Mapping BasicsMapping Basics

MUPGRET Workshop

June 18, 2004

Randomly IntermatedRandomly IntermatedP1 x P2

F1

SELF

F21 2 3 4 5 6 7 ……One seed from each used for next generationRecombination.

After recombination self to create line.

Randomly Intermated.Randomly Intermated.

Very high resolution.Accumulates recombination events across

generations and fixes them.Excellent for fine mappingOnly homozygous genotypes.

Population SizePopulation Size

Dependent on type of populationGenerally 200-300 individualsIf doing trait analysis, the number of

individuals determines the maximum number of QTL you can find.

Two samples from the same population will produce different maps because they sample different gametes.

Genetic Mapping BasicsGenetic Mapping Basics

Gene: a particular sequence of nucleotides among 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)

More terminologyMore 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.

More termsMore terms

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 products of exchange of alleles from parental types as a result of crossing-over.

TerminologyTerminology

Phenotype: the observable properties of an organism, produced by the interaction between the organism’s genotype and the environment (Johannsen, 1909).

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

RecombinationRecombination

Parental Recombinant

Recombination and MappingRecombination and Mapping

Assume 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 far apart.

Recombination and MappingRecombination 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– Fewer recombinants = close together

Two Point AnalysisTwo Point Analysis

Parental Types

Tall, Green

42

Short, White

39

=81%

Recombinant Types

Tall, White7

Short, Green

12

=19%

Map UnitsMap 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.

ChallengeChallenge

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 AnalysisThree-Point Analysis Single cross-over

A B C

a b cDouble cross-over

Double cross-overs and Map Double cross-overs and Map DistanceDistance

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 AnalysisThree-Point Analysis

Distance = # Singles +2 * Doubles

TotalIf cross-overs are equally likely along the

chromosome and closer genes have few cross-overs, then the likelihood of two cross-overs close to one another would be small.

Double cross-oversDouble cross-overs

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

Maximum Likelihood MethodMaximum Likelihood Method

Gives an estimate of the distances and the relative orders of the loci which would maximize the probability that the observed data would have occurred.

BHBBAHBHHBHHBHB umc157

HHBBABBHHBBBBAB umc76

BHBBABHAHHBHBAB asg45

BHBBABBAHHBHBAB zb4

BHBBHBHAHHBHBAB csu3

How Maximum Likelihood How Maximum Likelihood WorksWorks

BHBBAHBHHBHHBHB umc157

BHBBABHAHHBHBAB asg45

HHBBABBHHBBBBAB umc76

BHBBABBAHHBHBAB zb4

BHBBHBHAHHBHBAB csu3

MapMakerMapMaker

Mapping program that uses maximum likelihood method.

Initially calculates what is linked (< 50% recombination).

MapMakerMapMaker

Works one linkage group at a time.Randomly picks two genes with the group

and calculates the distance between them.Adds another gene from the group and

determines the correct placement by using maximum likelihood to minimize the double cross-overs.

MapMakerMapMaker

Does this by calculating a LOD value for the placement of the gene in each of the intervals.

Accepts the placement with the highest LOD value.

Can be used for molecular markers or for trait data.

LODLOD

Log likelihood.LOD = log 10 (Probability that the observed

data would have occurred /probability that the gene is unlinked).