Genetics Lecture 3

Why was Mendel’s experiment so successful?

-He used a pea plant as a model organism.

-Easily assessed characteristics

-Experimental approach with mathematical interpretation.

Outcomes of Mendelian genetics

-Inheritance is controlled by genes.

-Genes are passed down through chromosomes.

-In diploid organisms, you have a copy of a gene from each parent. These paired chromosomes allow you to inherit from both parents.

-During gamete formation, homologous chromosomes segregate from one another and assort independently with other segregating homologs.

-Predicted genetic ratios aren’t exact—they can change by chance, and we use statistics to study this.

-Studying family trees helps predict how traits are inherited.

Locus

Specific place on a chromosome, occupied by an allele.

Genotypes

Genetic makeup of an organism. A set of alleles occupied by an individual organism.

Heterozygote

An organism possessing two different alleles at a locus.

Homozygote

An organism possessing two of the same alleles at a locus.

How do alleles work? How do alleles influence a phenotype?

Different alleles for a particular gene occupy the same locus on homologous chromosomes.

The combination of the allele is what determines the phenotype.

Mendels hypothesis

When peas with 2

different traits (round/wrinkled seeds) are

crossed, will their progeny exhibit one of the

traits, both traits, or an intermediate trait?

How did Mendel test his hypothesis?

He crossed two parent pea seas that differ only in one trait(like if seed is round or wrinkled):

1) Find parents that are homozygous. (have two identical alleles for the same trait).

First generation

When you cross RR × rr, all offspring get one R and one r → Rr

R is dominant, so all F1 seeds are round

Second generation

Cross F1 plants: Rr × Rr

Punnett square gives:

RR, Rr, Rr, rr

Phenotypes (what we see):

• Round seeds → RR or Rr = 3 out of 4

• Wrinkled seeds → rr = 1 out of 4

So the phenotypic ratio = 3 round : 1 wrinkled

Monohybrid cross

a genetic cross between two organisms that differ in only one trait (or characteristic).

ex)Crossing a plant with round seeds (RR) with a plant with wrinkled seeds (rr).

Mendel’s first principle of inheritance

derived from monohybrid

test crosses

Genes exist as pairs!

A gene is a unit factor! Each gene carries a trait.

1. Every gene has two allele versions of it, one from mom and one from dad.

2. Possible allele combinations → Because there are two alleles, you can get three possible genotypes:

   • AA → both alleles are the same dominant

   • Aa → one dominant, one recessive

   • aa → both alleles are recessive

Key point: The combination of alleles determines the organism’s genotype and influences its phenotype.

Mendel’s second principle of inheritance

derived from monohybrid

test crosses

- When 2 unlike alleles are present, one allele is dominant over the other, recessive, allele.

-When a dominant allele is present, its trait shows up, and the recessive trait is hidden in the F1 offspring.

Mendel’s third principle of inheritance

derived from monohybrid

test crosses

-Segregation → also called the Law of Segregation. It describes how alleles separate during the formation of gametes (sperm or egg). Each gamete recieves one or the other with equal probability.

-If an individual is heterozygote, each gamete has a 50% probability of receiving either allele

The concept of dominance

when two different

alleles are present in a genotype, only the “dominant”

allele―is observed in the phenotype. The other

trait that is not seen in the offspring, is encoded

by the recessive allele.

Principle of segregation

Each individual diploid

organism possesses two

alleles for any particular

characteristic. These two

alleles segregate when

gametes are formed, and

one allele goes into each

gamete.

Probability

The chance that a particular event will happen.

In genetics, it’s used to predict the likelihood of certain genotypes or phenotypes in offspring.

Addition rule

Add the probabilities of each event. Events cannot happen at the same time.

Genetics example:

• Cross Aa × Aa, probability of getting a dominant phenotype (AA OR Aa):

  • P(AA) = 1/4

  • P(Aa) = 2/4

  • P(AA OR Aa) = 1/4 + 2/4 = 3/4

Multiplication rule

Used when you want the probability of two or more independent events happening together.

Cross Aa × Aa, probability of offspring being Aa AND another offspring being aa:

• P(Aa) = 2/4 = 1/2

• P(aa) = 1/4

• P(Aa AND aa) = 1/2 × 1/4 = 1/8

Dihybrid cross

-2 traits are being inherited.

-Each trait follows its own probability rules

• To find the chance of inheriting both traits in a particular combination, you multiply the probabilities for each trait (using the Multiplication Rule)

• Each trait has 2 alleles.

  Therefore, each parent has 2

  alleles per trait (2 alleles x 2

  traits = 4 alleles). Ex. AaBb

Possible outcomes for dihybrid crosses

There are 4 possible gametes potentially created in a dihybrid cross that must be considered in the

If both parents were heterozygous for the 2 genes (A and B), they would have the genotype AaBb.

Each parent therefore has the potential for creating 4 different gamete genotypes

Foil method

F: first set

O: outer set

I: inner set

L: last set

How do you determine the phenotypic ratio in a dihybrid cross

You use the multiplication rule

Principle of Independent Assortment

Alleles for different genes assort independently. One does not affect the other.

Trihybrid Cross

-Segregation and

independent assortment

applied to three pairs of

constraining traits

-Punnet square with 64 boxes.

Fork Lined Method

When the monohybrid cross is

made, we know that:

• All individuals have the

genotype Aa and express the

phenotype represented by the

A allele, which is called the A

phenotype in the discussion

that follows.

• The generation consists of

individuals with either the A

phenotype or the a phenotype

in the ratio of 3:1.

What can happen to these observed ratios?

May deviate from expected

Chi Square analysis

Determines whether differences in genetic results are caused by random chance or by another factor.

Chance deviation

Chance-based processes naturally show variation, not exact consistency.

As the sample size increases, random variation has less effect on the results. Basically, with more samples, random differences cancel out, so results are closer to what’s expected.

Two factors in analyzing or

predicting genetic outcomes

Independent assortment: Outcomes vary because alleles separate randomly by chance.

Sample Size: As more individuals are observed, chance deviations become smaller and results move closer to the expected ratio.When sample size is small, results can be far off because of chance. As sample size gets larger, the difference (deviation) between what you expect and what you actually observe becomes smaller, so the results are more accurate and consistent.

What is wrong with Mendel’s monohybrid and dihybrid ratios?

They are based on assumptions. These assumptions include:

What are these assumptions?

• Dominance/recessiveness – Mendel assumed one allele is completely dominant over the other, but sometimes alleles show incomplete dominance or codominance.

• Unimpeded segregation – He assumed alleles separate cleanly during meiosis, but sometimes chromosomal abnormalities or gene linkage interfere.

• Independent assortment – He assumed genes on different chromosomes assort independently, but linked genes on the same chromosome can be inherited together.

• Random fertilization – He assumed every gamete has an equal chance of combining, but environmental or biological factors can bias fertilization.

Which assumptions are influenced by chance events?

independent assortment and random

fertilization, which leads to random fluctuation. so because they are due to chance, the actual results fluctuate from expected/predicted ones

Null hypothesis:

assumes no real difference between measured and predicted values, attributing any differences to chance. Any deviations is due to chance.

Statistical analysis

-Determines whether the null hypothesis is

rejected or fails to be rejected.

What does rejection of stat analysis mean?

Rejection implies that observed deviations are not due to chance,necessitating a reexamination of the hypothesis and assumptions.

What does fail to reject of stat analysis mean?

Fail to reject the hypothesis assumes that the deviations are due to chance.

Chi-Square goodness of fit test

can be used to determine the magnitude of deviation between observed and

expected. A way to measure how much your observed data differs from what you expected.

How do you know to reject or fail to reject based on this goodness of fit test?

If 𝑥2 > critical value → reject null hypothesis

If 𝑥2 < critical value → fail to reject null

hypothesis

Degrees of freedom

“df”: The max number of independent values, which have the freedom to vary.

=n-1

n

number of different categories into

which data may fall (different

outcomes)

x²

The χ² (chi-square) value is a statistic you calculate when you perform a chi-square test, which measures how much your observed data deviate from what you expected under the null hypothesis.

The larger the χ² value, the greater the difference between observed and expected frequencies

P value

(P=0.05)= statistically

significant probability of error is less

than 5%

• A small p-value (usually < 0.05) means the observed data are unlikely under the null hypothesis, so you reject H0H_0H0​.

• A large p-value means the data are consistent with the null hypothesis, so you fail to reject H0H_0H0​.

Pedigree

A pedigree is a map that depicts the different members of a family and

their connections. It is a graph, and it makes assessing who is

connected and their relationships — such as parent, sibling, cousin —

apparent by visual inspection.

A pedigree can also help determine how a trait or condition might be

passed down through the generations and what might accompany it.

Symbols on pedigrees and what they mean

Square: Male

Circle: Female

Diamond: unknown

Fully colored in: Affected

Half colored in: Carrier

Generations are labeled with roman numerals

Eldest child on left.

“Individual designation II:2” The roman numeral is the generation and the number is the second person listed (left to right) in that generation.

Animal Pedigree

-Records the ancestral and mating relationship.

-Often include birth date, sex, and registration number

-Used to document breed purity.

-Shows an animals registration within breed or group.

-Can list physical traits or genetic info. (eye disease, hip score)

-May include the owners information.

Horse pedigree

-Sire (father) written on top

-Dam (mother) written on bottom.

-Physical appearance notes

Angus pedigree

-Has genetic merit scores (EPD): a number that estimates an animal’s ability to pass on desirable traits to its offspring based on its genetics

-Performance data

-Progeny data

Autosomal recessive trait

-traits affect males and females equally.

-Recessive traits typically skip generations.

-You must have two recessive alleles (aa) to show the trait.

-Someone with one normal allele and one recessive allele (Aa) is a carrier but looks unaffected. The male parent (I-1) is affected → his genotype must be aa. The female parent (I-2) is unaffected, so she could be:

• AA (homozygous normal), or

• Aa (a carrier)

The unaffected female must be homozygous normal because none of the offspring exhibit the trait.

-If the parent was heterozygous (a carrier) than ½ of her offspring would show the trait.

-II-3 does not show the trait but passes it on, meaning he is a carrier, which supports autosomal recessive inheritance.

-II-3 and II-4 are both carriers, so about ¼ of their children are expected to be affected (2 out of 6 observed).

-The small sample size (n=3) limits the

certainty of these conclusions

Autosomal dominant traits

-all affected offspring will have a parent that also expresses the trait. If none of the offspring inherit the dominant allele, the trait will cease to exist in future generations.

-Affected individuals with a rare autosomal dominant disease are usually heterozygous,

resulting in approximately half of the offspring inheriting the trait.

-Homozygotes for a dominant mutation are often more severely affected, sometimes failing

to survive, as seen with familial hypercholesterolemia.

Heterozygotes for familial

hypercholesterolemia have

elevated

LDL levels and are prone

to heart attacks by their fourth

decade, while homozygotes have

extremely high LDL levels and are

likely to have heart attacks very

early in life.

What is wrong with pedigrees?

Pedigree analysis is valuable in

genetic studies but does not provide

the same certainty as experimental

crosses with large numbers of

offspring.

How can you draw consistent conclusions from pedigrees?

Consistent conclusions can often be

drawn from analyzing many

independent pedigrees of the same

trait or disorder.