Basic genetics

Haixu Tang

School of Informatics

Mendel’s two innovations

• Developed pure lines – a population that breeds true for a particular

trait

• Counted his results and kept statistical notes

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

Results from Mendel's Experiments

Parental Cross F1 Phenotype F2 Phenotypic Ratio F2 Ratio

Round x Wrinkled Seed

Round 5474 Round:1850

Wrinkled 2.96:1

Yellow x Green Seeds Yellow 6022 Yellow:2001 Green 3.01:1

Red x White Flowers Red 705 Red:224 White 3.15:1

Tall x Dwarf Plants Tall l787 Tall:227 Dwarf 2.84:1

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

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.

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

F1: Symbol representation

F2: Punnett Square

Union of GametesAt Random

D d

D DD(Tall)

Dd(Tall)

d Dd(Tall)

dd(Short)

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

Test the hypothesis

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 recessiveThus the F2 is genotypically 1/4 Dd : 1/2 Dd : 1/4 dd

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

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.

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;

Pedigree Analysis

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

Traits exhibiting recessive gene action

• unaffected parents can have affected offspring

• affected progeny are both male and female

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.

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)

Mendel’s 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

Parental cross

Female Gametes

GW Gw gW gw

GWGGWW (Yellow,round)

GGWw (Yellow,round)

GgWW (Yellow,round)

GgWw (Yellow,round)

MaleGw

GGWw (Yellow,round)

GGww (Yellow,wrinkled)

GgWw (Yellow,round)

Ggww (Yellow,wrinkled)

GametesgW

GgWW (Yellow,round)

GgWw (Yellow,round)

ggWW (Green,round)

ggWw (Green,ROUND)

gwGgWw (Yellow,round)

Ggww (Yellow,wrinkled)

ggWw (Green,round)

ggww (Green,

wrinkled)

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

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.

backcross - F1 dihybrid x

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

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

An example

Let's test the following data to determine if it fits a 9:3:3:1 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

A Chi-Square TableProbability

Degrees of

Freedom0.9 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

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.

• 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 yellow:1 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.

Testcross

• All testcross data with the yellow mice give a 1:1 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 2:1 ratio is the typical ratio for a lethal gene.

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

Gene Interactions

Rose                                              Pea

Single                                               Walnut

Phenotypes Genotypes Frequency

Walnut R_P_ 9/16

Rose R_pp 3/16

Pea rrP_ 3/16

Single rrpp 1/16

Epistasis

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

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.

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 9:3:3:1 ratio when the F1 plants were crossed.

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

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

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

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