Transcript DNA Polymorphisms: DNA markers

Transmission Genetics
• Transmission genetics is the sub-field of
genetics that is concerned with the study of
inheritance in individuals.
• Individuals reproduce sexually (crosses) and
the appearance of traits in the offspring is
studied.
• Farmers since the dawn of agriculture used
transmission genetics to improve varieties.
• Gregor Mendel used the scientific method to
study inheritance.
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Mendel and Transmission Genetics
• Gregor Mendel, monk, Czech Republic, 1856-1863
– Studied 7 traits in pea plants, Pisum sativum
– Established basic rules of transmission genetics
• Good science, but ignored for >30 years
• Why peas?
– Many varieties w/ contrasting traits
– Self-pollinating, with true-breeding varieties
– easy to snip parts to cross pollinate
– Need little space, produce lots of offspring
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Basics of Mendelian Genetics
• Terminology
– Traits: characteristic of appearance that can
come in different forms, such as different flower
colors.
– Hybrid: offspring formed by crossing of parents
that differ in a trait
• Monohybrid, dihybrid, etc: based on how
many traits parents differ by.
– Reciprocal crosses: matings with traits
swapped in parents
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More definitions
P1 generation:
the parents
F1: first
generation of
offspring
F2: second
generation of
offspring
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Scientific and historical context
• Ideas about heredity
• Every organism carries all the traits
to be found in its descendants
• Blending: when traits are inherited
from 2 sources, they blend and lose
their individual identities.
• Mendel: sources of traits are
discrete (particulate)
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First observations
• Mendel did many monohybrid crosses
– Multiple generations looking at seeds, pods, flowers, stems
• In each case, he crossed parents with contrasting
traits, obtained seeds, and grew the F1 generation.
Phenotype of the
offspring was that of
one parent, not any
blend of the two traits.
(e.g. round x
wrinkled = all
round).
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First observations-2
• Crossing plants of the F1 generation: F2 generation
Missing trait
returned (e.g.
wrinkled seeds)
Missing trait always
about ¼ of the
offspring.
(3:1 ratio)
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Mendel’s postulates
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• Genetic characters controlled by “unit factors”
– These exist in pairs in organisms
– Unit factors are genes; contrasting forms are alleles
– 3 combos possible (e.g. 2 factors for tall, 2 factors
for dwarf, or 1 each for tall and dwarf).
Terminology
Homozygous: both alleles are the same.
Heterozygous: alleles are different (1 of each)
Mendel’s postulates continued
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• When the 2 factors are different, one masks the
other (is dominant; the other is recessive)
– In F1 generation, the recessive factor was hidden,
e.g. the round seed allele masks the wrinkled one.
• Segregation: during formation of gametes, the
paired unit factors separate (segregate) so that
each gamete gets one of them (at random).
– For a plant with one allele each for round seeds and
wrinkled seeds, a gamete has a 50% chance of
having either.
Law of Segregation
• Punnett Square
– Two units for each trait; during meiosis, each
gamete gets only one unit.
– Single gamete from each parent combines to
produce diploid offspring.
• Law of Segregation:
– Each gamete equally likely
to receive either unit.
• Nomenclature “W” & “w”
Genotype: 1:2:1 ratio
Phenotype: 3:1 ratio
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When is dominant dominant?
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• Visual phenotype:
– Pea plants homozygous for the wrinkled seed allele
make wrinkled seeds.
– Homozygous for round seed allele: round seeds
– Heterozygous plants also make round seeds.
• Molecular phenotype:
– What do alleles code for? The presence (or
absence) of a starch-branching enzyme.
– The normal gene is disrupted by insertion of a
transposon, so enzyme is not made, resulting in the
wrinkled trait .
Molecular analysis of “wrinkled”
• When DNA fragments
are separated, larger
pieces move slower (are
at top of gel).
• Seeds made by
heterozygous plants
show dominant visual
phenotype, but the
molecular phenotype
shows co-dominance
(neither allele masks the
other).
DNA which includes
gene for the enzyme.
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Dominance
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• Dominance is a situation in a diploid organism
in which one allele masks another.
• Dominant does NOT mean most common
• Dominance can be co-dominance (neither trait
masks the other) or partial dominance (both
traits are partially seen, neither completely
masks the other).
Crosses Mendel did to confirm his predictions
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• When the F1 generation was selfed, a 3:1 ratio of
round to wrinkled seeds was produced (3/4 round).
– Of that ¾, 2 were heterozygous, 1 homozygous
dominant
– Therefore, when all the round-seeded plants were
selfed, 1/3 would produce only round seed, but the
other 2/3 would produce round and wrinkled seeds
(in a 3:1 ratio)
Crosses Mendel did to confirm his
predictions
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• Testcross: kind of backcross in which the parent has a
known genotype (homozygous recessive!)
•Backcross: any cross between offspring and parent
Problem: individuals with the dominant
phenotype could be either homozygous or
heterozygous.
By crossing with the homozygous recessive,
offspring will either all have the dominant
phenotype or will be 50:50 dominant and
recessive.
Possible results of testcross
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The Dihybrid Cross
G (dominant) = yellow
W (dominant) = round
ω (recessive) = wrinkled g (recessive) = green
WW GG x ωω gg
Wω Gg (all heterozygous)
Wω Gg x Wω Gg (self the F1 generation)
W
G
W
g
ω G
ω g
WG
WW GG
WW Gg
Wω GG
Wω Gg
Wg
WW Gg
WW gg
Wω Gg
Wω gg
ωG
Wω GG
Wω Gg
ωω GG
ωω Gg
ωg
Wω Gg
Wω gg
ωω Gg
ωω gg
Dihybrid cross (continued)
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• Phenotypic classes: 9:3:3:1
• Genotypic classes: 1:2:1:2:4:2:1:2:1
• Actual data (phenotypic)
– Round, yellow
315
– Round green
108
– Wrinkled, yellow
101
– Wrinkled, green
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• Independent Assortment
– During gamete formation, segregating pairs of
alleles assort independently of each other
– Because 2 traits are inherited independently, the
“product law” can be use to calculate probabilities.
Events in Meiosis I provide the cytological
basis for Mendel’s Independent Assortment
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Disjunction (separation of chromosomes)
of homologues is a random event, that is,
any combination of maternal and paternal
chromosomes can separate together.
Alleles present on these chromosomes can
likewise be expressed in different
combinations. This is what Mendel saw
when the F2 generation of peas produced
seeds that showed a 3:1 ratio for both the
yellow/green trait and for the round/
wrinkled trait. Neither affected the other.
Trihybrid cross
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• Mendel also crossed peas and looked at
inheritance of 3 traits simultaneously.
– These showed independent assortment also.
• A Punnett square to determine the phenotypic
ratios would be unwieldy
– It would require an 8 x 8 matrix: 64 squares
• Because independent events are involved, one
can use the product law
– Multiply each probability.
– Simplest way: forked-line method = branch diagram
Branch diagram for figuring trihybrid cross
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Crossing 2 individuals
heterozygous for all 3 traits:
Ww Gg Pp x Ww Gg Pp
What proportion of the
offspring are expected to
have round, green peas and
purple flowers, where W is
round, w is wrinkled; G is
yellow, g is green; and P is
purple and p is white?
W_ gg P_
¾ x ¼ x ¾ = 9/64