Plant Genetics and Molecular Biology

Republic of the Philippines
PARTIDO STATE UNIVERSITY

Goa, Camarines Sur
PARTIDO STATE UNIVERSITY TINAMBAC CAMPUS

Name of Campus/ College
Module II
PLANT GENETICS AND MOLECULAR BIOLOGY
Name of Student: _________________________________ Week No: Weeks 12 – 13

Course Code: CSBIO2 Name of Faculty: For. Ceazar Ian B. Pesimo
Course Title: GENERAL BOTANY
I. OBJECTIVES
At the end of the lesson, the student must be able to:

 Explain the basic concepts of Genetics and discuss the concept of plant heredity and variation in the
context of Mendel’s Principles and Sutton’s Chromosomal Theory of Inheritance;
 Learn the concepts in Central Dogma of Molecular Biology and understand the complexity of the
process that makes the genetic information in genes be utilized for the daily needs of the plant;
 Describe the different Plant Breeding Techniques and relate associated concepts of plant genetics; and
 Define population and discuss the forms of evolution, speciation, how does it happen and the main
evolutionary factors affecting plant genetic diversity.
II. LESSON
Basic Concepts of Plant Genetics

- Genetics
o is a branch of biology that deals with heredity and variation of organisms;
o study of genes and inheritance.
- Plant Genetics
o Sub-discipline of genetics concerned with the genetic variation and inheritance in botanical
species.
Two Viewpoints of Heredity
- “Blending” Hypothesis:
o genetic materials from two parents blends together;
o offsprings were essentially a "dilution" of the different parental
characteristics
- “Particulate” Hypothesis:
o parents pass on discrete heritable units (genes)
- Between the two viewpoints, it is the Particulate hypothesis that is
scientifically accepted nowadays as established by the theory of Mendel.
Concept of Variation
- Absence of uniformity among trees considering their individual traits
- Variation in trees generally recognized to be wide reaching to almost
infinity and results in GE or Genetic x Environment Interactions
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- Categories:
o Variation among species o Stands within sites
o Among provenances of a species o Individual trees within stands
(geographic variation) o Within individual trees (limited
o Sites within provenances extent)
Genes vs. Traits vs. Alleles
- Genes (Character)
o Functional units or a portion of DNA that code for specific traits
o Ex. Plant height; Fruit Color
- Allele
o Refers to a specific form or portion of the gene that is responsible for the variations in which the
trait can be expressed.
o Ex. AA/Aa/aa
- Traits
o Specific characteristics that vary from individual to individual as coded by the DNA
o Ex. Short/tall; Yellow/Green
- To explain further:
Allele
Gene Traits
Dad Mom
Eye color B b Brown/blue
Hair color D D Dark/blond
Smartness s S Smart/non-smart
Ability to tongue roll T T Tongue roller
Genotype vs. Phenotype

- Genotype
o Genetic make-up of a particular gene or the set of alleles carried by an organism
o Alleles are always in pairs.
 Dominant vs. Recessive Alleles
 Dominant (A)
o The allele of a gene that masks or suppresses the expression of an
alternate allele
o The trait appears in the heterozygous condition.
o Represented by a capital letter and is always written first when present.
 Recessive (a)
o An allele that is masked by a dominant allele
o Does not appear in the heterozygous condition, only in homozygous.
o Represented by a small letter
 Homozygous vs. Heterozygous Allele Pairing
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 Homozygous (AA) or (aa)

o having identical alleles for a particular characteristic
o AA or Homozygous Dominant
 dominant trait will be exhibited
o aa or Homozygour Recessive
 recessive trait will be exhibited
 Heterozygous (Aa)
 having identical alleles (one from each parent) for a particular characteristic
 If A is dominant then a will be masked
- Phenotype
o the physical or observable expression of the gene or as dictated by the genotype
o Result of Genetic and Environmental Interaction
o Using the example in the Genes vs Trait vs Alleles:
Genotype
Phenotype
Characteristics Trait Allele
Eye color B-brown; b-blue Bd Brown eyes
Hair color D-dark; d-blond Dd Dark hair color
Smartness S-Smart; s-nonsmart Ss Smart
Ability to T-Tongue roller;
TT Tongue roller
tongue roll t-non-tongue roller
The Punnett Square

- Invented during the early 20th Century by an English geneticist named Reginald Punnett.
- A graphical way of discovering all the possible combinations of genotypes that can occur in an offsprings
using the genotypes of the parents.
- To use this,
o the genotype of the parents must be identified
o draw the P-square and utilize it
o split the alleles of the parental genotype and put it outside the p-square
o determine the possible genotype of the offspring by filling in the p-squares
o summarize the results of the offspring’s genotype and use it to determine its phenotype
Three (3) Principles of Mendelian Inheritance

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- In 1866, Gregor Mendel (Father of Genetics) published Experiments in Plant Hybridization (Versuche über
Pflanzen-Hybriden) that first established these principles.
- Mendel looked at seven traits or characteristics of pea plants:
- Terminologies:
o True-bred (pure bred): all offspring of same variety
o Hybridization: crossing of 2 different true-breds
o Monohybrid cross:
 a genetic cross involving a single pair of genes (one trait); parents differ by a single trait.
 P = Parental generation
 F1 = First filial generation; offspring from a genetic cross.
 F2 = Second filial generation of a genetic cross
o Dihybrid cross
 Matings that involve parents that differ in two genes.
- Mendel’s 1st Experiment

o Mendel bred two (2) purebreds: 1 Homozygous Dominant (Purple flower) x Homozygous
Recessive (White flower)
o F1 generation: Genotype = 100% have Heterozygous trait (Pp)
Phenotype = 100% purple flowers
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o As what can be observed, despite crossing purple flowers with white ones, the offsprings always
come out to have purple flowers. This proposes that some traits are dominant over others: the
purple color being the dominant while the white as the recessive one.
o This caused the formulation of the first principle of inheritance: Law of Dominance
 In a cross of parents that are pure for contrasting traits, only one form of the trait will
appear in the next generation.
 Offspring that are hybrid for a trait will have only the dominant trait in the phenotype
- Mendel’s 2nd Experiment

o For this, Mendel continued breeding the offsprings from the 1st experiment: 1 Heterozygous pair
(Purple flower) x 1 Heterozygous pair (Purple flower)
o F2 generation: G = 1 Homozygous dominant: 2 Heterozygous pairs: 1 Homozygous recessive
P = 3 Purple flowers: 1 White flower
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o In the whole experiment, it is only in the F2 generation that the white flower was expressed and it
constantly happens in the ratio of 3:1 with 1 being the occurrence of white flowers.
o This result caused the formulation of the second principle: Law of Segregation
 When gametes (egg/sperm) are formed, the pairs of hereditary factors (genes) become
separated, so that each sex cell (egg/sperm) receives only one kind of gene.
 The allocation of gene copies is random.
 To review, this is supported in the process of meiosis as to why the daughter cells are
haploids.
- Mendel’s 3rd Experiment

o Mendel continued the experiment by considering two traits in
crossing to plants.
o For the P1 of the dihybrid cross: 1 purebred of pea plant with
Homozygous Dominant genes both in flower color (Purple)
and stem length (Tall) and 1 with Homozygous Recessive
genes (White flower and short stem length).
o The F1: G = 100% heterozygous trait
P = 100% Tall and purple flowers
o This dihybrid crossing was continued where F1 generation were allowed to crossbreed or self-
pollinate with each other.
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o In this last part, it resulted to a ratio of 9 Tall, Purple: 3 Tall, White: 3 Short, Purple: 1 White, Short.
This phenotypic ratio was consistent throughout the experiment and it is consistent when four (4)
attributes are randomly mathematically assorted.
o This leads to the 3rd principle of inheritance: Law of Independent Assortment
 Alleles for different traits are distributed to sex cells independently of one another.
 The allele a gamete (egg/sperm cell) receives for one gene does not influence or affect
the allele received for another gene. The segregation of one trait (flower color) is not
affected by the segregation of the other trait (stem length).
- Besides being the core principle in genetics as a science, here are some other applications of the Principles:
o Test cross (Breeders)
 The process used to identify the genotypes of an individual just by looking at its
phenotype.
 It is done by crossing the genotype of the individual to a homozygous recessive individual.
o Back cross
 The process used to achieve an offspring/F2 having a genetic identity to be closer to that
of the parent.
 It is done by crossing the F1 x Parental genotype (Pure breed)
- In connection to the Law of Dominance, There are types of dominance:

o Complete dominance
 offspring always looked like one of their two parents (Mendel’s experiment)
o Incomplete dominance
 full expression of 2 alternative alleles in a heterozygote, resulting in a phenotype in which
the presence of both alleles can be detected
 individuals with heterozygous alleles exhibit a phenotype intermediate between those with
homozygous alleles
Complete dominance Incomplete dominance
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The Chromosomal Theory of Inheritance
- This theory was proposed by Walter Sutton and Theodor Boveri in 1902.
- It identified Chromosomes as the genetic material responsible for the
Mendelian inheritance.
- It states that genes (as hereditary units) are found at specific locations on
chromosomes and that the behaviour of chromosomes during meiosis is
consistent with Mendel’s Law.
- The series of experiments led to the following observations:
o During meiosis, homologous chromosome pairs migrate as discrete
structures that are independent of other chromosome pair.
o The sorting of chromosomes from each homologous pair into pre-
gametes appears to be random.
o Each parent synthesized gametes that contain only half of their
chromosomal complement.
o Even though the male and female gametes differ in size and morphology, they have the same
number of chromosomes suggesting equal genetic contributions from each parent.
o The gametic chromosome combine during fertilization to produce offspring with the same
chromosome number as their parents.
The Chromosome
- A thread-like structure composed of DNA, carrying the hereditary information (gene)
- Review the Cell Cycle as how chromosome are duplicated and recombine
- Main functions:
o It ensures that DNA are copied accurately and distributed among cells.
 This is essential in making sure that the organism properly grow and function.
o Provides packaging to DNA. Without this, DNA molecules won’t fit inside the cell
 If the DNA of a human cell is stretched, it would reach 6 feet.
 Order of coiling: DNA – Histones – Nucleosome – Chromatin – Chromosome
 Histones – protein where the DNA binds itself forming the Nucleosome
 Nucleosome – repeating unit of Chromatin with 8 histone proteins and about `146 base pairs of DNA
 Chromatin coils itself into higher order structures, such as the Chromosome
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The DNA:
- Review of previous notes:
o Gene - a unit of heredity
o Genome - the entire set of genes in an organism; totality of genetic component
o Locus (Loci) - a fixed location on a strand of DNA where a gene or one of its alleles is located
o Alleles - two forms of a gene that occupy the same position on homologous chromosomes and that
cover the same trait
- DNA or Deoxyribonucleic Acid is the material basis of heredity
o Biological macromolecule for the storage of genetic information
o Universal for all bacteria and higher organisms
o DNA can be found in:
 Nucleus (biparental inheritance)
 Plastids (uniparental inheritance)
 Mitochondria: maternal
 Chloroplasts:
o Angiosperms usually maternal
o Gymnosperms (Conifers) usually paternal
- DNA Structure
o The repeating units of DNA: Nucleotides

 Nucleotides:
 Pentose sugar = Deoxyribose
 Phosphate (PO4 )
 Nitrogen Bases:
o Purines
 Adenine (A)
 Guanine (G)
o Pyramidines
 Thymine (T)
 Cytosine (C)
o A DNA molecule consists of two nucleotide chains

(strands), running in opposite directions and coiled
into a double helix
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o Nitrogen bases in DNA strands can pair in only one way

 Purines pair Pyramidines:
 Adenine always pairs with Thymine
 Guanine always pairs with Cytosine
 The sequence of bases is the genetic code.

 Variation in base sequences gives life diversity
 Chargaff’s Rule
 The amounts of thymine and adenine in DNA are the same, and the amounts of
cytosine and guanine are the same: A = T and G = C
 Base pairs form on the inside of the helix, held together by hydrogen bonds (A-T and G-C)
 Adenine forms 2 H2 bonds to Thymine, Guanine forms 3 H2 bonds to Cytosine
o DNA vs RNA
Ribonucleic Deoxyribonucleic
Parameters
Acid (RNA) Acid (DNA)
Sugar Ribose Deoxyribose
Structure Single-stranded Double-stranded
Nitrogen Bases Uracil Thymine
Prominent Nucleus and
Nucleus
Location Cytoplasm
Central Dogma of Molecular Biology
- This is simply the flow of genetic information

- Involves Three (3) Major processes: DNA Replication,
Transcription and Translation
- Four (4) Requirements for DNA to be a genetic
material:
o Must carry information
 Cracking the genetic code
o Must replicate
 DNA replication
o Must allow for information to change
 Mutation
o Must govern the expression of the phenotype
 Gene function
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- To utilize the genetic information of DNA, it must first be made available and be accessed
o DNA stores information in the sequence of its nitrogen bases (A=T, C=G)
 Much of DNA’s sequence-specific information is accessible only when the double helix is
unwound or split.
 Proteins read the DNA sequence of nucleotides as the DNA helix unwinds.
 Proteins can either bind to a DNA sequence, or initiate the copying of it.
DNA Replication
Definition
- Process of duplication of the entire genome prior to cell division
- Biological significance
o extreme accuracy of DNA replication is necessary in order to preserve the integrity of the genome
in successive generations
o In eukaryotes, replication only occurs during the S phase of the cell cycle.
 Replication rate in eukaryotes is slower resulting in a higher accuracy of replication in
eukaryotes
The summarized mechanism of DNA replication
- Initiation
o Proteins bind to DNA and open up double helix
o Prepare DNA for complementary base pairing
- Elongation
o Proteins connect the correct sequences of nucleotides into a continuous new strand of DNA
- Termination
o Proteins release the replication complex
Basic rules of replication
- Semi-conservative –
o DNA Replication would produce 2 copies that each contained 1 of the original strands and 1 new
strand
- Starts at the ‘origin’

o Initiator proteins identify specific base sequences on DNA called sites of origin.
 Prokaryotes – single origin site
 Eukaryotes – multiple sites of origin
- Semi-discontinuous and synthesis is always in the 5-3’ direction
o Antiparallel strands replicated simultaneously
 Leading strand synthesis continuously in
5’– 3’ direction
 Lagging strand synthesis in fragments in
5’-3’ direction
- RNA primers required
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o RNA primase provides base pairs at the site of origin to which the main enzyme synthesizing
nucleotides (DNA polymerase 3) can attach itself and continue the DNA Replication.
Detailed discussion of the DNA Replication process
- DNA Replication is the process by which the original DNA is used as a template for the production of a new
complementary DNA strand.
- Initiation
o The process starts at the origin of the replication site. Plant, like any eukaryotes have many of these.
o It begins in the nucleus when an enzyme: Helicase breaks
the hydrogen bonds between the two strands of DNA,
unwinding the double helix DNA into two single strands
that serve as template for the replication of DNA.
 The resulting structure is called the Replication
Fork.
 DNA Gyrase relieves strain by unwinding helicase
o Single-strand Binding Protein (SSBP)
 SSBP prevents the separated strands from
binding again too early during the replication
process.
o Enzyme Primase assembles an RNA primer at the origin
of replication site
 RNA primer – short sequence of RNA
nucleotides, complementary to a small, initial
section of the DNA strand prepared for replication
- Elongation
o The Leading Strand is formed from its 5’ to its 3’ strand by the enzyme DNA Polymerase 3.
o DNA Polymerase 3 then adds nucleotide units to leading strand.
 Nucleotides contain sugars (deoxyribose), phosphate and nitrogen bases (A,C,T,G)
o The other strand known as the Lagging Strand is

formed backward from its 3’ to its 5’.
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 It does not form continuously like the leading strand; instead it forms in pieces known as
Okazaki fragments.
 Okazaki fragments are series of short DNA fragments, and each requires a separate RNA
primer.
o Primase again adds RNA nucleotides which is short sequence of RNA nucleotides, complementary
to a small, initial section of the DNA strand to the lagging strand.
o DNA polymerase 3 lays down a new DNA in lagging strand. This process is repeated as new DNA
is added to the strand.
Termination
o As eukaryotes have multiple initiation sites, DNA replication happens simultaneously and so as
DNA Polymerase 3 making new DNA strands.
o DNA Polymerase 3 will stop once it encounters an already replicated part of the DNA. Once this
happen it will remove itself from the replication fork.
o To end the DNA Replication process, the RNA Primer must be replaced by DNA nucleotides by
another type of DNA polymerase known as DNA Polymerase 1.
 DNA Polymerase 1 will
replace all the RNA primers
with DNA nucleotides.
o The enzyme DNA Ligase links the
Okazaki fragments in the lagging
strand and other discontinuities within
the new strand.
o Finally, all other enzymes will
unattached themselves closing the
Replication Fork and terminating the
DNA Replication process.
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Regulation of DNA Replication

- Cell cycle regulation by protein phosphorylation ensures that
activities before DNA replication can only occur in G1 phase
and that the actual DNA replication shall only occur in the S
phase. Other checkpoint regulation include making sure that
cell cycle does not progress not until DNA replication is
complete, accuracy of DNA replication and stabilizing the
replication fork.
Review:
- Genes and Proteins
o Genes are a sequence of nucleotides in DNA that code for a particular protein
o Proteins drive cellular processes, determine physical characteristics, and manifest genetic
disorders by their absence or presence
o Genetic information (DNA) is contained within the nucleus (mostly) of a cell, which directs protein
synthesis, but protein synthesis occurs in ribosomes located in the cytoplasm
- Gene Expression
o A multistep process by which genetic information encoded by a gene is converted into a structural
or functional part of a cell or body
o DNA codes for RNA and RNA makes protein
 DNA transcribed to mRNA by a process called transcription.
 Ribosomes use mRNA as a blueprint to synthesize proteins composed of amino acid by a
process called translation.
- One Gene – One Enzyme
o The Beadle and Tatum experiment showed that one gene codes for one enzyme.
o One gene codes for one polypeptide.
 Polypeptide - a chain of covalently bonded amino acids.
 Proteins are made of one or more polypeptide
Transcription
Definition
- Enzymes use the nucleotide sequence of a gene to synthesize a complementary strand of RNA
- The process of transcribiing DNA into RNA (mRNA)
- Transcription is the process of taking one gene (DNA) and converting into a mRNA strand and happens at
the Nucleus of the cell.
RNA or Ribonucleic Acid

o RNA vs DNA
Ribonucleic Deoxyribonucleic
Parameters
Acid (RNA) Acid (DNA)
Sugar Ribose Deoxyribose
Structure Single-stranded Double-stranded
Nitrogen Bases Uracil Thymine
Prominent Nucleus and
Nucleus
Location Cytoplasm
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o There are three types of RNA:

 mRNA – Messenger RNA
 is the “blueprint” for building a protein
 carries genetic information from DNA in the nucleus to direct protein synthesis in
the cytoplasm
 rRNA – Ribosomal RNA
 is the “site” where the proteins are made
 associates with protein to form the ribosomes
 tRNA – Transfer RNA
 is the “vehicle” delivering the proper amino acid to the site of protein synthesis
 transports amino acids to the ribosome
Detailed discussion of the Transcription process
- Initiation
o RNA polymerase binds to the promoter of a gene and unwinds the DNA
 RNA polymerase recognizes the promoter region which is a sequence of DNA rich in A
and T bases (TATA box) found only on one strand of the DNA.
 Promoter serve as the start signal region of transcription.
- Elongation
o RNA polymerase uses only one of the strands of DNA as a template for mRNA synthesis.
 RNA polymerases can add nucleotides only to the 3’ end of a DNA sequence. Thus, an
RNA molecule elongates in the 5’ to 3’ direction.
o RNA polymerase makes the mRNA copy by producing RNA nucleotides complementing the
nitrogen bases of the coding strand of the DNA.
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o As the RNA polymerase molecule passes, the DNA helix re-forms.
- Termination
o Synthesis continues until the end of a gene is reached where RNA polymerase recognizes a
terminator sequence.
 Terminator serve as the signal that stops the transcription process.
o The two strands of DNA rejoin and a strand of mRNA is produced.
- Post-Transcriptional Processing
o Once the RNA polymerase leaves the promoter region, a new RNA polymerase can bind there to
begin a new mRNA transcript.
o In eukaryotes, the mRNA released at the end of transcription is called pre-mRNA.
o The pre-mRNA from eukaryotic cells needs some modification before it leave the nucleus and
proceed with Translation.
o Importance of processing of Pre-mRNA
 Pre-mRNA undergoes several changes before it is exported out of the nucleus to protect it
from the cytoplasmic environment.
 Modifications help the RNA molecule to be recognized by molecules that mediate RNA
translation into proteins
 Helps increase the efficiency of protein synthesis as it allows only specific protein- coding
RNA to go on to be translated
o Activities in the processing of Pre-mRNA:
 The 5’ end of the pre-mRNA is capped with a modified form of the G nucleotide. At the 3’
end, an enzyme in the nucleus adds the poly A tail, a long series of A nucleotides.
 Portions of the RNA chain that are not supposed to be

translated into proteins are cut out of the sequence.
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 Introns - non-coded sections

 Exons - codes for a protein
 The initial pre-mRNA contains introns that are removed from the pre-mRNA by
Spliceosomes while the exons are spliced together.
o After processing the Pre-mRNA:
 mRNA leaves the nucleus through the nuclear pores
 mRNA reaches the ribosomes
Review
Proteins
- Are polymers of amino acids
o There are only 20 different amino acids
o But, there are hundreds of thousands of different proteins
- Amino acids bond to form polypeptide chains
o Peptide Bonds – Link each amino acids together to form proteins
Translation
Definition
- Simply the production of proteins from mRNA
- mRNA goes to the ribosomes in the cytoplasm or the RER and produces proteins
- Ribosomes synthesize different proteins by reading the coding sequence on mRNA
Codons
- The mRNA is read in triplets of nucleotides or Codons
- There are 61 different codons for amino acids
o 1 “start” codon (AUG) – starts the translation process
o 3 “stop” codons (UAA, UAA, UGA) – stops the translation
process
- The order of the codons in the mRNA determines the order of the
amino acids in the polypeptide chain.
- Each codon encodes an amino acid.
o The figure beside enumerates the amino acid being coded by
every available codon
Transfer RNA or tRNA
- Refers to an adapter molecule composed of RNA and is typically 76 to 90
nucleotides in length.
- Serves as the physical link between the mRNA and the amino acid
sequence of proteins
- It is three-lobed like “cloverleaf” due to base pairing between
complementary nucleotides on different regions of each tRNA molecule
causing it to fold
- At the end of one lobe of tRNA, a sequence of three bases called the
anticodon is present.
o Anticodon is complementary to a codon of the mRNA and binds
to it through base pairing.
- The other end of the tRNA carries the amino acid that’s specified by the
codon.
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Ribosome
- Ribosomes are the site of protein synthesis.
- It’s a complex structure and contains a cluster of different kinds of proteins and rRNA which
are linear strands of RNA
- The ribosome has binding sites for the mRNA transcript and the amino acid-tRNA molecules.
- Each active ribosome has 3 different binding sites for tRNA molecules:
o P (peptide) site – holds one amino acidtRNA and the growing chain of amino acids;
o A (acceptor) site – holds the tRNA bringing the next amino acid to be added to the
chain;
o E (exit) site – releases the tRNA molecules back into the cytoplasm
- There are also two subunits to the ribosome and they lock together with a mRNA trap inside to synthesize
chains of amino acids.
o Large ribosomal subunit
o Small ribosomal subunit
Detailed discussion of the Translation process
- Initiation
o To begin the process, there must be the following:
 Ribosome (Large + small subunits)
 mRNA strand
 “Initiator” tRN carrying the start codon forming: Formylmethionine or Fmet
o The initiator tRNA attaches to the small ribosomal subunit and bind to the 5’ end of the mRNA.
o After binding, the tRNA scans the mRNA in 5’ to 3’ direction until it finds the start codon (AUG).
o When all these happen, the “initiation complex” is said to be formed and the protein synthesis
process begins.
- Elongation
o The Fmet-carrying tRNA starts in the middle slot of the ribosome, the P site.
o This makes the codon right after the start codon to be exposed to the A site of the ribosome which
serve as the “landing site” for the next tRNA
 This next tRNA must contain the complementary anticodon to match that of the exposed
codon in the mRNA.
o Once the matching tRNA has landed in the A site, a peptide bond forms.
 This peptide bond connects one amino acid to another.
o The presence of the peptide bond allows the transfer of the Fmet to the amino acid of the tRNA in
the A site.
o As the tRNA becomes “empty” from amino acid that had just transferred, it will drift out through the
E site in the ribosome which exposes a new codon in the A site.
o The whole cycle repeat and form a chain of amino acids of polypeptide.
- Termination
o The production of polypeptide end when a stop codon (UAA, UAG or UGA) enters the A site.
o The stop codons are recognized by proteins called release factors which fits into the P site, despite
not being a tRNA.
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 This release factor stops the formation of peptide bonds and the newly made protein is
released.
o Finally, the ribosome will disintegrate into its subunits and will separate from the mRNA strand it
has been translating.
 The materials are said to be reusable and can take part to another round of translation.
Termination
Introduction to Plant Breeding and Improvement
Plant Breeding
- Application of Plant Genetics
- Plant species are genetically manipulated to produce types suitable to man’s
needs
- A directed activity where efforts are geared to solve specific problems on plant
production, or a desired product from plants
- Genetics as the cornerstone of all breeding programs as it uses the principles of
heredity in tapping the potential of plant heredity.
History
- Started with the fist domestication of agricultural plants about 9,000 to 11,000
years ago.
o Initially farmers simply selected food plants with desirable
characteristics and employed this as the parental for the next
generations.
- Grafting was first practiced in china before 2000 BCE and is well-
established by 500 BCE.
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o A technique that vegetatively joins two plants into one.

o Grafted plants use the roots and the bottom part of one plant (rootstock) and attach it to a tender
shoot (Scion)
- It is through Gregor Mendel’s work that genetics was employed in Plant Breeding.
Goal of Plant Breeding

- The aim of plant breeders is to produce an ideal plant having the maximum number of desirable
characteristics:
o Resistance to disease and pests
o Tolerance to heat, soil salinity, or frost
o Appropriate size, shape and time to maturity
 Uniformity of plant crops are essential to maximize field operations and use of machines.
- Other essential traits are:
o improved adaptation to environment
o faster growth
o easier handling
o greater yield
o overall better quality
- Another common goal of plant breeders are to extend the area of
production of a crop species.
- Breeding can also be used to improve nutritional quality of
plants.
o This Biofortification of food crops has been proven to improve nutrition which is essential to
developing countries such as the Philippines. (example: yellow rice biofortified with vitamin A)
Mating Systems of Angiosperms

- Before discussing the Plant Breeding methods, let us understand first plant mating systems.
o The mating system of angiosperms devolve about their type of pollination.
o Pollination is the process of transferring pollen from one flower to another
o Flowers can be:
 Self-pollinated – (selfer) if pollen is transferred from a flower to any flower of the same
plant.
 Cross-pollinated – (outcrosser or outbreeder) if the pollen comes from a flower on a
different plant.
o About half of the more cultivated plants are naturally cross-pollinated with
their reproductive organs encouraging such type of pollination.
 Protandry – pollen matures first before the ovules preventing self-
pollination of the same plant.
 Protogyny – ovule matures first before the pollen preventing self-
pollination of the same plant.
 Dioecy – male and female flowers are formed in different plant
individuals.
 Self-incompatibility – there exist a gene that recognizes the similar
gene and does not permit the growth of pollen tube to connect the
pollen and the ovary
 Heterostyly – stigma and anther are placed at different levels.
This prevents the pollen from reaching the stigma and
Goa, Camarines Sur
pollinating it.

o In controlled
breeding
procedures, it is
essential that the
pollen is from the
desired male parent
only.
Methods of Plant Breeding
o Selection
 The process of selectively propagating plants
with desirable characteristics while eliminating
those with less desirable characteristics.
 Among the 4 plant individuals, you will choose
the most desirable and propagate it.
 This served as the most primitive form of plant
breeding that have allowed the exponential
domestication of agricultural products we are
familiar nowadays.
 The food crops we daily consume are far
different from its native or wild counterpart so much so that tracing
its ancestor through morphological characteristics is very difficult.
o Crossing or Deliberate Interbreeding

 Breeding two individuals of closely or distantly related species to produce a new variety of
that species maximizing the traits of their chosen parents
 Distantly-related species may mean they are in the same genera but different
specific epithet (Oryza sativa and Oryza glaberrima or Asian and African rice)
 Crossing a red but small apple with a pink one but big in size to produce a big red apple.
 Backcrossing is usually employed in this technique to ensure that
the offspring is similar to that parent having the desired
characteristics.
 Crossing is usually done using deliberate e pollination.
 However, crossing of distantly related species sometimes produce
problems such as:
 Aborting of embryo before it reaches maturity or become
functional seed
o To solve this, Embryo rescue is a method used to
assist the development of plant embryos that
might not survive. A common method is
culturing the embryos and placing them
in onto media culture.
 Sterility or having
no seeds
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o To solve this, plant tissue culturing or vegetative reproduction is

employed
o Another method is to apply Colchicine which is a chemical that is given
to plant hybrids to increase cell division and double the number of
chromosome producing fertile lines or hybrids with seeds.
o Use of CMS plants
 CMS or Cytoplasmic Male Sterility is a maternally inherited trait that makes the plant
produce sterile pollen.
 The use of this plants, in corn, enables the production of hybrids without the need for
labour-intensive detasseling promoting deliberate pollination.
o Plant Tissue Culture
 Technique used to maintain or grow plant cells, tissues or organs
under sterile conditions on a nutrient culture medium. It is used to
produce clones of plants that are products through crossing related
species that don’t normally sexually reproduce with each other.
 This new hybrids already contain the desired characteristics from
crossing distant species that are usually fruitless.
o Use of Mutagens or Mutation Breeding
 Mutagens are chemical or physical agents that change the genetic
material, usually DNA of an organism and thus increase the
frequency of mutations.
 It is applied to plants in order to generate mutants with desirable
traits.
 Common types used in Plant Breeding are: Ethyl methanosulfunate
(EMS), Dimethyl sulphate (DMS), Radiation, and Transposons.
 Their application in breeding is that they try to apply these
mutagens to plants to promote mutations in the hope of producing
desirable traits such as variation in color, high yield, high amount of
commercially-important secondary compounds. Application of this in
plants are highly experimental.
o Induced Polyploidy and Chromosomal Engineering
 This refers to the addition or removal of chromosomes in plants to increase mutations with
a goal of increasing the desired traits by editing the set of chromosomes or ploidy level.
 The most common chemicals being used in this technique are Colchicine and
Dinitroanilines.
o Protoplast or Somatic Fusion
 Refers to a type of genetic modification in plants by which the protoplast of two distinct
species of plants are fused together to form a new hybrid plant with the characteristic of
both protoplast sources.
 Protoplast are plant cells without the cell wall (but with cell membrane).
 After the two protoplast adheres to one another,
membranes of the protoplast fuse until their
cytoplasms fully intermingle.These fusion can be done
with mechanical aid or using chemicals instead.
 After doing so, the fused protoplast are cultured to
grow and develop into a new hybrid.
o Transgenesis
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 The process of introducing a gene (referred as transgene) from one organism into the
genome of another organism.
 The aim is to produce plant crops (referred as transgenic
organism) that will express the gene and exhibit the
desired property or trait.
 For example, is the BT Corn. The BT stands for Bacillus
thurengensis which is a soil bacteria that produces the
crystal toxin protein poisonous to insects. By inserting this
trait to corn, the corn now has the attributes of being pest-
resistant.
 There are many transgeneric organisms now in the
market all which have undergone the approval of
appropriate agencies.
o Genome Editing
 This refers to a group of technologies that provides
the ability to change an organisms DNA by
allowing the addition, removal or alteration of
particular locations in the genome.
 By being able to identify the location of the genes
that functions for the trait of interest, scientist are
able to breed the most ideal plants they want.
 However, there are still precautions in doing so because if the genetic alteration is too
severe, a new species is actually being created and have implications in biosafety.
Population
Mendelian Population
- Group of individuals from the same species (or with a relatively close degree
of genetic relationship) that lives in the same geographic area that actually
or potentially interbreeds;
- A unit of organisms capable of sexual reproduction;
o Each pair of organisms has the chance to have at least one
common offspring
- Members of species often range over a wide geographic area.
Species concept: Biological vs. Botanical species
- Biological species concept
o Defines a species as members of population that actually or potentially interbreed in nature and not
according to similarity of appearance.
o Environmental conditions exist under which two populations behave like a single population
o Genetically defined unit of reproduction.
- Morphological species concept
o Plant organisms with similar trait expressions, usually morphological features are identical
o Gene flow of plant species within tropical forests:
 Gene flow refers to the transfer of genetic variation from
one population to another.
 Many botanical species are not biological species
 Extensive and far-reaching and
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 Even different botanical species may belong to same biological species, ‘hybridization” is
frequent
- The
scientific community follows more the biological species concept especially with the employment of genetics
in species identification. There are many other species concepts that will be discussed in Taxonomy and
Systematics.
- Both species concepts are non-identical and frequently lead to different conclusions regarding species
borders.
- It is often difficult to prove that two organisms belong to the same biological species or even to the same
population.
Distinction of Population
- The distinction of populations requires certain knowledge of important aspects of the genetic system.
o For complete self-fertilisation (selfers or self-pollinators), each organisms is
regarded as a single, closed population
o For outcrossing, the realised gene flow via pollen or seeds will be crucial for the
delineation of populations.
o The distinction of populations is often possible if the distribution area of a species
is disconnected and populations are small.
o The distinction of populations is difficult for plant species with a large,
continuous distribution and particularly problematical in species-rich forests --
the "metapopulation" concept.
 Metapopulation refers to a group of spatially-separated populations of
the same species which still interact at some genetic level.
Evolution
Background and Definition
- Common misinterpretations about evolution:
o Evolution can only be noticed over long periods of time
 In fact, evolution occurs from time to time depending on the
classification of evolution (microevolution).
 It is only the noticeable expression of genes that are not easily
seen (microevolution).
o Evolution is the only responsible for the formation of new, "higher"
developed species
 There are many factors affecting the formation of new species.
- Two aspects are often neglected:
o Most evolutionary chance occurs within species and does not lead to the
development of a new species.
o Evolution is a permanent process which can directly be observed by
suitable experiments.
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- Evolution is a change of the genetic structures of a population, and are brought about by evolutionary
factors.
- Biological evolution is based on heritable variation within species or populations.
o Heritable or genetic variation in plants refers to the genetic diversity of a single plant species in the
wild
- Describes how an organism change and adapt over time as a result of inherited physical and behavioural
characteristics that are passed from parents to offsprings.
Scale of Evolution
- Microevolution
o Evolutionary change in a small scale
o Change in allele frequencies within the gene pool resulting
from natural selection, genetic drift, gene flow and
mutation
o Microevolutionary changes may accumulate that
sometimes (not always) over long periods of time may
result to major evolutionary changes (macroevolution)
- Macroevolution
o The large scale patterns, trends, and rates of change
among families and other form of inclusive group of
species.
o Generally refers to evolution above the species level.
Hardy-Weinberg Principle
- States that with random mating, a large population with alleles A and a
and their corresponding frequencies at a locus, will attain in one
generation the frequencies p2, 2pq, and q2 for genotypes AA, Aa, and aa,
respectively, regardless of its phenotypic array, and it will remain in these
proportions in the absence of those factors that causes changes in
frequencies (natural selection, genetic drift, gene flow and mutation).
- Assumptions of HWP:
o Population is infinitely large and random mating
o No selection is operative
o No migration
o No mutation
o Meiosis is normal
Evolutionary Factors Affecting Genetic Variation
- Natural selection
o Inherited ability of organisms to survive and reproduce
(fitness) with time, superior genotypes increase their
frequency in the population
o Survival of the fittest
o Contributes to maintenance or increase genetic diversity
(rare alleles or heterozygous genotypes)
o Types of Natural Selection:
 Stabilizing Selection
Goa, Camarines Sur
 Extreme alleles (homozygous) are culled out

and intermediate (heterozygous) forms of
trait in a population is favoured
 Causes reduction in within population
variation
 Directional Selection
 Selection favouring individuals at one
extreme of the phenotype in the population
 Causes reduction in within population
variation
 Allele frequencies underlying a range of
variation tend to shift in a consistent direction
in response to directional change in
environment.
o For example, alleles expressing modifications of stem as water storage
as the environment becomes too humid are being more selected to
facilitate the survival of the plant species.
 Disruptive Selection
 Intermediate forms (heterozygous) are selected less as extreme forms
(homozygous) in the range of variation are more favoured.
 Causes increase in within population variation
- Mutation
o Random changes of genetic information and are usually errors in DNA replication
o The simplest mutation produces a change in a single nucleotide in the DNA sequence of a gene.
o It can also occur at the chromosomal level, changes in the number of genes or polyploidism
o o Prerequisite for any genetic variation;

o It is the ultimate source of variation;
o It increases diversity but because spontaneous mutations are rare, the rate of change in gene
frequency is very low;
o Often lethal/detrimental but sometimes increases biological fitness of a population
- Genetic drift
o The effect of random fluctuations of genetic structures (like
mutation, independent from environmental conditions)
o Consequence of limited population size
 small population size-strong genetic drift, hence, high
genetic differentiation among populations
 A bottleneck develops when population size is reduced
 Bottleneck effect – gene pool randomly drifts
when a population is reduced by a disaster
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randomly eliminating individuals.

 Founder effect occurs when a few individuals
colonize and become established in a new habitat
or environment
o Genetic drift does not increase genetic multiplicity but can
lose gene as a result of drift
o Drift decreases diversity within a population because it tends
to cause the loss of rare alleles, reducing the overall number
of alleles.
o Events that reduce population size:
 Domestication
 Subpopulations (inbreeding, clonal reproduction)
 Long-range dispersal (founder effect)
 Regeneration of genetic resources collections
- Gene flow or Migration
o Movement of individuals or any form of introduction of genes
from one population to another;
o Transport of pollen (gene flow) or seeds (migration)
o Types:
 Emigration: population loses alleles when new
individuals permanently leave it
 Immigration: population gains alleles when new
individuals permanently move in
o Migration, leading to a gene flow, increases diversity
(population’s genetic variability) and its rate can be large,
causing significant changes in gene frequency (i.e. initial
effect of migration)
 blends populations and prevent their divergence
(ultimate, if no other factors are acting upon the population)
o Physical flow of alleles between populations, tend to counter genetic differences that we expect to
arise through mutation, natural selection, and genetic drift
o Main factors affecting gene flow/migration in crop species:
 Pollinators or Pollen vectors
 Pollen vectors 1: wind (anemophily)
 Pollen vectors 2: mammals (zoophily)
o Bats – pollinates big, often pale flowers (white/light
yellow); large quantities of nectar.
o Flying foxes
o Non-flying mammals – Monkeys, opossums, rodents
 Pollen vectors 3: birds
 Pollen vectors 4: bees and wasps (Hymenoptera) – single most important insect
order pollinators in both Temperate and Tropical regions.
 Pollen vectors 5: butterflies and moths
o Butterflies – Brightly coloured, nectar producing
flowers and are less efficient than bees
o Moths – Are attracted to pale colour, but strong
smell.
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 Pollen vectors 6: flies and beetles

o Pollinators only in tropical forests
o Flies – Flowers often unattractive smell, traps
o Beetles – Pollinates primitive families as it
destroys flowers often partially
 Pollen vectors 7: other insects such as thrips, cicadas
and other bugs.
 Seed dispersal Breeding (mating) system
 Wind (anemochory) – seeds with wings, hairs and are
light in weight
 Water (hydrochory) – common to mangrove, river and
peat forests
 Gravity (barochory) – common to large seeded and are
for short distance transport; typical for climax species
o Climax species
 Animals (zoochory) – mainly vertebrates such as
mammals and birds
o Endozoochorous – seed dispersal via ingestion
are for usually long distant transport
o Exozoochorous – seed dispersal via “carrying”
of animals
o Migration is crucial for “neighbourhood” formation in a population:

 Short distance transport would mean that there are less number of species within an area,
thus less biodiversity.
 Long distance transport would mean that there are more number of species within an
area, thus more biodiversity.
- Effects of gene flow natural selection, genetic drift, and mutation:
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Origin of Species: Speciation

- Refers to the evolutionary process by which the populations evolve to become distinct species.
- The end product of the macroevolution.
- Four (4) Geographic Modes of Speciation:
III. ACTIVITIES
To better understand the lesson, provide the answers to the following questions. Write your answers on a separate
paper (1 whole yellow pad).
 Identify the ratio of Genotypes and Phenotypes of the cross:
AaBb x AABb
Where: A – Pricked seeds
a – smooth seeds
B – Thick seed coat
b – Thin seed coat
 Practice exercise:
o Convert the DNA sequence below to RNA sequence:
CGGACCGCTATC
o Then convert the RNA sequence to a polypeptide chain
and its amino acids. To identify the amino acid, refer to
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the figure beside this.

 List at least Three (3) plant crops in your household that is a product of plant breeding.
 Create your own diagram of how the Four (4) evolutionary factors can affect population variation in
terms of within and among populations. (Will it increase or decrease?)
IV. ASSESSMENT
To assess your understanding of the lesson, provide the answers to the following questions. Write your answers on a
separate paper (1 to 2 whole yellow pads only).
1. In a tabular form, compare and contrast plant heredity in the context of Mendel’s
Principles and Sutton’s Chromosomal Theory of Inheritance. (Are the two concepts opposing or
supporting each other?)
2. Identify the word by performing the main activities in the Central Dogma of MB:
*DNA Replication: Provide the complementary DNA Strand of the DNA template
3’ ATG GCC GGA GCA CTT ATA AAT GGG TGA 5’
*Transcription: Provide an RNA template from the Complementary DNA strand you made.
*Translation: Then convert the RNA sequence to a polypeptide chain and its amino acids. *To
identify the amino acids, refer to the figure used in the activity part of the module.
*To identify the word, convert the amino acids into single-letter code. Refer to this figure:
3. Create your own plant crop and explain why did you created it and how will you make
it using any of the discussed plant breeding techniques.
4. Create your own species and discuss how the Four (4) evolutionary factors would
have affected its creation.
V. SUGGESTED REFERENCES
Nabors, Murray W., (2005). Botany: An Introductory Approach. Pearson Education.

Evangelista, E. V., & Evangelista, L. T. (2009). Worktext in General Botany. C & E Publishing Inc.
Berg, L. R., (2012). Introduction to Botany. Cengage Learning.
San Felipe, V. O., (2000). General Botany: Laboratory Manual. Booklore Pub. Corp.
Magdamo, L., (1986). Manual in General Botany. Goodwill Trading Co., Inc.
Fuller, H. J., (1970). General Botany. (5th ed.). Barnes & Noble, Inc.
Mauseth. (1998). Botany: An Introduction to Plant Biology. (2nd ed.) Jones & Bartlett Publishing, Inc.

Plant Genetics and Molecular Biology

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Republic of the Philippines

PARTIDO STATE UNIVERSITY

PARTIDO STATE UNIVERSITY TINAMBAC CAMPUS

Name of Student: _________________________________ Week No: Weeks 12 – 13

At the end of the lesson, the student must be able to:

Basic Concepts of Plant Genetics

Genotype vs. Phenotype

 Homozygous (AA) or (aa)

The Punnett Square

Three (3) Principles of Mendelian Inheritance

- Mendel’s 1st Experiment

- Mendel’s 2nd Experiment

- Mendel’s 3rd Experiment

- In connection to the Law of Dominance, There are types of dominance:

The Chromosomal Theory of Inheritance

o The repeating units of DNA: Nucleotides

o A DNA molecule consists of two nucleotide chains

o Nitrogen bases in DNA strands can pair in only one way

 The sequence of bases is the genetic code.

Central Dogma of Molecular Biology

- This is simply the flow of genetic information

- Starts at the ‘origin’

Detailed discussion of the DNA Replication process

o The other strand known as the Lagging Strand is

Regulation of DNA Replication

RNA or Ribonucleic Acid

o There are three types of RNA:

Detailed discussion of the Transcription process

o As the RNA polymerase molecule passes, the DNA helix re-forms.

 Portions of the RNA chain that are not supposed to be

 Introns - non-coded sections

Detailed discussion of the Translation process

Introduction to Plant Breeding and Improvement

o A technique that vegetatively joins two plants into one.

Goal of Plant Breeding

Mating Systems of Angiosperms

Methods of Plant Breeding

o Crossing or Deliberate Interbreeding

o To solve this, plant tissue culturing or vegetative reproduction is

Evolutionary Factors Affecting Genetic Variation

 Extreme alleles (homozygous) are culled out

o o Prerequisite for any genetic variation;

randomly eliminating individuals.

 Pollen vectors 6: flies and beetles

o Migration is crucial for “neighbourhood” formation in a population:

Origin of Species: Speciation

the figure beside this.

Nabors, Murray W., (2005). Botany: An Introductory Approach. Pearson Education.

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