Chapter 4: Mapping Eukaryote Chromosomes by Recombination

Recombination

combinations of genes that differ from parental traits

- closely linked genes: recombination frequency is lower than 50%; they are more likely to be inherited together; not enough space, need a double strand break to occur

- unlinked genes: frequency is 50% due to independent assortment, do not need a double strand break, results in 1:1:1:1 ratio

Double Strand Breaks

two non sister chromatids make contact in the chiasmata

- break and swap DNA strands

- occurs during prophase I

- allows for crossing over to occur

Crossing Over

allows for recombination to occur

- result of DNA double strand breaks

- multiple can occur, the greater the number the rarer they are

Chiasmata

physical chromosome conformations

- give rise to crossing over

How are DNA Double Strand Breaks Distributed on a Chromosome

randomly occurring

- some positions where DNA breakage occur at a higher frequency

- repairs are also random; do not always occur through a DNA heteroduplex

Cis

two dominant alleles are on the same chromosome

Trans

two dominant alleles on different chromosomes

Recombination Map

chromosome map based on recombination frequencies

- represent spatial arrangement of genes on chromosomes

Three Point Cross

look at what the parental genotypes do not have

- the double crossovers are the rarest genotypes; the ones with the least amount of progeny

Calculating Recombination Frequencies

determine the total number of recombinants from the parents

- add them

- divide each recombinant by total progeny and multiple by 100

Making Recombination Map

recombination frequencies become map units

- the ones furthest apart go on the ends

Diagnostics of Linkage

genes are linked if they are on the same chromosome

- can be referred to as loci

- discovered by mendel’s laws

Linkage Map

spatial map of genes based on recombination frequencies

Genetic Map Units

distance between genes for which 1% of meiosis is recombinant

- corresponds to the progeny that has 1% of that specific recombinant

Unlinked Genes

independent assortment

- results in equal ratios for all phenotypes

- 50% chance of recombination

Linked Genes

genes on same chromosomes that are inherited together

- less than 50% chance of recombination due to being close together; the more close the less chances

Monohybrid Test Cross With No Linkage Ratio

1:1

Monohybrid Selfed Cross Ratio

3:1

Dihybrid Testcross with No Linkage Ratio

1:1:1:1

Dihybrid Selfed Crossed Ratio

9:3:3:1

Trihybrid Testcross with No Linkage

1:1:1:1:1:1:1:1

Molecular Markers

sequence variants used to map phenotypes to chromosomal regions

- used to find the genes for traits

- detected by whole genome sequencing and PCR primers

- neutral markers with no phenotypic effect

- minisatellites and microsatellites

Minisatellite Marker

variants are 15-100 bp long

Microsatellite Marker

variants that are 2 or 3 bp long

Chi-Square Test

used to infer genotypes and linkage between genes

- for linkage plug in observed progenies in chi square test to see if they deviation from the expectations of no linkage

- no linkage expectation: 1:1:1:1

- always four phenotypic classes, 3 df

Physical Maps

more accurate than linkage maps

- sequence based map of actual genomic DNA

- recombination maps represent hypothetical arrangement of genes on chromosome