Promoter: A DNA sequence preceding a gene that contains regulatory sequences controlling the rate of RNA transcription of that gene In effect, promoters control when and in which cells a given gene will be expressed Protein: A molecule composed of amino acids arranged in a special order determined by the genetic code Proteins are required for the structure and function of all living organisms Pure line: The progeny of a single homozygous individual produced by repeated selfing Recessive: A phenotype that is expressed in organisms only if it is homozygous for the corresponding allele Recombinant DNA: A hybrid DNA molecule produced in the laboratory by joining pieces of DNA from different sources Recombinant DNA technologies: Procedures used to join together DNA segments in a cell-free system (an environment outside a cell or organism) Under appropriate conditions, a recombinant DNA molecule can enter a cell and replicate there, either autonomously or after it has become integrated into a cellular chromosome Recombination: The process by which progeny derive a combination of genes different from that of either parent In higher organisms, this can occur by crossing over Recurrent selection: A breeding method whereby plants are repeatedly selected and intercrossed to increase the frequency of favorable alleles Regeneration: The process of growing an entire plant from a single cell or group of cells Reporter gene: A gene sequence that is easily observed when it is expressed in a given tissue or at a certain stage of development Restriction enzyme: An enzyme that recognizes a specific nucleotide base sequence (usually four to six base pairs in length) in a double-stranded DNA molecule and cuts both strands of the DNA molecule at every place where this sequence occurs Restriction fragment length polymorphism (RFLP): The presence of two or more variants in the size of DNA fragments produced by a restriction enzyme These different sized fragments result from an inherited variation in the presence of a restriction enzyme’s target sequence RFLPs are used for gene mapping and DNA profiling Ribonucleic acid (RNA): A molecule that translates the instructions encoded in DNA to build proteins Ribosomes: Small cellular components composed of specialized ribosomal RNA and protein; site of protein synthesis Selection (field): The process of discriminating among genetic variability to advance a fraction to the next generation or breeding cycle Selection (in vitro): A method to retain specific cells (or clones of cells) expressing a specific trait, such as antibiotic or herbicide resistance, while killing off all other cells that not express that trait 560 GLOSSARY OF TERMS Somatic cell: Cells in the body that are not involved in sexual reproduction (that is, not germ cells) Southern blotting: Transfer by absorption of DNA fragments separated in electrophoretic gels to membrane filters for the detection of specific base sequences by radiolabeled complementary probes Tissue culture: Growing cells, tissues, or tissue fragments (from complex, multicellular organisms) on a nutrient medium in a dish, test tube, or flask Totipotent: A cell that is capable of regenerating an entire adult organism by itself Trait: A distinguishing characteristic or quality of an organism Transcription: The transfer of information from specific sequences in a DNA molecule to produce new strands of messenger RNA, which then carry this information from the nucleus to the cytoplasm (where the messenger RNA is translated into protein) Transformation: Introduction of an exogenous DNA molecule into a cell, causing it to acquire a new phenotype (trait) Transgenic: An organism that has been transformed with a foreign DNA sequence Translation: Synthesis of protein using information contained in a messenger RNA molecule Vector: A type of DNA molecule, usually a plasmid or virus, that is used to move recombinant DNA molecules from one cell to another Appendix Internet resources Chapter http://www.foodfirst.org/media/opeds/2000/ 4-greenrev.html Lessons from the Green Revolution http://www.arches.uga.edu/~wparks/ppt/green/ Biotechnology and the Green Revolution Interview with Norman Borlaug http://cuke.hort.ncsu.edu/cucurbit/wehner/741/ hs741hist.html History of plant breeding Chapter http://agronomy.ucdavis.edu/gepts/pb143/pb143.thm Gepts, P 2002 The evolution of crop plants http://cucurbitsvr.hort.ncsu.edu/breeding/ usplantbreeding/uspbmain.html Plant breeding in the USA List of land grant institutions and seed companies http://pas.byu.edu/AgHrt100/evolutio.htm Synopsis on plant breeding and evolution http://billie.btny.purdue.edu/apomixis/apomixis.html Excellent overview of apomixis Chapter http://www.barc.usda.gov/psi/ngrl/ngrl.html Website of National Germplasm Resources Lab http://www.plantstress.com/admin/WRFiles/ germplasmwr.htm List of websites for plant germplasm resource centers worldwide http://www.ciesin.org/docs/002-256a/002–256a.html Paper on current status of biological diversity by E O Wilson of Harvard University Chapter http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/ H/Hardy_Weinberg.html Excellent discussion of population genetics Chapter Chapter 10 http://molvis.sdsc.edu/atlas/atlas.htm#dnarna Colorful animated figures of DNA and other macromolecules http://www-scf.usc.edu/~chem203/resources/DNA/ doublehelix.html DNA structure http://biog-101-104.bio.cornell.edu/BioG101_104/ tutorials/cell_division.html Well illustrated tutorial site on cell division http://csf.colorado.edu/perma/stse/isolate.htm Basic isolation practices for reducing or eliminating natural cross-pollination in field crossing http://www.actahort.org/books/200/200_3.htm Application of wide crosses in tomato improvement Chapter 11 Chapter http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/ A/AsexualReproduction.html Asexual reproduction in plants http://www.emc.maricopa.edu/faculty/farabee/BIOBK/ BioBookflowers.html Excellent illustrations and discussion of aspects of reproduction in flowering plants http://www.ukans.edu/~bio152/17/sld001.htm Excellent slides on plant reproduction http://aggie-horticulture.tamu.edu/tisscult/microprop/ microprop.html Links to numerous aspects of plant micropropagation http://billie.btny.purdue.edu/apomixis/apomixis.html Excellent overview of apomixis http://www.sprrs.usda.gov/apomixis.htm Comments from foremost scientists in field of apomixis http://www.blogontheweb.com/tissue_culture Excellent discussion on tissue culture 562 APPENDIX Chapter 12 Chapter 22 http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/ M/Mutations.html Detailed discussion of mutations in nature http://www.plantmutations.com/ Excellent discussion of mutagenesis in plant breeding http://www.ext.colostate.edu/PUBS/CROPS/00307.html Brief overview of pharming in plants http://www.molecularfarming.com/molecularfarming-patents.html Site to various products and companies engaged in pharming Chapter 13 Chapter 25 http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/ P/Polyploidy.html Good discussion on polyploidy http://wheat.pw.usda.gov/ggpages/BarleyNewsletter/ 42/oral04.html Application of doubled haploids in barley breeding http://www.cgiar.org http://impact.cgiar.org http://www.cgiar.org/centers/index.html Chapter 26 Chapter 15 http://www.wipo.org/about-ip/en/about_patents.html General information about patents http://www.3bsproject.com/html/ip.html European perspectives on intellectual property http://www.cid.harvard.edu/cidbiotech/comments/ comments117.htm Biotechology and morality debate http://www.aphis.usda.gov/biotech/OECD/usregs.htm US biotechnology regulatory oversight http://www.agwest.sk.ca/saras_reg_int.shtml Links to international regulations on biotechnology http://www.codexalimentarius.net/ Codex Alimentarius Commission http://www.enn.com/enn-features-archive/ 2000/03/03052000/gefood_5991.asp Raging debate over biotechnology food http://www.cid.harvard.edu/cidbiotech/comments/ comments117.htm Debate over morals in biotechnology http://uk.fc.yahoo.com/g/genetic.html GM foods debate Chapter 18 http://www.ontariocorn.org/ocpmag/dec99feat.html Historical account of corn hybrids http://www.anth.org/ifgene/breed2.gif A scheme for organic plant breeding Chapter 31 http://www.notrans.iastate.edu/research.html#breeding Breeding for low linolenic acid http://www.ag.uiuc.edu/~stratsoy/research/ind10.html Breeding for high seed protein http://www.indianasoybeanboard.com/Links.shtml Soybean links Chapter 32 http://www.vaes.vt.edu/tidewater/peanut/ Peanut production guide Chapter 33 http://oregonstate.edu/potatoes/potliv.html Potato links http://www.umaine.edu/paa/Breeding/ B&Gsec31802.htm Site of the Potato Association of America http://www.aphis.usda.gov/bbep/bp/potato.html Brief overview of the crop Appendix Conversion rates Imperial unit Metric conversion Volume/Capacity Cubic inch Bushel Pint Quart Gallon 16.39 cubic centimeters 0.036 cubic meters 0.57 liters 1.14 liters 4.55 liters Area Acre Acre Square yard Square feet 4046.86 square meters 0.4 hectares 0.8 square meters 0.09 square meters Mass Ounce (avoirdupois) Pound Hundredweight Ton 28.35 grams 0.45 kilogram 50.80 kilograms 1.02 tonnes Length Inch Foot Yard Mile 2.54 centimeters 0.31 meter 0.91 meter 1.61 kilometers Index A-chromosomes, 229 A-line, 344 abiotic resistance, 385 active collections, 99 adaptation, 9, 427 additive effect, 125 additive gene action, 125 additive variance, 127 advanced backcross breeding, 96, 252 advanced yield trial, 419 adventitious shoot production, 183 agamospermy, 64 agriculture, 3, alien addition lines, 228 alleles, 38, 40–43 multiple, 40 recessive, 40 allogamous (cross-pollination), 56 alloploidy (alloploid), 215, 221 allozymes, 42, 248 alternative hypothesis, 147 alternative splicing, 51 amphiploidy (amphiploid), 215 amplified fragment length polymorphisms (AFLP), 249 androecium, 58 androgenesis, 64 angiosperms, 76 annuals, 57 ANOVA (analysis of variance), 154 Anther culture, 186 antibiotic selection, 235 antiparallel, 48 anueploidy, 227 apomictic cultivar, 283 apomixis, 63–67, 196 apospory, 64 artificial hybridization, 165 see also hybridization Association of Official Seed Analysis, 445 Association of Official Seed Certifying Agencies, 447 autogamous (self-pollination), 56 autoploidy (autoploids), 215, 220 avirulent, 369 avoidance, 369, 379 axillary shoot production, 183 B-chromosomes, 229 B-line, 344 backcross breeding, 303–308, 331 backup collections, 99 base collections, 99 better-parent heterosis, 340 biennials, 57 binomial system of classification, 7, 76 biochemistry, 26 bioinformatics, 26, 238, 240 biological variation, 75 biological yield, 353 biomass, 353 biopharming, biotechnology, 231–255 cloning genes, 233 definition, 231 gene transfer, 234–237 general steps in rDNA technology, 231 genomics, 237 landmark discoveries, 232 legal risks of adoption of GM crops, 278 public perception and fears, 276 regulation of the industry, 269 biotechnology in developing countries, 459 biparental inheritance, 37 blends (cultivar), 308 boom and bust cycles, 375 Borlaug, N., 10, 11–13 botany, 25 breeder seed, 436, 438 breeders’ equation, 131 breeder’s eye, 24 breeders’ rights, 258 breeders’ trials, 418 breeding objectives, 495, 507, 517, 527, 535, 544, 553 breeding potato, 537–545 breeding value, 126 bridge crosses, 178 broad sense heritability, 128 bt resistance, 377 bulbosum method, 187 bulk population breeding, 294–297 Calyx, 58 Camerarius, R.J., canonical correlation, 161 Cartagena Protocol on biosafety, 274 cDNA library, 233 cell, 35 central dogma of molecular biology, 49 centralized plant breeding, 462–468 certified seed, 436, 441 CGIAR centers, 453 chemical mutagens, 203 chiasma, 80 chimera, 200, 206 chimerism, 194 chi-square test, 153 chromosomal mutation, 202 chromosome deletion, 228 chromosome elimination, 187 chromosome mapping, 46 chromosome substitution, 229 chromosomes, 37 classification, 75–78 operational system, 77 rules, 76 cleistogamy, 60 clonal cultivar, 283 clonal propagation, 61 clonally propagated species breeding, 193–196 breeding apomictic cultivars, 196 breeding approaches, 195 genetic issues, 194 clones, 194, 284 cloning vectors, 233 cluster analysis, 161 coat protein mediated viral resistance, 382 codominance, 42 codon, 50 coefficient of inbreeding, 116 coefficient of variation, 151 cold stress breeding, 392 combining ability, 139–141, 328 comparative genomics, 237 complementary DNA (cDNA), 49 complete block designs, 430 complete flower, 58 complete linkage, 43 INDEX complex inheritance, 42 composite cultivar, 310 composites, 310 compositional traits, 9, 404 congruency backcross, 308 constitutive expression, 52 constitutive promoters, 235 Consultative Group of International Agricultural Research (CGIAR), 452–455 conventional breeding, 29 convergent crosses, 170 cool season plants, 78 copyrights, 257 corn breeding, 485–497 corolla, 58 correlated response, 133 correlation coefficient, 151 cotton breeding, 546–554 coupling phase, 45 crop introduction, 20–22 crop registration, 432 cross-pollinated, 60 crossing, 165 crossing over, 38 cryopreservation, 100 cultivar, cultivar release process, 438 cuttings, 62 cybrids, 186 cytoplasmic inheritance, 37 cytoplasmic male sterility (CMS), 335, 345, 488 Darwin, C., 17 decentralized participatory plant breeding, 463 delayed ripening, 412 determinacy, 364 developing countries (breeding), 451 diallel cross, 143, 170 diallel cross test, 328 dichogamy, 61 dicots, 76 differential cultivars, 374 differential expression, 52 dihaploid, 214 dioecious plants, 59 dioecy, 61, 68, 349 diploidization, 219 direct organogenesis, 184 directed selection, 193 directional selection, 115 disease, 368 disease resistance, 367 disease triangle, 369 disruptive selection, 115 divergent crossing, 170 DNA, DNA amplification fingerprinting (DAF), 249 DNA markers, 247 DNA microarrays, 239, 243 DNA sequencing, 232, 237 domestication, 18–24 centers of diversity, 19 law of homologous series, 20 patterns, 19 syndrome, 23 dominance, 39 dominance effect, 12 dominance gene action, 126 dominance theory (of heterosis), 339 dominant mutation, 201 double cross, 170 double dwarfs, 363 double fertilization, 60 double helix, 48 doubled haploids, 187, 190 drought stress, 387 drought stress breeding, 387–392, 393–396 ear-to-row selection, 317 early generation testing, 139 economic yield, 353 ecosystem, emasculation, 26, 166, 481 embryo rescue, 185 end-use quality breeding, 412 environmental index, 424 environmental variation, 79 epidemics, 383 epistasis, 43 ethics, 263 evolution, 17 ex situ conservation, 91, 98 exons, 51 experimental design, 427 experimental unit, 148, 427 explant, 183 expressivity, 46 factor analysis, 155 Fairchild, T., female gametophyte, 59 fertilization, 59 field plot designs, 429 field plot technique, 427 filament, 58 565 first division restitution (FDR), 216 “FlavrSavr” tomato, 413 flood stress, 402 flowers, 58 food allergy, 271 forward mutation, 200 foundation seed, 436, 440 frame shift mutation, 202 full-sib family selection, 318 functional genomics, 238 G × E interaction, 386, 420–423 gametic incompatibility, 172 gametogenesis, 59 gene action, 125 gene banks, 91 gene-for-gene hypothesis, 372 gene frequency, 110, 113 gene mutation, 200 gene pool, 109 gene pyramiding, 247, 374 general worth, 139 genes, genetic advance, 130 genetic code, 50 genetic determination, 128 genetic engineering, genetic erosion, 96 genetic gain, 130 genetic linkage, 43–46 genetic markers, 25 genetic transformation, 80, 234 genetic use restriction systems (GURT), 244–246 genetic variation, 79 genetic vulnerability, 90 genetically modified (GM), genome, 36, 237 genomic DNA library, 233 genomic formula, 214 genomic mutation, 200 genomics, 477 genotype, 40 genotype × environment (G × E) interaction, 386, 420–423 germplasm, 29, 87–107 collection, 98 conservation, 91, 98, 103 enhancement, 93 gene pools, 89 genetic vulnerability, 89, 95 importance, 87 sources, 88 storage technologies, 100 germplasm collection, 98 566 germplasm composites, 327 germplasm enhancement, 91, 102 gigas, 216 “Golden Rice”, 5, 410 green revolution, 10 growing degree days, 347 gymnosperms, 76 gynoecium, 58 half-sib family selection, 315 haploid number, 214 haploids, 186–188 anther culture, 186 definition, 189 doubled haploids, 187, 191 ovary culture, 187 Hardy–Weinberg equilibrium, 110, 112 Harlan, J.R., 23, 89 harvest index, 355 harvest maturity, 365 heat stress breeding, 399 heat units, 347 herbicide resistance engineering, 382 heredity, 18 heritability, 127–130 applications, 130 computation, 129 definition, 128 types, 128 hermaphrodity, 55 heterosis, 339 biometrics of heterosis, 340 dominance theory, 340 genetic basis, 339 overdominance theory, 340 heterostyly, 61 heterotic relationship (groups), 341 definition, 342 heterotic groups and patterns, 342 methods for developing groups, 342 heterozygote, 40 high lysine, 405 homeologous chromosome, 222 homologous chromosomes, 37 homozygote, 40 horizontal resistance, 371 host, 369 hybrid, hybrid breeding, 491–494 hybrid cultivar, 283, 334 definition, 335 genetic basis of heterosis, 339 hybrid vigor, 335 inbreeding depression, 336 types of hybrids, 343 INDEX hybrid cultivation, 336 hybrid seed production, 448 hybrid vigor, 335 hybrid weakness, 172 hybridization, 164–172 artificial hybridization, 165 genetic issues, 168 linkage drag, 169 types of population generated, 170 identity preservation, 275 ideotype concept, 354 in situ conservation, 91, 98 in vitro culture, 182 in vitro selection, 188 inbred line, 285, 344, 346 inbreeding, 116–119 inbreeding depression, 61, 335 incomplete block designs, 431 incomplete dominance, 42 incomplete flower, 59 incomplete linkage, 45 independent curling, 133 indexing, 195 indirect organogenesis, 184 inflorescence, 59 insect resistance engineering, 377 intellectual property, 257–262 concept, 257 patents, 258–263 international agricultural research centers, 106, 452–455 International Board of Plant Nomenclature, 76 international centers, 452 International Crop Improvement Association, 447 international crop research centers, 453 International Seed Testing Association, 445 interspecific cross, intrapopulation improvement, 315 ear-to-row selection, 317 full-sib family selection, 318 half-sib family selection, 316 half-sib reciprocal recurrent selection, 326 modified half-sib selection, 318 introns, 50 intuitive index, 135 ionizing radiations, 203 isolines (near isogenic lines, NIL), 283, 308 isozymes, 248 Jones, D.F., Koelreuter, J., law of independent assortment, 39 law of segregation, 39 legal risk, 278 line cultivar, 288 linkage, genetic, 43 linkage block, 123 linkage drag, 169, 307 linkage group, 43 Linneaus, C., living modified organisms (LMO), 274 local control, 148, 429 locus, 39 lodging resistance, 362 long-day plants, 364 low phytate breeding, 412 male gametophyte, 59 male sterility, 70–72 marker-assisted selection (MAS), 251–254, 478 mass selection, 286–288 maternal effect, 37 maternal inheritance, 37 Mather, C., mating design diallel cross, 143 North Carolina design I, 142 North Carolina design II, 142 polycross, 142 mating system, 60, 115, 119 maturity (early), 365 McClintock, B., measures of central tendency, 149 measures of dispersion, 150 meiosis, 38 Mendel, G., 42 Mendelian concepts, 39, 42 Mendelian ratios, 43 Mendel’s laws, messenger RNA, 48 metric traits, 84 microarrays (DNA), 239 microprojectile bombardment (biolistics), 234 micropropagation, 62, 183 see also tissue, culture middling resistance, 374 midparent heterosis, 340 migration, 113 mineral deficiency stress, 401 mineral toxicity breeding, 400 INDEX minor gene resistance, 371 minor genes (polygenes), 43, 84 missense mutation, 202 mitosis, 38 modified pedigree method, 297 modifying genes, 124 molecular breeding, 246, 231 molecular markers, 247–250 monocarps, 57 monocistronic gene, 52 monocots, 76 monoecious plants, 59 monoecy, 61, 68, 349 monoploid, 214 morals, 263 morphological markers, 247 multiline breeding, 308, 374 multilines, 283 multivariate analysis, 155 mutagenesis, 8, 199 mutation, 81, 113 mutation breeding, 196, 199–215 breeding clonally propagated species, 206 breeding seed-bearing plants, 205 factors affecting mutagenesis, 204 limitations of mutagenesis in breeding, 211 mutagenic agents, 203 types of materials used, 204 types of mutation, 200 narrow sense heritability, 128 natural selection, 17 new world crops, 20 Nilsson, H., non-disjunction, 227 non-vascular plants, 76 Norin 10 dwarfing genes, 475 normal distribution, 150 North Carolina designs, 142 novel traits (breeding), 415 nuclear division, 37–39 nucleic acids, 47–49 DNA, 47 RNA, 48 nucleoside, 47 nucleotide, 47 null hypothesis, 147 obsolete cultivars, 97 official trial, 419 oil quality breeding, 411 old world crops, 20 oligogenes (major genes), 43 oligonucleotide, 47 open-pollinated cultivar, 283 open reading frame (ORF), 51 organic agriculture, 468 organic plant breeding, 468 orthodox seed, 98 overdominance gene action, 117, 126 overdominance theory (of heterosis), 339 ovule culture oxidative stress, 401 oxygen enhancement ratio, 204 panicle, 59 parent–offspring regression, 129 parthenogenesis, 188 particle gun, 234 passport data, 100 patents, 258–262 path analysis, 161 pathogen, 369 pathogeneticity, 369 peanut breeding, 529–535 Pearson correlation coefficient, 151 pedigree, 285 pedigree selection, 289–294 penetrance, 46 peptide bonds, 50 perennials, 57 perfect flower, 59 periclinal mutants, 206 phenology, 390 phenotype, 40 photoperiod, 364 photoperiod-insensitive, physical mutagens, 203 physiological maturity, 365 physiological race, 373 physiological traits, 352 pin, 68 plant breeder, 3, 30 plant breeding, 14 art and science of, 24–27 conducting, 28–30 cost, 33 industry, 30–32 international, 32 plant exploration, 102 plant genetic resources, 96, 99 plant genomics, 36, 237 plant ideotype, 354 plant introduction, 102, 104 plant physiology, 25 plant taxonomy, 75 plant variety protection, 262, 442 567 pleiotropy, 43 ploidy modification, 81 pollination, 59–61, 167 cross-pollination, 61 self-pollination, 60 polycistronic gene, 52 polycross test, 328 polygenes, 123 polygenic inheritance, 43, 84 polymerase chain reaction (PCR), 232 polynucleotide, 47 polypeptide synthesis (protein synthesis), 49 polyploidy, 214–230 aneuploidy, 227 autoploidy, 216 breeding alloploids, 226 breeding autoploids, 220 cytology, 217 effects on plants, 216 genetics of autoploids, 218 origin, 216 terminology, 214 variation in chromosome number, 215 polyploidy series, 215 population genetics, 109 population improvement, 119 population mean, 149 population variance, 149 position effect, 47 prebreeding, 102 precautionary principle, 273 preliminary yield trial, 419 primary gene pool, 89 primary trisomics, 227 principal component analysis, 160 progeny test, promoters, 235 protandry, 61 protein, 51–53 regulation, 52 structure, 52 synthesis, 51 protein content engineering, 409 protein markers, 247 proteomics, 238 protogyny, 61 protoplast, 185 pro-vitamin A, 5, public sector breeding, 32 pure line, 282 pure-line selection, 288–290 pure-line theory, purines, 47 568 purity test, 446 pyrimidines, 47 QTL mapping, 251 qualitative variation, 83 definition, 121 polygenes and polygenic inheritance, 123 quantitative traits, 122 see also Variation quality protein maize (QPM), 406–409 quantitative genetics, 121–127 quantitative (polygenic) inheritance, 123 quantitative trait loci (QTLs), 250 quantitative traits, 122, 127 quantitative variation, 84 see also variation r-line, 346 random amplified polymorphic DNA (RAPD), 248 random mating, 111, 115 random sampling, 147 randomization, 148, 429 recalcitrant seed, 98 recessive (recessivity), 39 recessive mutation, 201 recognition sequence (site), 232 recombinant, 45 recombinant DNA, 29 recombination frequency, 45 recurrent mass selection, 136 recurrent selection, 136, 310 concept, 314 genetic basis, 315 types, 315 regeneration, 222 registered seed, 436, 441 regulation of biotechnology, 270–275 biosafety regulation at international level, 274 concept of substantial equivalence, 272 concept of precautionary principle, 273 labeling of biotech products, 274 Reid, R., replicated tests, 430 replication, 49, 148, 429 reporter genes, 235 reproduction, 55–74 alternation of generation, 56 asexual, 62 mode, 55 sexual, 56 INDEX types, 56 types of flowers, 58 reproductive isolation barriers, 171–178 overcoming challenges, 173 resistance (disease), 368, 370 breeding strategies, 373 durable resistance, 371 gene pyramiding, 374 genetic resistance, 371 genetics, 372 horizontal resistance, 371, 375 pest resistance, 373 polygenic resistance, 374 vertical resistance, 371 vertifolia effect, 375 response to selection, 130 restriction enzymes (restriction endonucleases), 232 restriction fragment length polymorphism (RFLP), 248 reverse mutation, 200 ribosomes, 49 rice breeding, 498–507 risk analysis, 264–269 salinity stress breeding, 398 salt tolerance, 399 sample, 147 sample mean, 149 second division restitution (SDR), 216 secondary gene pool, 89 sectorial mutants, 206 seed certification, 435, 441, 445, 447 seed germination test, 445 seed industry, 436 seed testing, 445 seedlessness (breeding), 414 segmental alloploids, 216, 221 selection, 6, 18, 113 index, 133 intuitive index, 134 modes, 115 for multiple traits, 133 response in breeding, 130–134 selection differential, 131 selection index, 133 selective (preferential) pairing, 219 selfed family selection, 319 self-incompatibility, 68 self-pollinated, 60 semidwarfs, 363 sequence characterized amplified regions (SCAR), 249 sequence tagged sites (STS), 249 sexual hybridization, 164 shattering resistance, 362 shoot culture, 183 short-day plants, 364 silent mutation, 202 Simmonds, N.W., 23 simple linear regression, 152 simple sequence repeats (SSR), 249 single-cell selection, 193 single cross, 170 single nucleotide polymorphisms (SNP), 249 single-seed descent, 297–303 site-directed mutagenesis, 83 somaclonal variation, 188, 193 see also variation somatic embryogenesis, 183 somatic hybridization, 185 sorghum breeding, 509–518 southern hybridization, 232 soybean breeding, 519–527 spike, 59 spontaneous mutation, 200 stability analysis, 423–425 stabilizing selection, 115 stamen, 58 standard deviation, 150 standard error of the mean, 151 statistical hypothesis, 147 statistical significance, 147 statistics, 146–162 analysis of variance, 154 chi-square test, 153 coefficient of variation, 151 experimental design, 148 hypothesis, 147 measures of central tendency, 149 measures of dispersion, 150 multivariate statistics, 155–161 normal distribution, 150 population versus sample, 147 probability, 149 simple linear regression, 152 t-test, 153 structural genes, 52 structural mutation, 200 substantial equivalence, 272 supernumerary chromosomes, 229 suspension culture, 182 synteny, 53 synthetic cultivars, 327 synthetic seed, 184 t-test, 153 tagging commercial seed, 446 tandem selection, 133 INDEX technology protection system (TPS), 244 template strand, 50 tertiary gene pool, 89 testcross, 41 three-way cross, 170 thrum, 68 tissue 181–188 applications, 184–186 culture, 181–185 culture medium, 182 directed selection, 193 in vitro selection, 188 micropropagation, 183 somatic embryogenesis, 184 topcross test, 328 totipotency, 181 trademarks, 258 traditional breeding, 29 transcription, 49 transfer RNA, 49 transgenic plants, 9, 377 transgressive segregation, 81, 123 transient expression, 235 translation, 49, 51 transposable elements, 82, 488 triangle of U, 221 triticale, 226 type II error, 147 variable gene expressivity, 47 variable gene penetrance, 46 variation, 18, 79–85 environmental, 79 genetic, 79 qualitative, 83 quantitative, 84 scale, 83 somaclonal, 83 types, 79 variety blend (composite), 310 variety protection, 433, 442–444 vascular plants, 76 Vavilov, N., 7, 19 vegetative propagation, 62 vertical resistance, 371 vertifolia effect, 375 Vigor test, 446 Vilmorin, L., viral resistance engineering, 382 virulence, 369 warm season plants, 78 wheat breeding, 472–483 569 wide crosses, 172–177 bridge crosses, 178 developing new species, 179 objectives, 172 successes, 173 wild type, 200 wobble hypothesis, 50 yield, 353 biological pathways to economic yield, 356 biological yield, 353 definition, 353 economic yield, 353 selecting for yield per se, 356 yield components, 356 yield plateau, 361 yield stability, 361 yield components, 356 yield gains, 435 yield plateau, 361 yield potential, 357, 386 yield stability, 361 yield trials, 418 xenia, 488 ... Generation 29 5 Number of plants Action P1 × P2 Year Year F1 50–100 Bulk and space plant F1 Year F2 2, 000–3,000 Bulk and plant at commercial seeding rate Year F3 2, 000–3,000 Bulk and plant at commercial... Year 10 Year 11 Year 12 Grow BC1F2 plants and screen for desirable plants Backcross 10? ?20 plants to the recurrent parent to obtain BC2F2 seed Grow BC2 plants Select 10? ?20 plants that resemble... harvest, and bulk the BC5F2 seed Grow BC5F2 plants, screen, and backcross Grow BC6 plants, harvest, and bulk the BC6F2 seed Grow BC6F2 plants and screen; select 400–500 plants and harvest separately