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INTRODUCTION

Chapter 02 MENDELIAN INHERITANCE

Many theories of inheritance have been proposed to explain transmission of t i i f hereditary traits

The most prominent are

Theory of pangenesis

Theory of preformationism

Blending theory Factors that control hereditary traits are maleable They can blend together generation after generation
Parent 1 Average Offspring Parent 2

Mendels Laws of Inheritance

1. Chose a very suitable organism: Pisum sativum

Gregor Mendels pioneering experiments with garden peas refuted all of the above Mendel was successful, when his predecessors were not, because he

2. Took time to ensure pure breeding 3. Concentrated on one or a few discontinuous characters at a time 4. Adopted quantitative form of analysis

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Mendels Experimental System

Figure 2.4

Used pure-breeding lines of garden peas Selected 7 traits to study, each of which had two distinguishable appearances Figure 2.4 He carefully designed his experiments and gathered mathematical data

Mendels Experimental System

Figure 2.3

1. Cross-fertilization Pollen and egg are derived from different plants Refer to Figure 2.3 2. Self-fertilization Pollen and egg are derived from the same plan

Figure 2.5

MONOHYBRID CROSSES

Mendel crossed individuals from two different lines that differ in only one trait Parental generation = Pure bred lines Fi First fili l generation = Off i of t filial ti Offspring f cross-fertilization of parentals Second filial generation = Offspring of self-fertilization of F1 plants Third filial generation = Offspring of selffertilization of F2 plants

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Mendel also performed the reciprocal cross, where dwarf plants were pollinated using pollen from tall plants The results were the same For all seven traits studied

DATA FROM MONOHYBRID CROSSES P Cross Tall X dwarf stem Round X wrinkled seeds Yellow X Green seeds Purple X white flowers Axial X terminal flowers Smooth X constricted pods Green X yellow pods F1 generation All tall All round All yellow All purple All axial All smooth All green F2 generation 787 tall, 277 dwarf 5,474 round, 1,850 wrinkled 6,022 yellow, 2,001 green 705 purple, 224 white 651 axial, 207 terminal 882 smooth, 229 constricted 428 green, 152 yellow Ratio 2.84:1 2.96:1 3.01:1 3.15:1 3.14:1 2.95:1 2.82:1

1. The F1 generation showed only one of the two parental traits 2. The F2 generation showed an ~ 3:1 ratio of the two parental traits 3. Reciprocal crosses yielded similar results

MONOHYBRID CROSSES

Mendel postulated the following

These results refuted a blending mechanism of heredity

1. A pea plant contains two discrete hereditary factors, one from each parent These factors are now referred to as alleles 2. The two factors may be identical or 2 Th t f t b id ti l different If the alleles are identical the organism is referred to as homozygous If the alleles are different the organism is referred to as heterozygous

Indeed, the data suggested a particulate theory of inheritance

3. When the two factors of a single trait are different, one is dominant and its effect can be seen, while the other is recessive and is not expressed 4. During gamete formation, the paired factors segregate randomly so that half of the gametes received one factor and half of the gametes received the other This is Mendels First Law, or the Law (Principle) of Segregation 5. The union of male and female gametes is a random process that reestablishes the paired units

Alleles are designated by letters derived from the specific characteristic they control Usually the letter chosen is the first letter of the dominant (or recessive) trait For example, T = Tall plants t = dwarf plants Alternatively, D = Tall plants d = dwarf plants

Lets introduce a few more terms

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Genotype = The specific allelic composition of an individual With respect to seed shape, a pea plant may have 3 different genotypes

Genotype Notation TT Tt tt

Genotype Description Homozygous dominant Heterozygous Homozygous recessive

Phenotype Tall Tall Dwarf

TT ; Tt ; tt

Phenotype = The physical appearance of an individual With respect to seed shape, a pea plant may have 2 different phenotypes

Tall ; Dwarf

Note that the phenotype is a product of the genotype and the environment

Information about parents can be used to predict genotypes and phenotypes of offspring Punnett square A grid that enables one to calculate the results of simple genetics crosses
Gametes

Refer to p. 24 We will illustrate the Punnett square approach using the cross of heterozygous tall plants as an example

1. Write down the genotypes of both parents M l Male parent = Tt t Female parent = Tt 2. Write down the possible gametes each parent can make. Male gametes: T or t Female gametes: T or t

Genotypes

3. Create an empty Punnett square

5. Determine the relative proportions of genotypes and phenotypes of the offspring

Genotypic ratio TT : Tt : tt 1 : 2 : 1 Phenotypic ratio Tall : dwarf 3 : 1

4. Fill in the Punnett square with the possible genotypes of the offspring

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Mendel verified his principle of segregation by performing a test-cross In a test-cross an organism with known phenotype but unknown genotype is crossed with an organism that has the recessive phenotype (and hence is homozygous recessive) For F example, if a pea plant is t ll it could b l l t i tall ld be homozygous dominant (true-breeding) or heterozygous This unknown genotype is designated T A test-cross will determine its correct genotype

Tall X Dwarf If all offspring are tall => the genotype is TT

If the offspring are in a ratio of 1 tall:1 dwarf Tt => the genotype is

To solve problems dealing with standard genetic crosses, follow these general rules: 1. Lay out the problem as a simple diagram 2 2. Assign letters for the alleles of the genes in question 3. Determine the genotypes of the parentals 4. Do a Punnett square

Application problem In humans, free earlobes are dominant to attached ear lobes. This characteristic is under the control of a single gene.

1. Elias and his wife Nadine have attached earlobes. What percentage of their children is expected to have attached earlobes?

DIHYBRID CROSSES
Mendel crossed individuals from two different lines that differ in two traits Refer to Experiment 2B P Round, yellow X Wrinkled, green

2. Peter and his wife Aida have free earlobes. Peters mom and Aidas dad have attached earlobes. What percentage of Peter and Aidas children are expected to have attached ear lobes?

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Figure 2.8

Trait 1 = Seed texture

Trait 2 = Seed color

Mendel looked at each trait in the F2 separately

DATA FROM DIHYBRID CROSSES

2.97 : 1

P Cross Round, R d Yellow seeds X wrinkled, green seeds

F1 generation F2 generation All round, d yellow 315 round, yellow seeds d ll d 101 wrinkled, yellow seeds 108 round, green seeds 32 green, wrinkled seeds

3.18 : 1

These values are very close to segregation expectations

Thus, Mendel proposed his second law, the law (principle) of independent assortment During gamete formation, the segregation of any pair of hereditary determinants is independent of the segregation of other pairs If the genes do assort independently, what will the predicted phenotypic ratio be? 9 3 3 1 9:3:3:1
F1 generation F2 generation Ratio 9.8 3.2 3.4 1.0

Figure 2.8

P Cross Round, Yellow seeds x Wrinkled, green seeds

All round, yellow 315 round, yellow seeds 101 wrinkled, yellow seeds 108 round, green seeds 32 green, wrinkled seeds

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Figure 2.9

Mendel verified this principle by, again, performing a test cross Cross F2 yellow, round plant with a Green, Wrinkled

If the offspring are 1 yellow, round plant : 1 yellow, wrinkled plant, what is the genotype of the dominant parent?

YYRr

Note: Offspring of a test-cross are always in equal proportions!

TRIHYBRID CROSSES

P
Gametes

Crosses that involve three pairs of traits

F1
Gametes

A Punnett square in this case will have 64 squares!

An alternative is the forked-line method Treat each gene separately Consider phenotypic (or genotypic) differences

In the F2 generation, 3/4 of all organisms will have the A phenotype, and 1/4 will ha e the a phenot pe ill have phenotype 3/4 of all organisms will have the B phenotype, and 1/4 will have the b phenotype 3/4 of all organisms will have the C phenotype, and 1/4 will have the c phenotype Refer to Solved Problem 4 (pp. 37-38)

Therefore it will be too cumbersome!

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General Rules for Multihybrid Crosses

If n = # of heterozygous gene pairs involved

One caveat: The genes must not be linked

Number of possible parental gametes n 2 Number of different genotypes in zygotes n 3 Number of different phenotypes in zygotes n 2 Proportion of homozygous recessive in F2 n 1/4

PEDIGREE ANALYSIS

PEDIGREE ANALYSIS

Refer to pp. 29-30 and 602-609 Determining the inheritance pattern of human traits is somewhat difficult

1. Controlled matings are not possible

2. Sibship sizes are relatively small 3. Complete penetrance is sometimes lacking 4. Degrees of expressivity sometimes vary

Pedigrees Diagrams that show the relationship among members of a family, as well as their status with respect to a particular hereditary condition

Figure 2.11

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Traits that are determined by a single gene are of five main types Autosomal dominant Autosomal recessive X-linked dominant X-linked recessive Y-linked

AUTOSOMAL DOMINANT TRAITS

1. Trait usually present in every generation 2. Members of both sexes affected equally 3. Unaffected parents produce unaffected offspring 4. Two affected parents can produce unaffected offspring 5. On average half the children of an affected parent will be affected

Autosomal Dominant Disorders

Polydactyly

Brachydactyly

Autosomal Dominant Traits

Achondroplasia

Syndactyly

AUTOSOMAL RECESSIVE TRAITS

Autosomal Recessive Disorders

1. Trait tends to skip generations 2. Members of both sexes affected equally 3. Unaffected parents can have an affected child 4. Two affected parents cannot have an unaffected child 5. Traits are more likely to occur in consanguineous marriages

Albinism Absence or partial deficiency of melanin in the skin, eyes and hair It occurs in a wide variety of animals

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Autosomal Recessive Disorders

X-LINKED RECESSIVE TRAITS

Cystic fibrosis

The most common lethal genetic disease among caucasians Mainly characterized by serious digestive and respiratory problems Average life expectancy ~ 30 yrs

1. Trait may skip generations 2. Most affected individuals are male 3. Affected males result from affected mothers or mothers who are carriers 4. Affected females come from affected fathers and affected or carrier mothers 5. Affected females will have affected sons 6. Trait can never be transmitted directly from father to son

X-linked Recessive Disorders

X-LINKED DOMINANT TRAITS

Red-green color blindness

Hemophilia

1. Trait does not skip generations 2. Affected males must come from affected mothers 3. Affected females come from affected mothers or fathers 4. Affected males have no normal daughters and no affected sons 5. Affected heterozygous females transmit the trait to approximately half of their children of either sex 6. Affected homozygous females transmit the trait to all their children

X-linked Dominant Disorders

Y-LINKED TRAITS

Faulty tooth enamel Vitamin D-resistant rickets

Rickets is disorder Ri k t i a di d involving softening and weakening of the bones (of children) primarily caused by lack of vitamin D This form of rickets is caused by lack of phosphate

1. Trait only affects males 2. Affected males get it from their fathers and give it to their sons

Hypertrichosis of the ear

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Penetrance

The proportion of individuals with a specific genotype who manifest the corresponding phenotype

Complete penetrance

% Penetrance = # of indiv. with correct phenotype

# of individuals with genotype coding for phenotype

Incomplete penetrance

Penetrance

The ABO blood group genes show almost complete penetrance You will find out later! Neurofibromatosis shows 50-80% penetrance Polydactyly also shows incomplete penetrance

Note: Incomplete penetrance may cause a phenotype to skip a generation Consider this pedigree that traces polydactyly in a family

Expressivity

The degree to which a penetrant gene is phenotypically expressed A range of phenotypes

is produced Identical known genotype

If Neurofibromatosis penetrates, it may be exhibited in various forms

Mildest form Caf-au-lait spots

Intermediate form Caf-au-lait spots Freckling

Variable Expressivity

Severe form Neurofibromas of various sizes Speech impediments

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If polydactyly penetrates, it may be exhibited in various forms

Note: Penetrance and expressivity are used most often with autosomal dominant traits What are the reasons for incomplete penetrance and variable expressivity? Gene interactions Environmental effects

Siamese cats have darker fur at their extremities

Phenylketonuria

Refer to pp. 8-9

Melanin

An autosomal recessive disorder Defect is in the gene that encodes phenylalanine hydroxylase
Figure 13.1 The metabolic pathway of phenylalanine breakdown

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Affected individuals cannot metabolize phenylalanine Phenylalanine will accumulate and be converted to phenylpyruvic acid These are toxic and will cause mental and physical abnormalities Newborns are now routinely screened for PKU Individuals with the disease are put on a strict dietary regimen Their diet is very low on phenylalanine These individuals tend to develop normally

Phenocopy

An organism whose phenotype has been modified to resemble the phenotype of a different mutant organism g Phocomelia Thalidomide

Phocomelia

PROBABILITY AND STATISTICS

Suppression of limb development Caused by a dominant allele with variable expressivity p y

Probability deals with chance or random events The laws of probability allow us to predict the outcomes of crosses, in addition to many other processes

Thalidomide

Sedative Between 1959-1962 children with shortened limbs were born to mothers who took the drug early in their pregnancy

Probability = # of favorable cases

total # of cases

Rules For Combining Probabilities

1. Product rule 2. Sum rule 3. Binomial expansion equation (binomial theorem)

It ranges from g 0 to 1 If an event has a probability of p, the probability of all alternative events is q

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1. Product rule The probability of the occurrence of independent events is the product of their respective probabilities Example: Probability of rolling a 3 AND then a 4 with a die? P(3 and 4) = P(3) X P(4) 1/6 X 1/6 1/36

2. Sum rule The probability of the occurrence of one of several mutually exclusive events is the sum of their respective probabilities Example: Probability of rolling a 3 OR a 4 with a die? P(3 or 4) = P(3) + P(4) 1/6 + 1/6 1/3

2. Sum rule
Note: If the 2 events are not mutually exclusive, then P(A or B) = P(A) + P(B) - [P(A) X P(B)] Example: Probability of drawing an ace OR a heart from a deck of cards

3. Binomial Expansion Equation The probability of the occurrence of unordered mutually exclusive events is defined by the binomial theorem P= n! px qn x x! ( x)! ! (n )!

P(A or ) =

P(A) + P() [P(A) X P()] 4/52 + 13/52 (4/52 X 13/52) 17/52 (1/52) 16/52

where p = probability that the unordered number of events will occur n = total number of events x = number of events in one category p = individual probability of x q = individual probability of the other category

Refer to the example on pp. 32-33 Question

Applying the binomial expansion equation Step 1: Calculate the individual probabilities This can be obtained via a Punnett square P(blue eyes) = p = 1/4 P(brown eyes) = q = 3/4

Two heterozygous brown-eyed ( ) yg y (Bb) individuals have five children What is the probability that two of the couples five children will have blue eyes?

Step 2: Determine the number of events n = total number of children = 5 x = number of blue-eyed children = 2 Step 3: Substitute the values for p, q, x, and n in the binomial expansion equation

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P= P= P=

n! px qn x x! (n x)! 5! (1/4)2 (3/4)5 2 2! (5 2)! 5X4X3X2X1 (1/16) (27/64) (2 X 1) (3 X 2 X 1)

Use Of Rules

1. What is the probability of rolling two dice together and obtaining a 3 and a 6?

P = 0.26 or 26%

Therefore 26% of the time, a heterozygous couples five children will contain two with blue eyes and three with brown eyes

2. Consider two parents heterozygous for albinism.

a) What is the probability that they will have an albino child? b) What is the probability that they will have 3 normal children in a row? c) What is the probability that they will have, in order, 2 normal children, an albino child, and then a normal child? d) What is the probability that they will have 3 normal children and an albino child, in any order?

CHI-SQUARE ANALYSIS

The 3:1 and 9:3:3:1 ratios are hypothetical ratios based on the following assumptions Dominance/recessiveness of alleles Complete segregation Independent assortment Random fertilization

CHI-SQUARE ANALYSIS

Independent assortment and random fertilization are chance events Therefore, they are subject to random y j fluctuations To minimize the possibility that chance deviation will significantly alter the outcome, we need to look at very large numbers

How can we evaluate the likelihood that deviations are NOT significant, but due to chance? The chi-square test is a statistical method e c squa e s stat st ca et od used to determine goodness of fit This refers to how close the observed data are to those predicted from a hypothesis

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The basic steps are the following: 1. Establish a NULL hypothesis It assumes that there is no real difference between the measured values and the predicted values

Consider the following example in Drosophila melanogaster (pp. 33-35)

Gene affecting wing shape + c = Normal wing c = Curved wing

Gene affecting body color + e = Normal (gray) e = ebony

2. Apply 2 formula

(O E)2 E

Note: Th wild-type allele i d The ild t ll l is designated with a + sign i t d ith i Recessive mutant alleles are designated with lowercase letters

The Cross:

3. Interpret 2 value This will ultimately lead to the acceptance or rejection of the null hypothesis

A cross is made between two true-breeding flies (c+c+e+e+ and ccee). The flies of the F1 generation are then allowed to mate with each other to produce an F2 generation.

The outcome

F1 generation All offspring have straight wings and gray bodies F2 generation 193 straight wings, gray bodies 69 straight wings, ebony bodies 64 curved wings, gray bodies 26 curved wings, ebony bodies 352 total flies

Step 2: Calculate the expected values of the four phenotypes, based on the hypothesis According to our hypothesis, there should be a 9:3:3:1 ratio on the F2 generation
Phenotype

straight wings wings, gray bodies straight wings, ebony bodies curved wings, gray bodies curved wings, ebony bodies

Applying the chi square test

Step 1: Propose a hypothesis that allows us to calculate the expected values based on Mendels laws The two traits are independently assorting

Step 2: Calculate the expected values of the four phenotypes, based on the hypothesis According to our hypothesis, there should be a 9:3:3:1 ratio on the F2 generation
Phenotype Expected probability 9/16 3/16 3/16 1/16 Expected number

Step 2: Calculate the expected values of the four phenotypes, based on the hypothesis According to our hypothesis, there should be a 9:3:3:1 ratio on the F2 generation
Phenotype Expected probability 9/16 3/16 3/16 1/16 Expected number 9/16 X 352 = 198 3/16 X 352 = 66 3/16 X 352 = 66 1/16 X 352 = 22

straight wings wings, gray bodies straight wings, ebony bodies curved wings, gray bodies curved wings, ebony bodies

straight wings wings, gray bodies straight wings, ebony bodies curved wings, gray bodies curved wings, ebony bodies

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Step 3: Apply the chi square formula (O1 E1)2 E1 (O2 E2)2 E2 + (O3 E3)2 E3 (O4 E4)2 E4

(193 198)2 198

(69 66)2 (64 66)2 (26 22)2 + + 66 66 22

Step 4: Interpret the chi square value The calculated chi square value can be used to obtain probabilities, or P values, from a chi square table These probabilities allow us to determine the likelihood that the observed deviations are due to random chance alone Low chi square values indicate a high probability that the observed deviations could be due to random chance alone High chi square values indicate a low probability that the observed deviations are due to random chance alone

0.13 + 0.14 + 0.06 + 0.73 1.06

By convention, the normal level of significance is 5 %

If p 0.05, the deviation is considered to be statistically insignificant => Null hypothesis is accepted >

If p < 0.05, the deviation is considered to be statistically significant => Null hypothesis is rejected

Before we can use the chi square table, we have to determine the degrees of freedom (df) The df is a measure of the number of categories that are independent of each other df = n 1 where n = total number of categories g In our experiment, there are four phenotypes/categories Therefore, df = 4 1 = 3 Refer to Table 2.1

With df = 3, the chi square value of 1.06 is slightly greater than 1.005 (which corresponds to P = 0.80) A P = 0.80 means that values equal to or greater than 1.005 are expected to occur 80% of the time based on random chance alone Thus, it is quite probable that the deviations between the observed and expected values in this expt. can be explained by random sampling error If the NULL hypothesis is rejected, then what???

1.06

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