Comprehensive Genetics Study Guide: Mendelian, Linkage, Pedigree, and Population Genetics

BLOCK 1: BASICS OF MENDELIAN GENETICS

Genetic Crosses and Mendelian Ratios

Genetic crosses involving F1 plants heterozygous for a given allele can produce characteristic phenotypic ratios in the F2 generation. The classic 3:1 ratio is a hallmark of Mendelian inheritance.

• Monohybrid Cross: A cross between two individuals heterozygous for a single gene (Aa x Aa), producing a 3:1 phenotypic ratio in the F2 generation.

• Dihybrid Cross: A cross between individuals heterozygous for two genes (AaBb x AaBb), producing a 9:3:3:1 phenotypic ratio if the genes assort independently.

• Reciprocal Cross: A pair of crosses between a male of one genotype and a female of another, and vice versa, to test for sex linkage or maternal effects.

Example: Crossing pea plants heterozygous for seed shape (Rr) and seed color (Yy) yields a 9:3:3:1 ratio in the F2 generation.

Meiosis and Gamete Formation

During meiosis, diploid cells undergo two rounds of division to produce haploid gametes. Each gamete contains one copy of each chromosome.

• Diploid (2n): Cells with two sets of chromosomes.

• Haploid (n): Gametes with one set of chromosomes.

• For a cell with n chromosome pairs, the number of possible gamete types is $2^n$.

Example: A tetraploid potato (4n) produces gametes with two copies of each chromosome.

Polyploidy in Plants

Polyploidy refers to organisms with more than two sets of chromosomes. Many crop plants, such as potatoes and bananas, are polyploid.

• Tetraploid: Four sets of chromosomes (e.g., commercial potatoes).

• Triploid: Three sets of chromosomes (e.g., commercial bananas, which are often seedless due to irregular meiosis).

Example: A triploid banana plant produces unbalanced gametes, leading to seedless fruit.

Genotype and Phenotype

The genotype is the genetic makeup of an organism, while the phenotype is the observable trait.

• Homozygous: Two identical alleles (e.g., AA or aa).

• Heterozygous: Two different alleles (e.g., Aa).

Inheritance Patterns

Different inheritance patterns can be observed depending on dominance, gene location, and interaction.

• Dominant: Only one allele needed for trait expression.

• Recessive: Both alleles must be present for trait expression.

• X-linked: Genes located on the X chromosome, often showing different patterns in males and females.

Example: Tongue rolling is a dominant trait; if both parents are heterozygous (Tt), their child may or may not be able to roll their tongue.

BLOCK 2: LINKAGE AND GENE MAPPING

Genetic Linkage and Recombination

Genes located close together on the same chromosome tend to be inherited together, a phenomenon known as genetic linkage. Recombination during meiosis can separate linked genes.

• Linked Genes: Genes on the same chromosome that do not assort independently.

• Recombination Frequency: The proportion of recombinant offspring, used to estimate genetic distance.

• Map Unit (centiMorgan, cM): 1% recombination frequency equals 1 cM.

Example: If two genes show a recombination frequency of 10%, they are 10 cM apart.

Test Crosses and Haplotype Analysis

Test crosses are used to determine the genotype of an individual by crossing it with a homozygous recessive individual. Haplotype analysis helps identify combinations of alleles inherited together.

• Test Cross: Cross between an individual of unknown genotype and a homozygous recessive individual.

• Haplotype: A set of alleles at multiple loci that are transmitted together.

Pedigree Analysis

Pedigrees are diagrams that show the inheritance of traits across generations. They are used to determine the mode of inheritance (autosomal dominant, autosomal recessive, X-linked, etc.).

• Symbols: Squares represent males, circles represent females, filled symbols indicate affected individuals.

• Autosomal Dominant: Trait appears in every generation.

• Autosomal Recessive: Trait may skip generations.

• X-linked Recessive: More common in males; affected males often have carrier mothers.

Table: Types of Genetic Crosses

Type of Cross	Genotype Example	Expected F2 Ratio
Monohybrid	Aa x Aa	3:1
Dihybrid	AaBb x AaBb	9:3:3:1
Test Cross	Aa x aa	1:1

BLOCK 3: PEDIGREE ANALYSIS AND GENETIC TESTING

Autosomal Dominant and Recessive Inheritance

Autosomal dominant traits appear in every generation, while autosomal recessive traits may skip generations. Pedigree analysis can help determine the probability of inheriting a disorder.

• Probability Calculations: Use Punnett squares and pedigree information to calculate the likelihood of offspring inheriting a trait.

• Penetrance: The proportion of individuals with a genotype who express the phenotype.

Example: Huntington's disease is autosomal dominant; if one parent is heterozygous, each child has a 50% chance of inheriting the allele.

X-linked Inheritance

X-linked recessive traits are more common in males, as they have only one X chromosome. Females can be carriers without showing symptoms.

• Examples: Hemophilia, red-green color blindness.

Types of Mutations

• Point Mutation: Change in a single nucleotide.

• Chromosomal Translocation: Rearrangement of chromosome segments.

• Trinucleotide Repeat Expansion: Increase in the number of repeats of a three-nucleotide sequence (e.g., Huntington's disease).

• Aneuploidy: Abnormal number of chromosomes.

BLOCK 4: POPULATION GENETICS AND HUMAN EVOLUTIONARY GENETICS

Hardy-Weinberg Equilibrium

The Hardy-Weinberg principle describes a population that is not evolving. Allele and genotype frequencies remain constant from generation to generation in the absence of evolutionary influences.

• Equation: $p^2 + 2pq + q^2 = 1$

• p: Frequency of the dominant allele

• q: Frequency of the recessive allele

Example: If 1 in 10,000 individuals is homozygous recessive (q^2), then $q = \sqrt{1/10,000} = 0.01$.

Selection and Fitness

Selection acts on phenotypes, altering allele frequencies. Fitness (w) measures reproductive success; selection coefficient (s) quantifies the reduction in fitness.

• Relative Fitness: $w = 1 - s$

• Selection Coefficient: $s = 1 - w$

Genetic Drift and Population Structure

Genetic drift is the random fluctuation of allele frequencies, especially in small populations. It can lead to loss of genetic variation.

• Bottleneck Effect: Sharp reduction in population size.

• Founder Effect: New population established by a small number of individuals.

Linkage Disequilibrium and Selective Sweeps

Linkage disequilibrium (LD) is the non-random association of alleles at different loci. Selective sweeps occur when a beneficial allele increases in frequency, reducing genetic variation nearby.

• Example: The SLC24A5 gene variant associated with lighter skin in Europeans shows evidence of a selective sweep.

Table: Types of Inheritance and Examples

Inheritance Pattern	Example Disease
Autosomal Dominant	Huntington's disease
Autosomal Recessive	Sickle cell anemia
X-linked Recessive	Hemophilia, red-green color blindness

Chi-Square Test for Hardy-Weinberg Equilibrium

The chi-square test is used to determine if observed genotype frequencies deviate from expected frequencies under Hardy-Weinberg equilibrium.

• Equation: $\chi^2 = \sum \frac{(O - E)^2}{E}$

• Degrees of Freedom: Number of genotypes minus number of alleles

Summary

This study guide covers fundamental concepts in genetics, including Mendelian inheritance, genetic linkage, pedigree analysis, population genetics, and evolutionary genetics. Mastery of these topics is essential for understanding genetic variation, inheritance patterns, and the genetic basis of human disease.