Molecular Mapping. Terminology Gene: a particular sequence of nucleotides along a molecule of DNA which represents a functional unit of inheritance. (

Molecular Mapping

Terminology

Gene: a particular sequence of nucleotides along a molecule of DNA which represents a functional unit of inheritance. (Johannsen, 1909)

Locus: the position of a gene on a chromosome or a genetic map. (Morgan, Sturtevant, Muller, and Bridges, 1915)

Terminology

Allele: one of two or more alternate forms of a gene occupying the same locus on a particular chromosome or linkage structure and differing from other alleles of that locus at one or more sites. (Johannsen, 1909).

Terminology

Linkage: the association in inheritance of certain genes and their associated phenotypes due to their being localized in the same chromosome. (Morgan, 1910)

Linked: two genes showing less than 50% recombination.

Terminology

Recombination: Any process which gives rise to cells or individuals (recombinants) associating the alleles of two or more genes in new ways. (Bridges and Morgan, 1923)

Recombinants are the end product of exchange of alleles from parental types as a result of crossing-over.

Terminology

Phenotype: the observable properties of an organism, produced by the interaction between the organism’s genotype and the environment. (Johannsen,

1909)

Terminology

Genotype: the genetic constitution in respect to the alleles at one or a few genetic loci under observation. (Johannsen, 1909)

AA Aaaa

A

a

B

b

A B

a b

A b

a B

Parental Type Recombinant

Two Point Analysis

Parental types

Tall, Green 42

Short, White 39 = 81 %

Recombinant types

Tall, White 7

Short, Green 12

=19%

Map Units

1 map unit is equal to 1% recombination.

Map units are also called centimorgans after geneticist

Thomas Hunt Morgan who won the Nobel Prize for discovering how

chromosomes govern inheritance.

Challenge

How do we merge the information about each pair of genes together into one common framework?

How do we order the genes relative to one another?

Three-Point Analysis

Single cross-overA B C

a b cDouble cross-over

Double cross-overs and Map Distance

If we only look at the outer markers A and C on the previous slide, we

will underestimate the true distance between them because we have not accounted for the

double cross-overs.

Three-point analysis

Distance =

# Singles + 2 ( # Doubles)Total

Double cross-overs

If cross-overs are equally likely along the chromosome and closer genes have few cross-overs, then the likelihood of two crossovers close to one another would be small.

Double cross-overs

If cross-overs are equally likely along the chromosome and closer genes have few cross-overs, then the likelihood of two crossovers close to one another would be small.

So, mapping algorithms can order genes by minimizing the number of double cross-overs.

Mapping Maize at UMC

Genetic mapping Genetic mapping is based on DNA is based on DNA fingerprint data of offspring from fingerprint data of offspring from two parents which differ in their two parents which differ in their appearance. appearance. Similar fingerprint data for two gene Similar fingerprint data for two gene

indicates they are physically close indicates they are physically close together on a chromosome. together on a chromosome.

Scoring your gel

Each parent A and B have different size DNA fragments.

Progeny are either: A (homozygous parent A) H (heterozygous) B (homozygous parent B) Can also use a – if missing or not

clear.

Molecular mappingDigest DNA

Electrophorese

-

+

Southern

blot

Hybridizewith probe

Scoring data

A B H H A B A H

Recombination and Mapping

Assume that the frequency of crossing-over is equal along the chromosome. Two genes that are very close to one another will have a lower likelihood of having a cross-over between them than two genes that are very far apart.

Recombination and Mapping

So, we can determine the relative distance between genes by counting the number of recombinant genotypes for each pair of genes. Lots of recombinants = far apart Few recombinants = close together

BHBBAHBHHBHHBHB umc157HHBBABBHHBBBBAB umc76BHBBABHAHHBHBAB asg45BHBBABBAHHBHBAB zb4BHBBHBHAHHBHBAB csu3

How Maximum Likelihood Works

BHBBAHBHHBHHBHB umc157BHBBABHAHHBHBAB asg45HHBBABBHHBBBBAB umc76BHBBABBAHHBHBAB zb4BHBBHBHAHHBHBAB csu3

SSR gel scoring

ABAABAAAAABABBBBBABABBAB

BAABAAABAAAAGBABAABBBBAA

ABBGAABABABAABABBAAABBAB

ABBBBAABBAAAABBBGBABABAB