Topic 9: Linkage and Mapping Flashcards
A/a; B/b
unlinked
AB/ab
linked
A/a - B/b
unknown linkage status
recombination
due to either independent assortment or crossing over between homologues
recombination frequency
independent assortment = 50%
linked genes = <50%
locus
gene or marker location on a genetic map
three point testcrosses
used to determine map order and distance (3 different genes used: A/a, B/b, C/c)
interference (I)
measure the effect of one crossover on crossovers in adjacent regions
- I= 1-coc
coc
coefficient of coincidence
observed # of double recombinants / expected
complete interference
I = 1
no interference
I = 0
negative interference
observed > expected
I < 0
positive interference
expected > observed
I < 0
conserved synteny
different species and how the segments of their chromosomes align with each other
SNPs
single nucleotide polymorphisms
- molecular marker
- always have 4 types, detected by direct sequencing, microarrays, RFLPs, or Southern blotting
RFLPs
restriction fragment length polymorphisms
- silent DNA variations may eliminate restriction sites causing variable distances between restriction sites (inherited)
SSLPs
simple sequence length polymorphisms
- molecular marker
- detected by PCR, flanking primers, Southern blotting
(AKA. VNTRs)
VNTRs
variable number of tandem repeats
(AKA. SSLPs)
minisatellite markers
based on numbers of tandem repeats of small sequences (15-100 nt)
microsatellite markers
based on di-, tri-, or tetra-nucleotide repeats
contigs
assembled clones into overlapping groups
- used for physical mapping
LOD scores
log of odds
- determining linkage in pedigree analysis
LOG= log(odds of linkage at specific distance/odds of independent assortment)
Hypothesis of linkage accepted at LOD >/=
3
