Genotyping: Key Terms and Concepts

Introduction to Genotyping

  • Genotyping: The process of determining the DNA sequence—the genotype—at specific positions within a gene of an individual.

    • Can be performed using various methods:
    • End-point PCR
    • Real-time PCR
    • Sequencing
    • Bead or microarray analysis
    • Mass spectrometry

  • Purpose: Understand genetic variations within a population related to phenotypic traits (e.g., fruit production, disease origins).

  • Genetic Variations: Include

    • Single Base Changes (Single Nucleotide Polymorphisms, or SNPs)
    • Insertions and Deletions (INDELs)
    • Gene Copy Number Variations

Essential Genotyping Vocabulary

  • SNPs (Single Nucleotide Polymorphisms): Variations in a single nucleotide present in more than 1% of a population.
  • Indels (Insertions/Deletions): Insertions or deletions of small DNA segments.
  • Alleles: Alternative forms of a gene found at a specific chromosomal locus.
  • Haplotypes: Sets of DNA variations (polymorphisms) inherited together at a locus.
  • Hemizygous: Possessing only one allele for a gene, as seen in XY males.
  • Nonsynonymous Variants: Variants that alter the amino acid sequence of proteins.

Genetic Terminology Explained

Alleles, Locus, and Haplotype

  • Allele:

    • Definition: The DNA sequence at a specific chromosomal location.
    • Humans possess two alleles at any given locus, one from each parent.
    • Types of Allelic States:
    • Polyallelic: Multiple alleles at a locus.
    • Biallelic: Two different nucleotides (e.g., A/G).
    • Triallelic: Three different nucleotides (e.g., A/C/T).
    • Quatra-allelic: Four distinct nucleotides (e.g., A/C/G/T).

  • Locus: A specific location on a chromosome.

  • Haplotype: Combination of alleles at adjacent loci that are inherited together.

Zygosity
  • Zygosity: Refers to the similarity or differences between alleles in an individual.
    • Types:
    • Homozygous (BB, bb): Two identical alleles.
    • Heterozygous (Bb): Two different alleles (one dominant, one recessive).
    • Hemizygous (B, b): One allele present (e.g., male sex chromosomes).

Genotype vs Phenotype

  • Genotype:
    • Definition: The genetic makeup of an organism; includes complete genes or specific alleles.
  • Phenotype:
    • Definition: The physical/observed traits arising from a genotype (e.g., flower color).