CS 253 PRINCIPLES OF PLANT BREEDING LECTURERS 1

CS 253: PRINCIPLES OF PLANT BREEDING LECTURERS: 1. Prof. Richard Akromah [BSc Agric. (Kumasi), MSc (Birmingham), Ph. D (Reading)] 2. Nabila Joshua [ph. D Brooklyn College of Agriculture] 3. Mr. Alexander Wireko Kena [BSc Agric. (Kumasi), MSc (Ibadan)] 1

Recommended Text Books 1. Principles of plant genetics and breeding (2007), by George Acquaah 2. Principles of plant breeding (1960), by R. W. Allard 3. Principles of cultivar development, vol 1. by Walter R. Fehr 4. Principles of crop improvement by N. W. Simmonds 2

• “That whoever could make two ears of corn, or two blades of grass, to grow on a spot of ground where one grew before, would deserve better of mankind and do more essential services to his country than the whole race of politicians put together”. Jonathan Swift, 1726 3

The Role of Plant Breeding in Agriculture What is Plant Breeding? ü Plant breeding is the art and science of the genetic improvement of plants (Fehr, 1993) ü Evolution directed by the will of man (Vavilov, 1951) ü The genetic adjustment of plants to the service of man (Frankel, 1958) ü The branch of agriculture that focuses on manipulating plant heredity to develop new and improved plant types for use by society (Acquaah, 2007) 4

Plant Breeding and Food Security Global Population (Billions) 1950 - 2050 Adapted from http: //www. census. gov/population/popclockworld. html 5

Urban sprawl encroaches rapidly on farmland How can we maintain or increase agricultural productivity? Source: http: //www. ars. usda. gov/is/graphics/photos/ 6

7

Give us this day our daily bread!! 8

9

Objectives of Plant Breeding • Primary objective is to increase crop yield and improve quality of crop produce • Increases in crop productivity come from careful attention to: Ø water Environment Øfertilizer component Ø pest control Øcrop variety Genotype • Phenotype, P= Genotype + Environment + (G*E) • Plant breeders concentrate on changing the crop variety (genotype). 10

Fertility Management and Nutrient Runoff v Nitrogen fertilizers - revolutionized agriculture v P, K, and micro-nutrient fertilizers v Liming Source: http: //www. ars. usda. gov/is/graphics/photos/ 11

Irrigation WATER – continues to be the most limiting factor in productivity Source: http: //www. ars. usda. gov/is/graphics/photos/ 12

Weed Control, Herbicides Source: http: //www. ars. usda. gov/is/graphics/photos/ 13

Integrated Pest Management Source: http: //www. ars. usda. gov/is/graphics/photos/ 14

Plant Breeding alone contributes > 50% of increased USA Agricultural productivity Source: http: //www. ars. usda. gov/is/graphics/photos/ 15

Ancillary Objectives q. Resistance diseases to pests and q. Earliness q. Tolerance to abiotic stresses (eg. Drought, Nitrogen deficiency, mineral toxicity, lodging, Photoperiod response) q. Adaptability to mechanization q. Appearance, taste, nutritional quality q- Aesthetic appeal q. Explain the difference between productivity and production? 16

Plant Breeding and Related Disciplines • Agronomy, horticulture and genetics are the core disciplines • Plant pathology and entomology is basic to developing cultivars for resistance to diseases and insects • Statistics is fundamental to the evaluation characters that are subject to variable environmental conditions • Biochemistry helps in understanding the physiological and molecular basis of phenomena in plants. • Botany is important in physiology, morphology and anatomy of plants. 17

Plant breeders need to: be observant of differences understand the genetics have imagination to visualize final product • foresight to predict demand for future plant products • • • 18

History of Plant Breeding 19

Selected milestones in plant breeding 9000 BC First evidence of plant domestication in the hills above the Tigris river 1694 Camerarius first to demonstrate sex in (monoecious) plants and suggested crossing as a method to obtain new plant types 1714 Mather observed natural crossing in maize 1761 -1766 Kohlreuter demonstrated that hybrid offspring received traits from both parents and were intermediate in most traits, first scientific hybrid in tobacco 1866 Mendel: Experiments in plant hybridization 1900 Mendel’s laws of heredity rediscovered 1944 Avery, Mac. Leod, Mc. Carty discovered DNA is hereditary material 1953 Watson, Crick, Wilkins proposed a model for DNA structure 1970 Borlaug received Nobel Prize for the Green Revolution Berg, Cohen, and Boyer introduced the recombinant DNA technology 1994 ‘Flavr. Savr’ tomato developed as first GMO 1995 Bt-corn developed 20

Evolution of Farming and Cultivated Plants • Agriculture is about 10, 000 years old. • It’s a man-made construct that is still developing. • Agriculture provides mankind with foodstuff, feedstuff, fibre and herbals; which are vital for man’s continued existence on earth. • The first farmer is believed to be a woman, who lived around the Neolithic period, somewhere in the tri-boundary of Iraq, Syria and Turkey (the fertile crescent; Garden of Eden? ) • She abandoned nomadic life as a gatherer of food from the wild, and settled in a fixed community to cultivate crops, due to the intermittent imbalance of food supply from the wild. 21

• Man began to direct the cause of evolution, leading to the domestication of few plant species through artificial selection. • This was made possible through the availability of natural diversity within plant species. • This deliberate effort to alter plants’ morphology, composition, performance, and consequently, usefulness to mankind through selection, established the art of plant breeding. • Through careful selection, seeds of species and individual plants that could best meet man’s need were obtained and propagated outside their ecological niche. • Natural vegetation was cleared to make room for large-scale planting of the chosen crops. • The choice of crop plants made by the primitive Plant Breeders for cultivation still remain as humankind’s most important crops. 22

Crop Domestication: Teosinte to Maize • Domestication actively changes the genetic constitution of living organisms to satisfy the needs of farmers and consumers. • This reflects in their morphologic appearance and behaviour. Teosinte, the progenitor of maize (top), modern maize (bottom), and a hybrid between teosinte and modern maize (middle). • This process is on-going through the work of modern Plant Breeders who design and construct the genetic architecture of plants. 23

Reproduction in Plants Floral structure 24

Terminology Ø Reproduction can be asexual (from vegetative parts--non-gametic/ non-fertilized) or by sexual (requiring effective fertilization/ hybridization forming botanic seed) methods Ø Alternation of sporophytic (2 n) and gametophytic (n) generations Ø In order to change from the sporophytic (2 n) to gametophytic (n) generation, meiosis must take place. Ø Among vascular plants, the diploid (2 n) phase dominates the gametophyte (pollen or embryo sac – n) phase. 25

Types of flowers üComplete flowers - have sepals, petals, stamen, and pistil üIncomplete flowers—lacking one of the above parts üPerfect flowers--stamens and pistils are in the same floral structure - wheat üImperfect flower--stamen and pistil not in the same floral structure üMonoecious ("one house")-stamens and pistils on the same plant (eg. maize, cassava) üDioecious ("two houses")-stamens and pistils on different plants. Ex. hemp, hops, buffalo grass, pawpaw, kiwi, nutmeg üFlowers may either be solitary or may be grouped together to form an inflorescence 26

Gametogenesis Formation of male and female gametes in higher plants 27

Pollination and Fertilisation ccompanied he nther ANTHESIS: the by Maturation of extension of the filament POLLINATION: Transfer of pollen grains from anther to stigma. • Method of transfer varies with crop • Pollen germinates on the stigma and the pollen tube enters the ovule via the micropyle • The generative nucleus divides -----> 2 male germ cells (gametes). These male gametes enter the embryo sac FERTILIZATION: • One male gamete(sperm) fuses with the egg ---> zygote. The other male gamete unites with the two polar nuclei. This triple fusion -----> the primary endosperm nucleus. 28

Mechanisms that promote Self Pollination • Cleistogamy • Chasmogamy • Stigma closely surrounded by anthers • Very few species are completely self pollinated • Rice, oats, wheat, barley, cowpea, soyabean, peanut, tomato, eggplant, okra etc 29

Mechanisms that promote Cross Pollination • Dioecy • Monoecy • Dichogamy (protoandry and protogyny) • Self incompatibility • Male sterility • Heterostyly (pin and thrum flowers) 30

Plant Breeding Vrs Evolution Vavilov (1951) Evolution is a population phenomenon Populations but not individuals evolve What is evolution? Evolution is simply, descent with modification It concerns the effect of changes in allele frequency within a genepool of a population, leading to changes in genetic diversity and the ability of the population to undergo evolutionary divergence The term was proposed by Charles Darwin in 1859 31

Principles of Evolution 1. Variation 2. Heredity 3. Selection The core of plant breeding principles • The process of evolution has parallels in plant breeding • Darwin’s theory of evolution relies on Natural Selection as the discriminating force, and Time • Plant breeders also employ these same principles in cultivar development • Breeders assemble or create variation and impose artificial selection to obtain the most desired individuals that meet their objectives 32

Breeders’ Activity • The work of the plant breeder can be described using six simple verbs (Burton, 1966): – Variate Intermate – Isolate – Evaluate – Multiplicate – Disseminate • The methods of plant breeding are based on the laws of heredity and the recognition that genes situated on chromosomes control hereditary differences between individuals • The phenomenon of segregation and recombination of genes in higher plants resulting from sexual reproduction 33

Review of Mendelian Genetics 34

Mendelian Inheritance Gregor Mendel published a small work with the title Experiments in Plant Hybridization in 1866 Gregor Mendel (1822 -1884) This work remained obscured, and was re -discovered in 1900 35

Mendel’s Experiments 1. Mendel developed pure lines of pea Pure Line - a population that breeds true for a particular trait e. g. , all seeds are either round or wrinkled, flowers purple or white for many generations. This was an important innovation because any non-pure (segregating) generation would and did confuse the results of genetic experiments. 2. Counted his results and kept statistical notes – this is essential for data analysis 36

Mendel had pure parental lines (P) that differed in single characters or traits Flower colour: Purple vrs white Seed colour: Green vrs yellow Seed shape: Round vrs wrinkled 37

Mendel crossed parents differing in these characteristics and obtained the following in the first offspring (F 1 or first filial generation): P 1 = yellow; P 2 = green seeds F 1 hybrids = All yellow P 1 = Purple; P 2 = white flowers F 1 hybrids = All purple 38

39

The Allele Concept Allele - one alternative form of a given allelic pair; purple and white are the alleles for the flower colour of a pea plant; more than two alleles can exist for any specific gene, but only two of them will be found within any diploid individual Allelic pair - the combination of two alleles which comprise the gene pair Homozygote - an individual which contains only one allele at the allelic pair; for example DD is homozygous dominant and dd is homozygous recessive; pure lines are homozygous for the gene of interest 40

Dominant - the allele that expresses itself at the expense of an alternate allele; an allele that determines the phenotype in a heterozygous condition Recessive - an allele whose expression is suppressed in the presence of a dominant allele; the phenotype that disappears in the F 1 generation from the cross of two pure lines and reappears in the F 2 generation. A recessive allele displays no influence on the phenotype in heterozygous individuals Homozygote - an individual which contains the same allele at a gene locus; for example DD is homozygous dominant and dd is homozygous recessive; pure lines are homozygous for the gene of interest Heterozygote - an individual which contains one of each member of the gene pair; for example the Dd heterozygote Monohybrid cross - a cross between parents that differ at a single gene pair (usually AA x aa) Monohybrid - the offspring of two parents that are homozygous for alternate alleles of a gene pair Remember --- a monohybrid cross is not the cross of two monohybrids 41

The phenotype is the appearance of an individual that is based on an underlying genotype and on the influence that the environment exerts 42

Mendel crossed the F 1 to themselves (selfed the F 1) He observed that white flowers that was absent in the F 1 appeared in the F 2 in a ratio of 3 purple flowers to one white flower i. e. , a phenotypic ratio of 3: 1 MENDEL's first law is the principle of segregation. It states that during gamete formation each member of the allelic pair separates from the other member to form the genetic constitution of the gamete. 43

Law of Segregation 44

Genotype vs. Phenotype = appearance = allele combinatio 45

According to this principle hereditary traits are determined by discrete factors (now called genes) that occur in pairs, one of each pair being inherited from each parent. This concept of independent traits explains how a trait can persist from generation to generation without blending with other traits. It explains, too, how the trait can seemingly disappear and then reappear in a later generation. The principle of segregation was consequently of the utmost importance for understanding both genetics and evolution 46

Confirmation of law of segregation The Testcross The F 1 phenotypic ratios tell whether the dominant phenotype is 47 homozygous (no segregation) or heterozygous ( ratio of 1: 1)

Mendel’s Second Law Mendel also performed crosses in which he followed the segregation of two genes e. g. , Yellow and round seeds x Green and wrinkled seeds. The dominance relationship between alleles for each trait was already known to Mendel when he made this cross Dihybrid cross - a cross between two parents that differ by two pairs of alleles (GGWW x ggww) Dihybrid - an individual heterozygous for two pairs of alleles (Gg. Ww) Example of dihybrid cross: Yellow, Round Seed x Green, Wrinkled Seed F 1 Generation: All yellow, round F 2 Generation: 9 Yellow, Round, 3 Yellow, Wrinkled, 3 Green, 48 Round, 1 Green, Wrinkled

49

Mendel selfed the F 1 and obtained individuals as shown in Punett Square below: GW Gw g. W gw GW GGWw Gg. WW Gg. Ww Yellow, round Gw GGWw GGww Gg. WW Ggww Male Gametes Yellow, round Yellow, wrinkled g. W Gg. Ww gg. WW gg. Ww Yellow, round Green, round gw Gg. Ww Ggww gg. Ww ggww Yellow, round Yellow, wrinkled Green, round Green, wrinkled Female Gametes 50

The phenotypes and general genotypes from this cross can be represented in the following manner: Phenotype General Genotype 9 Yellow, Round Seed G_W_ 3 Yellow, Wrinkled Seed G_ww 3 Green, Round Seed gg. W_ 1 Green, Wrinkled Seed ggww The results of this experiment led Mendel to formulate his second law. Mendel's Second Law - the law of independent assortment; during gamete formation the segregation of the alleles of one allelic pair is independent of the segregation of the alleles of another allelic pair It does inevitably cover the case that new combinations of genes, that were not existing before can arise. In MENDEL's experiment these are the combinations: Yellow wrinkled seeds; Green round seeds 51

PUNNETT-Square: The scheme shows the genotypes of the P-, F 1 - and F 2 generation of a dihybrid hereditary path. This kind of representation was introduced by the British geneticist R. C. PUNNETT at the beginning of 20 th century 52

Law of Independent Assortment 53

Note: MENDEL's fundamental work was forgotten for 35 years. It became known in 1900. The German C. CORRENS, the Dutchman HUGO de VRIES and the Austrian ERICH von TSCHERMAK-SEYSENEGG are regarded as its rediscoverers. Mendel’s work is today viewed as the fundament of modern genetics. The chromosome theory confirmed Mendel’s work 54

Complications to Mendelian Genetics 1. Gene actions • Intra-allelic interactions » Additivity » Incomplete or partial dominance » Dominance » Over-dominance • Inter-allelic interactions » Epistasis » Pleiotrophy 2. Linkage 55

Incomplete Dominance is an exception to Mendel’s general observations. In case of incomplete dominance, a homozygous dominant trait crossed with a homozygous recessive trait will produce an intermediate trait which allows some of the recessive trait to filter through, incompletely masked by the dominant trait. 56

Dominance • Dominance is not an inherent property of an allele • An allele may be dominant to a second allele, but co-dominant, incompletely dominant, or even recessive to a third 57

Epistasis Epistatic genes override or mask the phenotype of a second gene. Epistasis is not dominance. Compare the definitions: Epistasis One gene masks the expression of a different gene for a different trait Dominance One allele masks the expression of another allele of the same gene 58

Classical Epistatic Ratios • About 6 different epistatic gene actions have been observed 1. Complementary gene action (9: 7): also known as duplicate recessive epistasis 2. Duplicate gene action (15: 1): a. k. a duplicate dominant epistasis 3. Recessive suppressors (13: 3): a. k. a dominant and recessive epistasis 4. Additive gene action (9: 6: 1) 5. Dominant epistasis (12: 3: 1) 6. Recessive epistasis (9: 3: 4) 59

Pleiotropy One gene causes multiple effects on a phenotype, i. e. the control of two or more characters by a single gene Sickle cell anemia: one mutant gene, many symptoms Single amino acid substitution in the hemoglobin protein Pain, stroke, leg ulcers, bone damage, jaundice, gallstones, lung damage, kidney damage, eye damage, anemia, delayed growth 60

LINKAGE • T. H. MORGAN’S LAWS (1911): • Genes occur chromosomes • Linked genes chromosome in a are linear on order the • Genes can be exchanged chromosomes during meiosis on same between • The closer genes are located on a chromosome, the less likely they will separate and recombine in meiosis 61

Genes on the same chromosome are linked Gene loci Dominant allele a P P Genotype: PP Homozygous for the dominant allele B b a aa Homozygous for the recessive allele Recessive allele Bb Heterozygous Figure 9. 9 62

GENETIC RECOMBINATION 63

• If two genes are close enough together, they will not assort independently • If they are not close together, recombination or crossing over may occur to separate them • Linkage types – Two possible configurations • cis: • trans: A B // a b A b // a B 64

REVIEW OF MOLECULAR GENETICS: THE CHEMICAL BASIS OF HEREDITY 65

Discovery of DNA as the Hereditary Material • Nucleic Acids (DNA and RNA) were discovered in 1869 by Friedrich Mieschner as a substance contained within cells • During the ’ 30 s & 40’s proteins rather than DNA was thought to hold genetic information 66

What is DNA? • Deoxyribonucleic acid (DNA) is a Nucleic Acid • Nucleic acids are polymers of Nucleotides • A nucleotide consists of three molecules – A Pentose or 5 -carbon sugar – A nitrogenous base – Phosphate group • There are four N-bases in DNA – Adenine, Guanine, Thymine, Cytosine 67

Structure of DNA by J. Watson & F. Crick (1953) • Carbon 1 (C 1) is where the base is attached. • Carbon 2 (C 2) tells you if it is a ribose or deoxyribose. In deoxyribose, oxygen at C 2 is missing. • Carbon 3 (C 3) is the point of attachment for more nucleotides through a phospho-diesther bond • Carbon 4 (C 4) completes the ring via an oxygen (O) which bridges to the carbon 1 (C 1). Carbon 5 (C 5) hangs away from the ring and is the point of attachment for its phosphate(s). 68

• DNA is a double stranded helix • The two strands are Antiparallel • Strands are held together hydrogen bonds between bases by • A pairs with T, and C with G 69

Nucleotide Structure 70

DNA is Antiparallel 71

DNA Replication • Before mitosis and meiosis, all of the DNA in the cell must be copied or replicated • How does this happen? 72

DNA Replication 73

What is a gene? • A gene is a piece of DNA consisting of coding (exons) and non-coding (introns) base sequences with the inherent ability to be transcribed and translated to produce a protein 74

• Thus, a gene locus for any character or trait (eg. Flower colour, seed coat colour, disease resistance, dwarfism, etc) on any chromosome, can be viewed as a code of genetic information written with the four bases; A, C, G, T. • Alleles actually emanate from differences in base sequences on homologous chromosomes caused by mutations, resulting in different proteins being formed, hence different phenotypes. 75