introduction to genetic analysis 9/e - south carolina...
TRANSCRIPT
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Genetics
The scientific analysis of
inherited variation
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Genetics: the study of inherited variation
Gregor Mendel began
the formal study of
genetics.
In 1866 he published
his results: inherited
factors are passed
down unchanged
from one generation
to the next (no
blending or other
modification)
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Genetics: the study of inherited variation
Gregor Mendel developed
methods that are still used
today
• controlled crosses with
pure breeding lines
• followed traits for
multiple generations
• counted progeny
• developed, tested
hypotheses
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Modern Genetic Analysis Includes
Two Principal Components
• Classical or Mendelian Genetics – Inheritance patterns, transmission of genes
– Studied by making controlled crosses
– Genes identified by heritable phenotypic variation
• Molecular and Biochemical Genetics – The structure, function and regulation of
genes
– Studied by manipulating, analyzing DNA, RNA and proteins
– Genes identified by molecular variation
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Modern Genetics Combines
Mendelian and Molecular Genetics
+ Reverse Genetics
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Organisms are made of cells. Each cell contains
chromosomes. Chromosomes carry genes.
The organization of living things is based on
cells and directed by genes:
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Living things have many different
chromosome structures and organizations
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DNA is a double helix:
• two strands of
nucleotides
• held to each other by
hydrogen bonds
• pairing = – Adenine - Thymine
– Guanine - Cytosine
One AT or GC pair = one
base pair
The length of DNA is
measured in base pairs or
bp. 1,000 bp = 1kb
8 bp
A closer look at DNA
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DNA Replication: Semiconservative Normal replication – faithful due to complementary pairing
Mutation – replication error modifies DNA sequence
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DNA replication is the
molecular basis for
chromosomal replication
• DNA replication
two identical daughter
chromosomes
• passed on to the next
generation.
• The only difference
between daughters is
due to rare mutations
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Meiosis:
haploid
germline
cells
Mitosis:
diploid
somatic
cells
Germline
mutation:
may be
passed to
offspring
Somatic
mutation:
not
passed to
offspring
DNA replication is the core of cell reproduction
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Genetic distance
estimated from
(cytochrome c)
DNA
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DNA Ancestry
20 generations = 1,048,576 ancestors
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From Genes to Phenotype: Information from DNA is used to
synthesize enzymes that catalyze
biological chemical reactions.
transcription translation
DNA RNA protein
phenotype
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Transcription in a eukaryote
Figure 1-5 part 2
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Gene transcription is controlled by a promoter
• RNA polymerase binds to promotor to
initiate transcription
• Promoter open – transcription on
• Promoter blocked – transcription off
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The Biochemical Mechanism for
Transcription
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Transcription in a eukaryote - RNA processing
• Introns are removed
• Exons are spliced
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Transcription and translation in a eukaryote
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Translation
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Amino acid sequence of a
protein determines its folding
pattern and activity
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Genomes • Genome
– entire haploid genetic content of an organism
– usually measured in kilobase pairs (kb) or
megabase pairs (mb)
– human haploid genome ≈ 3,000,000 kb
• Coding Genome
– DNA that codes for protein (< 2% of human
genome)
• Noncoding Genome – everything else
– DNA involved in gene regulation or with no
known function (introns, for example)
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Genomic Structure in Different Organisms:
simpler organisms have relatively more coding
DNA and less noncoding DNA
13 genes / 20 kb
11 genes / 20 kb
0.8 genes / 20 kb
0.33 genes / 20 kb
Total coding DNA per segment
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Albinism: A mutant gene
nonfunctioning
enzyme
prevents melanin
synthesis
causes albinism
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Pigmentation results from two properly functioning genes
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One malfunctioning gene does not change pigmentation
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Two malfunctioning genes leads to albinism
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DNA can be
analyzed with gel
electrophoresis
See Genetics Links, Interactive Animation of Gel Electrophoresis
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DNA is
separated by
size during
electrophoresis
DNA on a gel may be
visualized by staining
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enzymes cut at
specific 6 base
sequence
every 46 = 4,096
bp on average
Fragments of DNA to be analyzed by electrophoresis can be
obtained by cutting DNA with restriction enzymes
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A probe can be used to detect specific
DNA fragments or chromosomal regions
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Probes can be used to detect specific macromolecules
Figure 1-12 part 2
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Probes can be used to detect specific macromolecules
Figure 1-12 part 3
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Probes can be used to detect specific macromolecules
Figure 1-12 part 4
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Polymerase Chain Reaction can be used to obtain specific DNA for analysis
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Polymerase Chain Reaction
Polymerase Chain Reaction (PCR) - YouTube
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Model Organisms in Genetics
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Application of animal models -
human medical and
developmental genetics:
• human genes often resemble those of other modern animals because humans share a common ancestor with them
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Application of animal models to
human developmental genetics:
extensive knowledge about human genes has been derived from the study of model organisms –
HOX genes regulate developement, control segment ID
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Examples from Medical Research:
• nematode worm – drug development
• one third of the worm's ~5,800 proteins are
similar to mammalian proteins
• yeast – molecular cancer research
• 38% of yeast’s 2,300 proteins are similar to
those of mammals
• fruit flies
• 75% of known human disease genes have
equivalents in fruit flies
• p53 gene in both plays a role in cell death
and uncontrolled growth
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Genetics: Study of Inherited Variation
• Wildtype – the common, typical phenotype
• Mutation
– Rare in population, usually harmful
– Usually discrete phenotype (albinism)
• Polymorphism – more than one wildtype
– Natural variation, common in population
– May be discrete
• Easily identifiable phenotypic categories
– Or continuous
• Phenotypic categories indistinct
Types of Phenotypic Variation
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Phenotypic Variation:
Wildtype vs. Mutation
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Manx cat:
dominant mutation
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There is a
broad
fascination
with mutants
and odd
hybrids
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Scientists successfully create human-bear-pig
chimera (manbearpig) posted April 1, 2008, Thinkgene.com
http://www.thinkgene.com/scientists-successfully-create-human-bear-pig-chimera
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Developmental Mutants: HOX genes
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Phenotypic Variation:
Discrete Wildtype Polymorphism
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Other discrete polymorphisms in nature
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Continuous Phenotypic Variation:
a common form of polymorphism
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Mutation, discrete
polymorphism or
extremes of continuous
variation?
Sultan Kösen
He Pingping
Svetlana Pankratova
8’ 3”
2’ 5”
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Sources of Phenotypic Variation Genetic and non-genetic factors may affect
phenotypic expression
• Genes only – no known environmental effects
― Human examples – eye color, blood type
• Environment only – no known genetic effects
— Human example – language and culture
• Both genetic and environmental effects
(Genotype X Environment Interaction)
— Human examples
• Developmental
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Eye Facets
(ommatidia)
Bristles Some Fruitfly Anatomy
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Environment
plays a role in
the expression
of wildtype eye
alleles.
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Eye Shape Mutants
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An example of
interaction
between
genotype and
environment
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• Curly wing mutation in Drosophila
– expression depends on temperature
during development
• 250C Cy mutant = curly wings
• 180C Cy mutant = normal wings
• Sickle cell anemia
– expression depends on oxygen tension in
blood, low O2 → sickling
• Type II Diabetes
– usually adult onset
– affected by diet, exercise
Other Examples of Genotype X
Environment Interaction
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Polypterus (“dragonfish”)
aquatic and
terrestrial
rearing on land
alters anatomy and
behavior to facilitate
terrestrial locomotion
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Genotype X Environment Interaction
• Expression of genotype depends at least partly
on environmental conditions
• Neither genotype nor environment alone are
sufficient to explain phenotype - both must be
known • (Like the length and width must both be known to
calculate the area of a rectangle)
• Norm of reaction = range of phenotypic
expression of a genotype over different
environments
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Norm of reaction
for bristle number:
different colored
lines represent
different inbred
homozygous
strains
Effect of
environment varies
among genotypes
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Effects of environment differ among
genotypes:
Different
growing
environments
have different
affects on
different
genotypes
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Genotype X Environment Interactions:
Implications for Selective Breeding
In all populations (plant,
animal, domestic, wild)
many characters: – vary continuously
– multiple genes contribute
– are subject to G X E
interactions
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Selective Breeding
Selective breeding occurs
when only relatively
extreme phenotypes are
used for the next
generation
Selective breeding has been important for
• modification of domestic plants and animals
• demonstration of genetic basis for variation in
specific traits
Genotype X Environment Interactions:
Implications for Selective Breeding
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• Phenotypic variation is the basis for
selective breeding
• Genetic variation is the basis for successful
selective breeding
Selective breeding over
several generations
can shift the phenotypic
distribution of a
population
Selective Breeding
Genotype X Environment Interactions:
Implications for Selective Breeding
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Genetic variation
determines the response to
selective breeding:
Traits with greater genetic
variation evolve more
rapidly under selective
breeding
Variation due to
environmental factors does
not respond to selection
Response to selective
breeding demonstrates
presence of genetic
variation
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Selective breeding can produce dramatic
changes over many generations:
flight speed of fruit flies in a wind tunnel
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Heritable traits can respond to selection in
either direction – increase or decrease in
trait expression
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Domestic dogs originated
with a wild species
Some retain
substantial similarity
to the ancestral
species
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Selective breeding has
produced some extreme
varieties of domestic
animals and plants.
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Voluntary wheel walking in mice:
selective breeding can reveal a
genetic component to behavior
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Maze running
ability in rats: a
cognitive trait that
can be altered by
selection
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Rearing Conditions Alter the Phenotypes of
Selected Maze Bright and Maze Dull lines
Rearing Conditions
Restricted Normal Enriched
Nu
mb
er
of
Mis
takes
80
100
120
140
160
180
Bright
Dull
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Heritability of Phenotypic Variation
• Heritability is the proportion of phenotypic
variation in a population that is attributable
to genes
• Genes only – no environmental effects
― Heritability of trait is 100% = 1.0
• Environment only – no genetic effects
— Heritability of trait = 0
• Genetic and environmental effects
— Heritability > 0 and < 1.0
• Higher heritability = greater likelihood of a
phenotype being transmitted faithfully,
greater response to selective breeding
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Heritability is
often expressed
as a range and
can differ
widely for
different traits
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Summary
• Agricultural plants, animals and laboratory
model organisms respond to selective
breeding:
– The response is repeatable, can be extended over
many generations and can result in a phenotype far
outside the range of normal variation
• Many complex traits respond to selective
breeding:
– Anatomical, physiological, behavioral
• Genetic variation contributes to variation in the
expression of complex traits
• Heritability is a measure of the extent to which
variation in a population is due to genes
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Human heritability: comparisons of
monozygotic (MZ) and dizygotic (DZ) twins
• MZ twins reared apart –
– Genetically identical, reared in different
environments
– Greater similarity between members of the
pairs = higher heritability
• DZ and MZ twins reared in birth families
– Rearing environment is the same for both
members of all pairs
– Greater similarity between MZ than DZ pairs
= higher heritability
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Measurements of identical twins reared apart permit estimates of heritability for human traits:
Correlation between members of the twin pair over many pairs provides the heritability for the trait
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fingerprint ridge count 0.97
height 0.85
IQ 0.5 - 0.7
scholastic achievement 0.40
good memory 0.20
Heritability of Some Common Traits
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Heritability of IQ is altered by
environmental factors: (based on MZ-DZ birth family comparisons)
Middle Income +
nutrition, healthy 0.74
Poverty (< $10,000/year)
nutrition, other
marginal health 0.39
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achievement (works hard, strives
for mastery) 0.38
social closeness (intimacy) 0.15
stress reaction (neuroticism) 0.48
aggression 0.67
absorption (imagination) 0.74
Human Personality Traits Show a
Range of Heritability
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Summary
• Genes do not “determine” phenotype
but set limits on variation − Norm of Reaction
• High heritability ≈ narrower limits
• Low heritability ≈ broader limits
• Individuals may be strongly or weakly
predisposed to specific phenotypes. − Environment plays a role in most traits
− Human microbiome - environmental
affects on many physiological traits