Basic genetics

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Basic genetics

• Haixu Tang
• School of Informatics

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Mendels two innovations

• Developed pure lines
• a population that breeds true for a particular
  trait
• Counted his results and kept statistical notes

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Phenotypes of Mendel's pea plants

• round or wrinkled seed phenotype
• yellow or green seed phenotype
• red or white flower phenotype
• tall or dwarf plant phenotype

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Results from Mendel's Experiments
Parental Cross F1 Phenotype F2 Phenotypic Ratio F2 Ratio
Round x Wrinkled Seed Round 5474 Round1850 Wrinkled 2.961
Yellow x Green Seeds Yellow 6022 Yellow2001 Green 3.011
Red x White Flowers Red 705 Red224 White 3.151
Tall x Dwarf Plants Tall l787 Tall227 Dwarf 2.841
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Phenotypes

• Dominant - the allele that expresses itself at
  the expense of an alternate allele the phenotype
  that is expressed in the F1 generation from the
  cross of two pure lines
• 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

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Conclusion

• The hereditary determinants are of a particulate
  nature. These determinants are called genes.
• Each parent has a gene pair in each cell for each
  trait studied. The F1 from a cross of two pure
  lines contains one allele for the dominant
  phenotype and one for the recessive phenotype.
  These two alleles comprise the gene pair.
• One member of the gene pair segregates into a
  gamete, thus each gamete only carries one member
  of the gene pair.
• Gametes unite at random and irrespective of the
  other gene pairs involved.

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Some terms

• Allele - one alternative form of a given allelic
  pair tall and dwarf are the alleles for the
  height of a pea plant more than two alleles can
  exist for any specific gene, but only two of them
  will be found within any individual
• Allelic pair - the combination of two alleles
  which comprise the gene pair
• Homozygote - an individual which contains only
  one allele at the allelic pair for example DD is
  homozygous dominant and dd is homozygous
  recessive pure lines are homozygous for the gene
  of interest
• Heterozygote - an individual which contains one
  of each member of the gene pair for example the
  Dd heterozygote
• Genotype - the specific allelic combination for a
  certain gene or set of genes

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F1 Symbol representation
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F2 Punnett Square
Union of GametesAt Random D d
Union of GametesAt Random D DD(Tall) Dd(Tall)
Union of GametesAt Random d Dd(Tall) dd(Short)
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Mendel's First Law

• The law of segregation during gamete formation
  each member of the allelic pair separates from
  the other member to form the genetic constitution
  of the gamete

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Test the hypothesis
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Genotype of the F2 individuals
Phenotypes Genotypes Genetic Description
F2 Tall Plants 1/3 DD2/3 Dd Pure line homozygote dominantHeterozygotes
F2 Dwarf Plants all dd Pure line homozygote recessive
Thus the F2 is genotypically 1/4 Dd 1/2 Dd
1/4 dd
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Backcross Dd x dd

• The cross of an F1 hybrid to one of the
  homozygous parents for pea plant height the
  cross would be Dd x DD or Dd x dd most often,
  though a backcross is a cross to a fully
  recessive parent

Backcross One or (BC1) Phenotypes 1 Tall 1
Dwarf BC1 Genotypes 1 Dd 1 dd
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Monohybrid

• 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.

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Variations to Mendel's First Law of Genetics

• Codominance - a relationship among alleles where
  both alleles contribute to the phenotype of the
  heterozygote
• Incomplete dominance - the F1 produces a
  phenotype quantitatively intermediate between the
  two homozygous parents

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Pedigree Analysis
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Traits exhibiting dominant gene action

• affected individuals have at least one affected
  parent
• the phenotype generally appears every generation
• two unaffected parents only have unaffected
  offspring

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Traits exhibiting recessive gene action

• unaffected parents can have affected offspring
• affected progeny are both male and female

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Mendel's Law of Independent Assortment

• We have followed the expression of only one gene.
  Mendel also performed crosses in which he
  followed the segregation of two genes. These
  experiments formed the basis of his discovery of
  his second law, the law of independent assortment.

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Dihybrid cross

• Dihybrid cross - a cross between two parents that
  differ by two pairs of alleles (AABB x aabb)
• Dihybrid- an individual heterozygous for two
  pairs of alleles (AaBb)

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Mendels experiment

• Parental 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

Seed Color Yellow G Green g
Seed Shape Round W Wrinkled w
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Parental cross
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Female Gametes Female Gametes Female Gametes Female Gametes
GW Gw gW gw
GW GGWW (Yellow,round) GGWw (Yellow,round) GgWW (Yellow,round) GgWw (Yellow,round)
Male Gw GGWw (Yellow,round) GGww (Yellow,wrinkled) GgWw (Yellow,round) Ggww (Yellow,wrinkled)
Gametes gW GgWW (Yellow,round) GgWw (Yellow,round) ggWW (Green,round) ggWw (Green,ROUND)
gw GgWw (Yellow,round) Ggww (Yellow,wrinkled) ggWw (Green,round) ggww (Green,wrinkled)
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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
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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.

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backcross - F1 dihybrid x
Female Gametes Female Gametes Female Gametes Female Gametes
GW Gw gW gw
MaleGametes gw GgWw(Yellow, round) Ggww(Yellow, wrinkled) ggWw(Green, round) ggww(Green, wrinkled)

• The phenotypic ratio of the test cross is
• 1 Yellow, Round Seed
• 1 Yellow, Wrinkled Seed
• 1 Green, Round Seed
• 1 Green, Wrinkled Seed

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The Chi-Square Test

• An important question to answer in any genetic
  experiment is how can we decide if our data fits
  any of the Mendelian ratios we have discussed. A
  statistical test that can test out ratios is the
  Chi-Square or Goodness of Fit test.

Degrees of freedom (df) n-1, where n is the
number of classes
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An example
Let's test the following data to determine if it
fits a 9331 ratio.
Observed Values Expected Values
315 Round, Yellow Seed (9/16)(556) 312.75 Round, Yellow Seed
108 Round, Green Seed (3/16)(556) 104.25 Round, Green Seed
101 Wrinkled, Yellow Seed (3/16)(556) 104.25 Wrinkled, Yellow
  32 Wrinkled, Green (1/16)(556)   34.75 Wrinkled, Green
556 Total Seeds                        556.00 Total Seeds
                                                
  Number of classes (n) 4
df n-1 4-1 3 Chi-square value 0.47
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A Chi-Square Table
Probability Probability Probability Probability Probability
Degrees ofFreedom 0.9 0.5 0.1 0.05 0.01
1 0.02 0.46 2.71 3.84 6.64
2 0.21 1.39 4.61 5.99 9.21
3 0.58 2.37 6.25 7.82 11.35
4 1.06 3.36 7.78 9.49 13.28
5 1.61 4.35 9.24 11.07 15.09

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Pleiotropic Effects and Lethal Genes

• In 1904, a cross was made between a yellow-coated
  mouse and a mouse with a gray coat. The gray-
  coated mouse was extensively inbred and therefore
  was considered to be pure bred.

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• Next a cross was made between two yellow mice.
  What genetic ratio would we expect to see? Yy x
  Yy should give a ratio of 3 yellow1 gray. The
  result, though, was a ratio of 2 yellow to 1 gray
  mice. How can this result be explained? Let's
  first set up a Punnett Square.

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Testcross

• All testcross data with the yellow mice give a
  11 ratio. This ratio is typical of what is seen
  with heterozygous individuals.
• All of the yellow mice from the cross of two
  heterozygous yellow mice are genotypically Yy.
  Somehow the YY genotype is lethal. The 21 ratio
  is the typical ratio for a lethal gene.

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Lethal gene

• Lethal Gene - a gene that leads to the death of
  an individual these can be either dominant or
  recessive in nature.
• Pleiotropic gene - a gene that affects more than
  one phenotype

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Gene Interactions
Rose                                            
  Pea Single                                   
            
Walnut
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Phenotypes Genotypes Frequency
Walnut R_P_ 9/16
Rose R_pp 3/16
Pea rrP_ 3/16
Single rrpp 1/16
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Epistasis

• The interaction between two or more genes to
  control a single phenotype

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Modifier Genes

• Instead of masking the effects of another gene, a
  gene can modify the expression of a second gene.
  In mice, coat color is controlled by the B gene.
  The B allele conditions black coat color and is
  dominant to the b allele that produces a brown
  coat. The intensity of the color, either black or
  brown is controlled by another gene, the D gene.
  At this gene, the dominant D allele controls full
  color whereas the recessive d allele conditions a
  dilute or faded expression of the color
  expression at the B gene. Therefore, if a cross
  is made among mice that are BdDd, the following
  phenotypic distribution will be seen
• 9 B_D_ (black)
• 3 B_dd (dilute black)
• 3 bbD_ (brown)
• 1 bbdd (dilute brown)
• The D gene does not mask the effect of the B
  gene, rather it modifies its expression.

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Gene linkage

• One experiment was performed by Bateson and
  Punnett with sweet peas. They performed a typical
  dihybrid cross between one pure line with purple
  flowers and long pollen grains and a second pure
  line with red flowers and round pollen grains.
  Because they knew that purple flowers and long
  pollen grains were both dominant, they expected a
  typical 9331 ratio when the F1 plants were
  crossed.

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Observed Expected
Purple, long (P_L_) 284 215
Purple, round (P_ll) 21 71
Red, long (ppL_) 21 71
Red, round (ppll) 55 24
Total 381 381
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Linked Genes On The Same Chromosome
F1 Gamete Testcross Distribution Gamete Type
pr vg 1339 Parental
pr vg 151 Recombinant
pr vg 154 Recombinant
pr vg 1195 Parental
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Coupling and repulsion
F1 Gamete Testcross Distribution Gamete Type
pr vg 1339 Parental
pr vg 151 Recombinant
pr vg 154 Recombinant
pr vg 1195 Parental
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Genotype Observed Type of Gamete
ABC 390 Parental
abc 374 Parental
AbC 27 Single-crossover between genes C and B
aBc 30 Single-crossover between genes C and B
ABc 5 Double-crossover
abC 8 Double-crossover
Abc 81 Single-crossover between genes A and C
aBC 85 Single-crossover between genes A and C
Total 1000
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