chapter 5 Flashcards
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what are genes on the same chromosome called?
syntenic genes
what can be quantified to map the positions of genes on chromosomes?
genetic linkage
what produced recombinant chromosomes?
when the alleles of syntenic genes can be reshuffled & crossing over occurs between them
what are chromosomes called that do not reshuffle alleles called?
parental chromosomes or non-recombinant chromosomes
what plots the position of genes on a chromosome
genetic linkage mapping
when does independent assortment of syntenic genes occur?
when they are far part on a chromosome
syntenic genes that are closer together will tend to ______ together
segregate
what occurs in prophase of meiosis 1?
crossing over that prevents linked genes from segregating together
linked genes are always syntenic to one another & always located near one another. T or F
True
what does genetic linkage lead to?
the production of significantly more gametes with parental allele combinations than nonparental combinations
T or F: If genes are linked, parental allele combinations will be observed at higher frequency than predicted by chance
True
complete genetic linkage is observed…
when no crossing over occurs between linked genes, only parental gametes are formed
what is an example of an organism that exhibits complete linkage?
drosophila males
-they have no crossing over
-biological bases for this is unkown
which is more common, incomplete linkage or complete linkage?
incomplete genetic linkage
what is recombination frequency?
a likely reflection of the physical distance between two genes
what type of test did morgan realize that the linkage of autosomal genes in Drosophila could be determined in?
two-point test-cross analysis
what type of relationship is genetic linkage?
a physical relationship among genes located near one another on a chromosome
what is crossover accompanied by?
chromosome breakage & rejoining in plants & animals
who was the first to demonstrate that genes are on chromosomes?
morgan
who created the genetic map for the five X-linked genes in drosophila?
Alfred Sturvant
what is a map unit (m.u), also called?
centiMorgan (cM)
where does recombination primarily occur?
at specific hotspots
what happened in mis-1980s
methods to identify polymorphic DNA sequences & improved-gene mapping software facilitated genome mapping efforts
what are the polymorphic DNA sequences called?
genetic markers
what lead to linkage groups?
the availibility of large numbers of DNA markers on each chromosome
what are linkage groups
clusters of syntenic genes that are linked to one another
where are genetic markers typically
in noncoding regions of the genome
genetic markers include
-variable number tandem repeats (VNTRs)
-single nucleotide polymorphisms (SNPs)
-restriction fragment length polymorphisms (RFLPs)
how long are VNTRs?
they are short- 3-20 bp
VNTRs
-sequences repeat end-to-end in a chromosomal region
-different chromosomes can carry different repeat numbers of the sequence
-repeat length can vary
how big are SNPs?
1 bp
SNPs
-more commonly used markers than VNTRPs
-involve variants where one base pair is substituted by another base pair, typically in a noncoding region
how many SNPs are there in the human genome?
3.3 million
which marker is more common, VNTRs or SNPs?
-SNPs
RFLPs
-changes in DNA sequence that are detected using DNA-cutting enzymes called restriction endonucleases (restriction enzyme)
-the restriction enzymes recognize & cut specific sequences of DNA
-peices of DNA resulting from restriction enzyme cutting are called restriction fragments
what are the pieces of DNA resulting from restriction enzyme cutting called?
restriction fragments
what is a haplotype?
-specific array of SNPs in a small region on a single chromosome
-they are closely linked variants & will tend to be passed on together during meisois
when will haplotype SNPs be passed on?
these specific arrays of SNPs will be passed on together during meiosis
what may haplotypes differ between?
members of a chromosome pair
what is the first obstacle when happing human genes?
the difficulty in determining the allelic phase
what is the allelic phase
the arrangement of alleles of linked genes on parental chromosomes
when can allelic phase be determined?
when a disease-causing allele is seen to segregate along with a known genetic marker
what does LOD score analysis do
compared the likelihood of obtaining the genotypes & phenotypes observed in the pedigree if two genes are linked versus the likelihood if they are unlinked
what does LOD stand for?
the logarithm of the odds ratio
what does the LOD score determine
the likelihood of linkage for many recombinant frequencies, called theta values
if theta equals 0 LOD score
complete linkage
if theta equals 0.5
not linked = independent assortment
if theta equals 0.1, how many map units is that?
10 m.u.
what does a LOD score of 3.0 or higher mean?
significant evidence in favor of linkage at the theta value
what does a LOD score of less than -2.0 mean
significant evidence against genetic linkage
LOD scores between 3.0 & -2.0 are what
inconclusive
what does the Zmax value indicate?
the recombination frequency most likley to be correct
what allows identification of the most likely recombination distance between genes?
the LOD score
what does Genome-wide association studies (GWAS) do?
-it detects & located genes that influence traits as a group of multiple genes
-the influenced genes may be scattered through the genome
-identifies where in the genome the genes influencing a single trait are located
what does GWAS look for?
-associtation between traits & groups of alleles in populations
why are SNPs typical genetic markers used in GWAS and what type of SNPs does GWAS use?
due to their frequent distribution in most genomes
-uses closely linked SNPs in haplotype groups with known chromosome locations
what are GWAS results represented in the form of?
a Manhattan Plot
what does the manhattan plot indicate?
the locations of genes contributing to the development of traits & conditions
reading a manhattan plot
-the higher the green bar, the stronger the association between a potential contributing gene & a chromosomal location
disequilibrium
nonrandom distribution of alleles for linked genes
linkage disequilibrium
when frequencies of haplotypes in a population deviate significantly from what is expected
what does linkage disequlibrium reflect?
the NON-RANDOM relationship between alleles of closely linked genes
-means the gene are are studying is closely associated to the SNP haplotype
how can linkage disequilibrium be separated?
by crossovers which are random & infrequent
what must be identified if linkage disequilibrium is found in a SNP haplotype?
all genes located in that chromosome region
-then activites associated with the identified genes are then identified to determine if their action may contribute to the condition
what gene was suggested to be associated to Crohn’s disease based of GWAS results?
CARD15 (recently named NOD2 gene)
