Gene mapping determines the order and relative distances between genes on a chromosome. Genes that are close together are less likely to assort independently during meiosis due to crossover events between them. The chance of recombination between two genes is directly related to their physical distance apart, with one map unit equaling a 1% chance of recombination. Gene mapping methods use recombination frequencies observed between alleles in offspring to calculate the relative distances between genes. Common markers used for gene mapping include RFLPs, SNPs, and SSRs, which identify polymorphisms that can be traced during meiosis.

1. Gene mapping
By Debajit Das
Ph.D. (Agricultural Biotechnology)

2. Gene Mapping – Basic requirements and principles
 Gene mapping determines the order of genes and the relative distances between them in map
units
 1 map unit = 1 cM (centimorgan)
In double heterozyote:
 Cis configuration = mutant alleles of both genes are on the same chromosome = ab/AB
 Trans configuration = mutant alleles are on different homologues of the same chromosome =
Ab/aB

3.  Gene mapping methods use recombination frequencies between alleles in order to
determine the relative distances between them
 Recombination frequencies between genes are directly proportional to their distance apart
 Distance measurement: 1 map unit = 1 percent recombination (true for short distances)
Gene Mapping

4. Calculation of Recombinant Fraction/Frequency

5. Gene mapping with recombination frequency

6. Principles
 Based on the fact that genes segregate via chromosomal recombination during meiosis.
 When two genes are close together on the same chromosome, they do not assort independently
and are said to be linked.
 The chance of a crossover producing recombination between genes is directly related to the
distance between two genes

7. Requirements for gene mapping
 Develope appropriate physical map and genetic map.
 Decide the type of molecular marker(s) to be used.
 Screen parents for marker polymorphism, and then go for genotyping (parents plus all
progenies).
 Perform linkage analyses (Calculate pairwise recombination frequencies between markers,
establish linkage groups, estimate map distances, and determine map order).

9. Markers used for gene mapping
RFLP
 Restriction endonucleases are used to map genes as they produce a unique set of fragments
for a gene
 There are more than 200 restriction endonucleases in use, and each recognizes a specific
sequence of DNA bases
 EcoR1 cuts double-stranded DNA at the sequence
5’-GAATTC-3’ wherever it occurs

10.  Differences in DNA sequence generate different recognition sequences and DNA cleavage
sites for specific restriction enzymes
 Two different genes will produce different fragment patterns when cut with the same
restriction enzyme due to differences in DNA sequence
RFLP

11.  Single-nucleotide polymorphisms (SNPs) are abundant in the human genome
 Rare mutants of virtually every nucleotide can probably be found, but rare variants are not
generally useful for family studies of heritable variation in susceptibility to disease
 To be considered as an SNP, the less-frequent base must have a frequency of greater than
about 5% in the human population.
SNP

12.  Results from differences in the number of copies of a short DNA sequence that may be
repeated many times in tandem at a particular site in a chromosome
 When a DNA molecule is cleaved with a restriction endonuclease that cleaves at sites
flanking the tandem repeat, the size of the DNA fragment produced is determined by the
number of repeats present in the molecule
SSR

13. Thank you very much