Molecular Markers - Genetics

1. Define the GENOTYPIC GROUPS in CONTINUOUS TRAITS using x and y.

Continuous traits (e.g., eye color, skin tone) are determined by multiple genes, each contributing a small additive effect:
For example: x⁶ + x⁵y + x⁴y² ..., where each term represents different allele combinations contributing to the phenotype. The overall phenotype results from the sum of these effects.

2. Define SNP vs. SNV.

  • SNP (Single Nucleotide Polymorphism): A variation in a single nucleotide occurring at a specific position in the genome, common in a population (>1%).

  • SNV (Single Nucleotide Variant): A single nucleotide change, whether common or rare.

3. For what types of traits are SNPs or SNVs so useful?

SNPs/SNVs are useful for studying:

  1. Cystic fibrosis

  2. Sickle cell anemia

  3. Diabetes

  4. Cancer susceptibility

  5. Cardiovascular disease

4. What is a haplotype? Are haplotype SNPs linked?

  • Haplotype: A group of alleles or SNPs inherited together due to physical proximity on the chromosome.

  • Linkage: Yes, haplotype SNPs are often inherited together because they are close on the chromatid, reducing the chance of recombination.

  • Only certain base positions are analyzed because they are informative for tracking genetic variation.

5. Molecular Markers like SNPs and SNVs are useful for what types of genetic disorders?

Molecular markers help identify genetic variations associated with:

  • Monogenic disorders (e.g., Huntington’s disease).

  • Complex traits (e.g., asthma, Alzheimer’s disease).

  • Predispositions to cancers or metabolic syndromes.

6. Why are SNP/SNVs that are close together on the chromatid most often inherited together?

They are tightly linked due to proximity, so recombination between them is rare. If far apart, recombination is more likely, leading to independent assortment.

7. How do we track SNP/SNVs that co-segregate with a disorder phenotype?

By analyzing pedigree data and performing genome-wide association studies (GWAS) to find correlations between specific SNPs and the disorder.

8. What does GWAS stand for? What is analyzed in a GWAS?

  • GWAS: Genome-Wide Association Study.

  • Analyzed: It scans the genome for SNPs associated with specific traits or disorders by comparing affected and unaffected populations.

9. Why scan genome-wide for SNPs/SNVs instead of analyzing one gene at a time?

Many traits are polygenic and influenced by multiple loci. GWAS allows for the identification of multiple genetic regions simultaneously.

  • QTLs (Quantitative Trait Loci): Genomic regions associated with quantitative traits.

10. What does a DNA restriction enzyme do, and how is it targeted?

  • Function: Cuts DNA at specific recognition sites, often palindromic sequences.

  • Targeting: Recognizes specific sequences of 4-8 base pairs.

11. What is cohesive vs. blunt end?

  • Cohesive (Sticky) Ends: Overhanging single-stranded DNA ends after restriction enzyme cutting.

  • Blunt Ends: No overhang; both strands are cut at the same position.

12. What is a palindrome in the restriction motif?

A sequence of DNA that reads the same in the 5’ → 3’ direction on both strands.
Example: 5’-GAATTC-3’ (EcoRI recognition site).

13. What is recombinant DNA? What do you need to clone a gene?

  • Recombinant DNA: DNA molecules formed by combining sequences from different organisms.

  • To clone a gene, you need:

    1. A vector (e.g., plasmid).

    2. Restriction enzymes to insert the gene.

    3. Ligase to join the fragments.

14. What does RFLP stand for, and how does it distinguish alleles?

  • RFLP (Restriction Fragment Length Polymorphism): A technique that uses restriction enzymes to cut DNA into fragments. Differences in fragment sizes reveal alleles due to sequence variations.

15. What is PCR? How do we view the DNA bands?

  • PCR (Polymerase Chain Reaction): Amplifies specific DNA sequences.

  • View bands: DNA is run on an agarose gel and visualized with dyes like EtBr or GelGreen.

  • Homozygote vs. Heterozygote: Homozygotes show one band; heterozygotes show two.

16. How is PCR used in combination with RFLP?

PCR amplifies the DNA region of interest. RFLP analyzes the amplified DNA to detect variations in restriction sites.

17. What does co-segregation mean?

The inheritance of two or more genetic markers together, often due to linkage.

18. In pedigree analysis, what two things co-segregate?

  1. The molecular marker (e.g., SNP).

  2. The phenotype (e.g., disease trait).

19. Do ALL restriction enzymes produce RFLPs that co-segregate with a disease?

No. Only enzymes that cut at polymorphic sites associated with the disease produce co-segregating RFLPs.

20. Is the molecular marker always located within the actual disease gene?

No. It is often near the gene but not necessarily within it.

21. Name at least two types of Molecular Markers:

  1. SNPs (Single Nucleotide Polymorphisms).

  2. Microsatellites (Short Tandem Repeats, STRs).

22. Define the difference between genetic predisposition and predetermination:

  • Predisposition: A higher likelihood of developing a condition due to genetic factors, but environmental influences play a role.

  • Predetermination: A genetic mutation guarantees the development of a condition regardless of environmental factors.