ch 4 mapping eukaryote chromosomes by recombination Flashcards
linkage
the association of two genes on the same chromosome
coupling configuration
arrangement of linked alleles in a dihybrid such that the two dominant alleles are on a chromosome, the two recessive alleles are on the other chromosome (AB/ab)
repulsion configuration
arrangement of linked alleles in a dihybrid such that a dominant and a recessive allele are together on each chromosome (Ab/aB)
cis dyhybrid
a dihybrid in which the alleles are coupled (AB/ab)
trans dihybrid
a dihybrid in which the alleles are in repulsion (Ab/Ba)
two process that generate recombinant products
- independent assortment of genes on different chromosomes
- crossing-over between genes on the same chromosome
what regions have higher recombinant frequencies
longer regions
map unit or cM
a recombinant frequency of 1%
why map the relative position of genes
calculated map distance is correlated to physical distance on a DNA molecule
- knowing the position of a gene on a chromosome allows us to find its sequence
- leads to an understanding of its structure and function
map distance formula
precent recombinant progeny
= # recombinant progeny/total progeny x 100%
recombination frequency never exceeds
50%
3-point test cross
mapping 3 genes relative to one another
rules for a 3 point test cross
- there should be 8 phenotypic classes
- progeny classes are grouped in pairs = reciprocal cross over events
- largest classes are the parentals
- smallest classes are the double cross over classes
interference
a measurement of the independence of two cross over events (does one cross over interfere with the possibility of another cross over)
interference formula
interference = 1 - (observed DCO/(p(SCO I) x p(SCO II) x total number of progeny))
negative interference
more double cross overs than expected (cross over in one region promotes cross overs in another region)
positive interference
(usually)
fewer double cross overs than expected (cross over in one region inhibits cross overs in another region)
spores: division I - separation of
homologues
spores: division II - separation of
sister chromatids
distance between 2 points =
% meiotic products showing recombination between the 2 points
the frequency of crossing over between any two points on a chromosome is proportional to the distance between those two points
1/2 MII octads / total x 100%
octad
an ascus containing eight ascospores, produced in species in which the tetrad normally undergoes a postmeiotic mitotic division
first division segregation
different alleles go into different nuclei at the first meiotic division producing an M1 division pattern of ascospores (4:4)
second division segregation
different alleles go into different nuclei at the second meiotic division producing an MII division pattern of ascospores (2:2:2:2)
molecular marker
a site of DNA heterozygosity (difference), not necessarily associated with phenotypic variation, used as a tag for a particular chromosomal locus
single nucleotide polymorphism (SNPs)
a nucleotide pair difference at a given location in the genomes of two or more naturally occurring individuals
- changes to a single nucleotide
- can be located within a gene or intergenic regions
simple sequence length polymorphisms (SSLPs)
the presence of different numbers of short or simple repetitive elements at one particular locus in different homologous chromosomes
- become subject to expansion or deletion
three methods of SNPs detection
- DNA sequencing - not always feasible as prior knowledge of the sequence is required
- RFLP analysis - restriction fragment length polymorphism
- CAPS analysis - cleaved amplified polymorphic sequences
RFLP analysis
restriction fragment length polymorphism
- restriction enzymes cleave DNA at a specific sequence
- detected by a Southern blot
- EcoR1 recognizes and cuts a specific sequence; but if the sequence is mutated, it will not cut
restriction enzyme
an enzyme that will recognize specific target nucleotide sequences in DNA and break the DNA chain at those points
4 steps of Southern blotting
- separate genomic DNA (cute with the restriction enzyme) via agarose gel electrophoresis
- DNA is transferred from the gel to a membrane
- expose the membrane to a labeled probe (P-32), complimentary to the region of interest; short DNA sequences of P-32 will stick to regions we are interested in following
- bound, radioactively labeled probe will expose x-ray film, and identify fragments to which the probe was bound
3 steps of CAPS analysis
- primers flanking a polymorphic R.E site are used to amplify region by PRC
- amplified region is then cut by R.E
- fragments are separated by electrophoresis
(less DNA needed and eliminates Southern blotting)
haplotypes
a genetic class described by a sequence of DNA or of genes that are together on the same physical chromosome (a chromosome segment defined by the array of markers it carries)
microsatellites
very short sequences of repetitive DNA <10nts
different alleles due to variable number of repeats
detection of microsatellites
use PCR to amplify the region containing the microsatellite and visualize fragments using agarose gel electrophoresis
minisatellites
short sequences of repetitive DNA, 15-100nts
different alleles due to variable number of repeats
detection of minisatellites
cut with R.E outside the minisatellite and southern blot using specific probe
minisatellites can be used to generate a
DNA fingerprint
microsatellites can show a linkage to a
disease gene
