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

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

3. “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

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

5. Global Population (Billions) 1950 - 2050
Plant Breeding and Food Security
Global Population (Billions)
Adapted from

6. Urban sprawl encroaches rapidly on farmland
How can we maintain or increase agricultural productivity?
Source:

8. Give us this day our daily bread!!

10. 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:
water
fertilizer
pest control
crop variety
Phenotype, P= Genotype + Environment + (G*E)
Plant breeders concentrate on changing the crop variety (genotype).
Environment component
Genotype

11. Fertility Management and Nutrient Runoff
Nitrogen fertilizers - revolutionized agriculture
P, K, and micro-nutrient fertilizers
Liming
Source:

12. Irrigation
WATER – continues to be the most limiting factor in productivity
Source:

13. Weed Control, Herbicides
Source:

14. Integrated Pest Management
Source:

15. Plant Breeding alone contributes > 50% of increased USA Agricultural productivity
Source:

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

17. 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.

18. 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

19. History of Plant Breeding

20. 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
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, MacLeod, McCarty 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 ‘FlavrSavr’ tomato developed as first GMO
1995 Bt-corn developed

21. 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.

22. 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.

23. 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.
This process is on-going through the work of modern Plant Breeders who design and construct the genetic architecture of plants.
Teosinte, the progenitor of maize (top), modern maize (bottom), and a hybrid between teosinte and modern maize (middle).

24. Reproduction in Plants
Floral structure 24

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

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

27. Gametogenesis
Formation of male and female gametes in higher plants

28. Pollination and Fertilisation
ANTHESIS: Maturation of the anther accompanied by the 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.

29. 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

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

31. 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

32. Principles of Evolution
Variation
Heredity
Selection
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
The core of plant breeding principles

33. Breeders’ Activity Intermate
The work of the plant breeder can be described using six simple verbs (Burton, 1966):
Variate
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
Intermate

34. Review of Mendelian Genetics

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

36. Mendel developed pure lines of pea
Mendel’s Experiments
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

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

38. Mendel crossed parents differing in these characteristics and obtained the following in the first offspring (F1 or first filial generation):
P1 = yellow; P2 = green seeds
F1 hybrids = All yellow
P1 = Purple; P2 = white flowers
F1 hybrids = All purple

39. Discuss dominant vs. recessive here39

40. 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
Each trait can have multiple states
Each individual carries two copies of each trait
One state can be dominant over another, such that heterozygosity leads to the dominant being expressed
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

41. 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 F1 generation from the cross of two pure lines and reappears in the F2 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

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

43. Mendel crossed the F1 to themselves (selfed the F1)
He observed that white flowers that was absent in the F1 appeared in the F2 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

44. Law of Segregation 44

45. Genotype vs. Phenotype
= appearance
= allele combination 45

46. 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

47. Confirmation of law of segregation
The Testcross
The F1 phenotypic ratios tell whether the dominant phenotype is homozygous (no segregation) or heterozygous ( ratio of 1:1) 47

48. 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 (GgWw)
Example of dihybrid cross: Yellow, Round Seed x Green, Wrinkled Seed
F1 Generation: All yellow, round
F2 Generation: 9 Yellow, Round, 3 Yellow, Wrinkled, 3 Green, Round, 1 Green, Wrinkled

50. Female Gametes GW Gw gW gw GGWW GGWw GgWW GgWw Yellow, round GGww Ggww
Mendel selfed the F1 and obtained individuals as shown in Punett Square below:
Female Gametes GW Gw gW gw
GGWW
GGWw
GgWW
GgWw
Yellow, round
GGww
Ggww
Male Gametes
Yellow, wrinkled
ggWW
ggWw
Green, round
ggww
Green, wrinkled

51. Phenotype General Genotype 9 Yellow, Round Seed G_W_
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
ggW_
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

52. PUNNETT-Square: The scheme shows the genotypes of the P-, F1- and F2-generation of a dihybrid hereditary path.
This kind of representation was introduced by the British geneticist R. C. PUNNETT at the beginning of 20th century

53. Law of Independent Assortment53

54. Note:
MENDEL's fundamental work was forgotten for 35 years. It became known in 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

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

56. Incomplete Dominance
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.

57. 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

58. Epistasis
Epistatic genes override or mask the phenotype of a second gene.
Epistasis is not dominance.
Compare the definitions:
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

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

60. 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

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

62. Genes on the same chromosome are linked
Gene loci
Dominant
allele P a B P a b
Recessive
allele
Genotype: PP aa Bb
Homozygous
for the
dominant allele
Homozygous
for the
recessive allele
Heterozygous
Figure 9.9

63. GENETIC RECOMBINATION

64. 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: A B // a b
trans: A b // a B

65. REVIEW OF MOLECULAR GENETICS: THE CHEMICAL BASIS OF HEREDITY

66. 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 ’30s & 40’s proteins rather than DNA was thought to hold genetic information

67. 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

68. Structure of DNA by J. Watson & F. Crick (1953)
Carbon 1 (C1) is where the base is attached.
Carbon 2 (C2) tells you if it is a ribose or deoxyribose. In deoxyribose, oxygen at C2 is missing.
Carbon 3 (C3) is the point of attachment for more nucleotides through a phospho-diesther bond
Carbon 4 (C4) completes the ring via an oxygen (O) which bridges to the carbon 1 (C1). Carbon 5 (C5) hangs away from the ring and is the point of attachment for its phosphate(s).

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

70. Nucleotide Structure

71. DNA is Antiparallel

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

73. DNA Replication

74. 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

75. Thus, a gene locus for any character or trait (eg
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.