chapter 5

Question 1

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what are genes on the same chromosome called?

Answer 1

syntenic genes

Question 2

what can be quantified to map the positions of genes on chromosomes?

Answer 2

genetic linkage

Question 3

what produced recombinant chromosomes?

Answer 3

when the alleles of syntenic genes can be reshuffled & crossing over occurs between them

Question 4

what are chromosomes called that do not reshuffle alleles called?

Answer 4

parental chromosomes or non-recombinant chromosomes

Question 5

what plots the position of genes on a chromosome

Answer 5

genetic linkage mapping

Question 6

when does independent assortment of syntenic genes occur?

Answer 6

when they are far part on a chromosome

Question 7

syntenic genes that are closer together will tend to ______ together

Answer 7

segregate

Question 8

what occurs in prophase of meiosis 1?

Answer 8

crossing over that prevents linked genes from segregating together

Question 9

linked genes are always syntenic to one another & always located near one another. T or F

Answer 9

True

Question 10

what does genetic linkage lead to?

Answer 10

the production of significantly more gametes with parental allele combinations than nonparental combinations

Question 11

T or F: If genes are linked, parental allele combinations will be observed at higher frequency than predicted by chance

Answer 11

True

Question 12

complete genetic linkage is observed…

Answer 12

when no crossing over occurs between linked genes, only parental gametes are formed

Question 13

what is an example of an organism that exhibits complete linkage?

Answer 13

drosophila males
-they have no crossing over
-biological bases for this is unkown

Question 14

which is more common, incomplete linkage or complete linkage?

Answer 14

incomplete genetic linkage

Question 15

what is recombination frequency?

Answer 15

a likely reflection of the physical distance between two genes

Question 16

what type of test did morgan realize that the linkage of autosomal genes in Drosophila could be determined in?

Answer 16

two-point test-cross analysis

Question 17

what type of relationship is genetic linkage?

Answer 17

a physical relationship among genes located near one another on a chromosome

Question 18

what is crossover accompanied by?

Answer 18

chromosome breakage & rejoining in plants & animals

Question 19

who was the first to demonstrate that genes are on chromosomes?

Answer 19

morgan

Question 20

who created the genetic map for the five X-linked genes in drosophila?

Answer 20

Alfred Sturvant

Question 21

what is a map unit (m.u), also called?

Answer 21

centiMorgan (cM)

Question 22

where does recombination primarily occur?

Answer 22

at specific hotspots

Question 23

what happened in mis-1980s

Answer 23

methods to identify polymorphic DNA sequences & improved-gene mapping software facilitated genome mapping efforts

Question 24

what are the polymorphic DNA sequences called?

Answer 24

genetic markers

Question 25

what lead to linkage groups?

Answer 25

the availibility of large numbers of DNA markers on each chromosome

Question 26

what are linkage groups

Answer 26

clusters of syntenic genes that are linked to one another

Question 27

where are genetic markers typically

Answer 27

in noncoding regions of the genome

Question 28

genetic markers include

Answer 28

-variable number tandem repeats (VNTRs) -single nucleotide polymorphisms (SNPs) -restriction fragment length polymorphisms (RFLPs)

Question 29

how long are VNTRs?

Answer 29

they are short- 3-20 bp

Question 30

VNTRs

Answer 30

-sequences repeat end-to-end in a chromosomal region -different chromosomes can carry different repeat numbers of the sequence -repeat length can vary

Question 31

how big are SNPs?

Answer 31

1 bp

Question 32

SNPs

Answer 32

-more commonly used markers than VNTRPs -involve variants where one base pair is substituted by another base pair, typically in a noncoding region

Question 33

how many SNPs are there in the human genome?

Answer 33

3.3 million

Question 34

which marker is more common, VNTRs or SNPs?

Answer 34

-SNPs

Question 35

RFLPs

Answer 35

-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

Question 36

what are the pieces of DNA resulting from restriction enzyme cutting called?

Answer 36

restriction fragments

Question 37

what is a haplotype?

Answer 37

-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

Question 38

when will haplotype SNPs be passed on?

Answer 38

these specific arrays of SNPs will be passed on together during meiosis

Question 39

what may haplotypes differ between?

Answer 39

members of a chromosome pair

Question 40

what is the first obstacle when happing human genes?

Answer 40

the difficulty in determining the allelic phase

Question 41

what is the allelic phase

Answer 41

the arrangement of alleles of linked genes on parental chromosomes

Question 42

when can allelic phase be determined?

Answer 42

when a disease-causing allele is seen to segregate along with a known genetic marker

Question 43

what does LOD score analysis do

Answer 43

compared the likelihood of obtaining the genotypes & phenotypes observed in the pedigree if two genes are linked versus the likelihood if they are unlinked

Question 44

what does LOD stand for?

Answer 44

the logarithm of the odds ratio

Question 45

what does the LOD score determine

Answer 45

the likelihood of linkage for many recombinant frequencies, called theta values

Question 46

if theta equals 0 LOD score

Answer 46

complete linkage

Question 47

if theta equals 0.5

Answer 47

not linked = independent assortment

Question 48

if theta equals 0.1, how many map units is that?

Answer 48

10 m.u.

Question 49

what does a LOD score of 3.0 or higher mean?

Answer 49

significant evidence in favor of linkage at the theta value

Question 50

what does a LOD score of less than -2.0 mean

Answer 50

significant evidence against genetic linkage

Question 51

LOD scores between 3.0 & -2.0 are what

Answer 51

inconclusive

Question 52

what does the Zmax value indicate?

Answer 52

the recombination frequency most likley to be correct

Question 53

what allows identification of the most likely recombination distance between genes?

Answer 53

the LOD score

Question 54

what does Genome-wide association studies (GWAS) do?

Answer 54

-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

Question 55

what does GWAS look for?

Answer 55

-associtation between traits & groups of alleles in populations

Question 56

why are SNPs typical genetic markers used in GWAS and what type of SNPs does GWAS use?

Answer 56

due to their frequent distribution in most genomes -uses closely linked SNPs in haplotype groups with known chromosome locations

Question 57

what are GWAS results represented in the form of?

Answer 57

a Manhattan Plot

Question 58

what does the manhattan plot indicate?

Answer 58

the locations of genes contributing to the development of traits & conditions

Question 59

reading a manhattan plot

Answer 59

-the higher the green bar, the stronger the association between a potential contributing gene & a chromosomal location

Question 60

disequilibrium

Answer 60

nonrandom distribution of alleles for linked genes

Question 61

linkage disequilibrium

Answer 61

when frequencies of haplotypes in a population deviate significantly from what is expected

Question 62

what does linkage disequlibrium reflect?

Answer 62

the NON-RANDOM relationship between alleles of closely linked genes -means the gene are are studying is closely associated to the SNP haplotype

Question 63

how can linkage disequilibrium be separated?

Answer 63

by crossovers which are random & infrequent

Question 64

what must be identified if linkage disequilibrium is found in a SNP haplotype?

Answer 64

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

Question 65

what gene was suggested to be associated to Crohn's disease based of GWAS results?

Answer 65

CARD15 (recently named NOD2 gene)