Title: Gene Linkage and Genetic Mapping
14 Gene Linkage and Genetic Mapping
2If two genes are on different chromosomes
3If two genes are on different chromosomes
Half look like they got a set of the parents
chromosomes
And half look like they got a mix of both parents
chromosomes
4Now suppose both gene A and B were next to each
other on the same chromosome.
What happens to the ratios in this diagram?
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7Gene Mapping
- Gene mapping determines the order of genes and
the relative distances between them in map units - 1 map unit 1 cM (centimorgan)
- Gene mapping methods use recombination
- frequencies between alleles in order to
determine the relative distances between them - Recombination frequencies between genes are
inversely proportional to their distance apart - Distance measurement 1 map unit 1 percent
recombination (true for short distances)
8Fig. 4.6
9Gene Mapping
- Genes with recombination frequencies less than 50
percent are on the same chromosome linked) - Linkage group all known genes on a chromosome
- Two genes that undergo independent assortment
have recombination frequency of 50 percent and
are located on nonhomologous chromosomes or far
apart on the same chromosome unlinked
10Mapping the distance between two genes
Starting with pure breeding lines, Cross Parent
1(AA BB) with Parent 2(aa bb) So Parental
chromosomes in the F1 have to be AB and ab
Now cross (AB ab) F1 progeny with (ab ab) tester
to look for recombination on these
chromosomes. Suppose you Get AB
ab 583 ltparental ab ab 597 ltparental Ab
ab 134 ltrecombinant aB ab 134 ltrecombinant
total 1448 so. 268 recombinants /1448
progeny 0.185 recombinants/progeny 18
.5 recombinants 18.5 mu
11Mapping (and ordering) three genes
Starting with pure breeding lines, Cross Parent
1(AA BB DD) with Parent 2(aa bb dd) So you know
the Parental chromosomes in the F1 have to be ABD
and abc
Cross (ABD abd) F1 progeny with (abd abd)
tester Suppose you Get ABD
abd 580 ltparental ABd abd 3 abD
abd 5 ltparental abd abd 592 AbD
abd 45 ltrecombinant Abd abd 89 aBD
abd 94 aBd abd 40 ltrecombinant
total 1448
Ab aB (4589)(9440) recom 268 recom/1448
total 0.185 A-B 18.5mu
Bd bD (340)(545) 93 recom/1448 total
0.064 B-D 6.4mu
Ad aD (389)(594) 191 recom/1448 total
0.132 A-D 13.2mu
so the order must be A-----D---B
-13.2--6.4- ----18.5----
12So How come 13.2 6.4 does not equal 18.5?
Cross (ABD abd) F1 progeny with (abd abd)
tester Suppose you Get ABD
abd 580 ltparental ABd abd 3 abD
abd 5 ltparental abd abd 592 AbD
abd 45 ltrecombinant Abd abd 89 aBD
abd 94 aBd abd 40 ltrecombinant
total 1448
Ab aB (4589)(9440) recom 268 recom/1448
total 0.185 A-B 18.5mu
A-----D---B -13.2--6.4- ----18.5----
13- Chromosome interference crossovers in one region
decrease the probability of a second crossover
close by - Coefficient of coincidence observed number of
double recombinants divided by the expected
number - \
- Interference 1-Coefficient of coincidence
If the two crossovers were independent, we would
expect that the probability of seeing two
recombination events occur would be 0.132
between A-D AND 0.064 between D-B 0.132 X 0.064
0.008 For every 1448 progeny, this would be
(1448x0.008)12.23 double recombinants We
actually observed only (53) 8 double
recombinants So the Coefficient of coincidence
observed / expected 8/12.23 0.65
Interference 1-Coefficient of coincidence
1- 0.65 0.35
14 Mapping Genes in Human Pedigrees
- Methods of recombinant DNA technology are used to
map human chromosomes and locate genes - Genes can then be cloned to determine structure
and function - Human pedigrees and DNA mapping are used to
identify dominant and recessive disease genes - Polymorphic DNA sequences are used in human
genetic mapping.
15Genetic Polymorphisms
- The presence in a population of two or more
relatively common forms of a gene or a chromosome
is called polymorphism - Changes in DNA fragment length produced by
presence or absence of the cleavage sites in DNA
molecules are known as restriction fragment
length polymorphism (RFLP) - A prevalent type of polymorphism is a single base
pair difference, simple-nucleotide polymorphism
(SNP) - A genetic polymorphism resulting from a tandemly
repeated short DNA sequence is called a simple
sequence repeat (SSR)
16RFLPs
- Restriction endonucleases are used to map genes
as they produce a unique set of fragments for a
gene - There are more than 200 restriction endonucleases
in use, and each recognizes a specific sequence
of DNA bases - EcoR1 cuts double-stranded DNA at the sequence
- 5-GAATTC-3 wherever it occurs
17Fig. 4.18
18RFLPs
- Differences in DNA sequence generate different
recognition sequences and DNA cleavage sites for
specific restriction enzymes - Two different genes will produce different
fragment patterns when cut with the same
restriction enzyme due to differences in DNA
sequence
Fig. 4.19
19SNPs
- Single-nucleotide polymorphisms (SNPs) are
abundant in the human genome - Rare mutants of virtually every nucleotide can
probably be found, but rare variants are not
generally useful for family studies of heritable
variation in susceptibility to disease - For this reason, in order for a difference in
nucleotide sequence to be considered as an SNP,
the less-frequent base must have a frequency of
greater than about 5 in the human population. - By this definition, the density of SNPs in the
human genome averages about one per 1300 bp
20SSRs
- A third type of DNA polymorphism results from
differences in the number of copies of a short
DNA sequence that may be repeated many times in
tandem at a particular site in a chromosome - When a DNA molecule is cleaved with a restriction
endonuclease that cleaves at sites flanking the
tandem repeat, the size of the DNA fragment
produced is determined by the number of repeats
present in the molecule - There is an average of one SSR per 2 kb of human
DNA
21Mapping Genes in Human Pedigrees
- One source of the utility of SNPs and SSRs in
human genetic mapping is their high density
across the genome - Additional source of utility of SSRs in genetic
mapping is the large number of alleles that can
be present in any human population.
22Mapping Genes in Human Pedigrees
- Human pedigrees can be analyzed for the
inheritance pattern of different alleles of a
gene based on differences in SSRs and SNPs - Restriction enzyme cleavage of polymorphic
alleles that are different in RFLP pattern
produces different size fragments by gel
electrophoresis
23A rare recessive disease that affects people late
in life is 90 linked to the RFLP marker on the
gel below.
Whats the probability that the grandchildren
(row III) are carriers?
90 10 9010 10 90 90
24A rare recessive disease that affects people late
in life is 90 linked to the RFLP marker on the
gel below.
Whats the probability that the grandchildren
(row III) are carriers?
10 90 10 90 90 10 10
25Tetrad Analysis
- In some species of fungi, each meiotic tetrad is
contained in a sac-like structure, called an
ascus -
- Each product of meiosis is an ascospore, and all
of the ascospores formed from one meiotic cell
remain together in the ascus - Several features of ascus-producing organisms are
especially useful for genetic analysis - They are haploid, so the genotype is expressed
directly in the phenotype - They produce very large numbers of progeny
- Their life cycles tend to be short
26Tetrad Analysis
- In tetrads when two pairs of alleles are
segregating, three patterns of segregation are
possible - parental ditype (PD) two parental genotypes
- nonparental ditype (NPD) only recombinant
combinations - tetratype (TT) all four genotypes observed
27Tetrad Analysis
- When genes are unlinked, the parental ditype
tetrads and the nonparental ditype tetrads are
expected in equal frequencies PD NPD - Linkage is indicated when nonparental ditype
tetrads appear with a much lower frequency than
parental ditype tetrads PD NPD - Map distance between two genes that are
sufficiently close that double and higher levels
of crossing-over can be neglected, equals - 1/2 x (Number TT / Total number of tetrads) x 100
28Neurospora Ordered Tetrads
- Ordered asci also can be classified as PD, NPD,
or TT with respect to two pairs of alleles, which
makes it possible to assess the degree of linkage
between the genes - The fact that the arrangement of meiotic products
is ordered also makes it possible to determine
the recombination frequency between any
particular gene and its centromere
29Tetrad Analysis Ordered Tetrads
- Homologous centromeres of parental chromosomes
separate at the first meiotic division - The centromeres of sister chromatids separate at
the second meiotic division - When there is no crossover between the gene and
centromere, the alleles segregate in meiosis I - A crossover between the gene and the centromere
delays segregation alleles until meiosis II
30- The map distance between the gene and its
centromere equals - 1/2 x (Number of asci with second division
segregation/ Total number of asci) x 100 - This formula is valid when the gene is close
enough to the centromere and there are no
multiple crossovers
31Gene Conversion
- Most asci from heterozygous Aa diploids
demonstrate normal Mendelian segregation and
contain ratios of - 2A 2a in four-spored asci, or 4A 4a in
eight-spored asci - Occasionally, aberrant ratios are also found,
such as - 3A 1a or 1A 3a and 5A 3a or 3A 5a. The
aberrant asci are said to result from gene
conversion because it appears as if one allele
has converted the other allele into a form like
itself - Gene conversion is frequently accompanied by
recombination between genetic markers on either
side of the conversion event, even when the
flanking markers are tightly linked - Gene conversion results from a normal DNA repair
process in the cell known as mismatch repair - Gene conversion suggests a molecular mechanism of
recombination
32- One of two ways to resolve the resulting
structure, known as a Holliday junction, leads to
recombination, the other does not - The breakage and rejoining is an enzymatic
function carried out by an enzyme called the
Holliday junction-resolving enzyme
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345 Human Chromosomes and Chromosome Behavior
35Karyotype stained and photographed preparation
of metaphase chromosomes arranged according to
their size and position of centromeres
36Human Chromosomes
- Each chromosome in karyotype is divided into two
regions (arms) separated by the centromere - p short arm (petit) q long arm
- p and q arms are divided into numbered bands and
interband regions based on pattern of staining - Within each arm the regions are numbered.
37Centromeres
- Chromosomes are classified according to the
relative position of their centromeres - In metacentric it is located in middle of
chromosome - In submetacentriccloser to one end of chromosome
- In acrocentricnear one end of chromosome
- Chromosomes with no centromere, or with two
centromeres, are genetically unstable
38Abnormal Chromosome Numbers
- Aneuploid unbalanced set of chromosomes
relative gene dosage is upset (example trisomy
of chromosome 21) - Monosomic loss of a single chromosome copy
- Polysomic extra copies of single chromosomes
- Most chromosome abnormalities lethal, frequently
in spontaneous abortions. - Exceptions are trisomy 13, trisomy 18, and
trisomy 21 (Down syndrome), and the Sex
chromosomes
39An extra X or Y chromosome usually has a
relatively mild effect. Why? 1) X chromosme
inactivation/Dosage Compensation 2) Not much
(essential) on the Y
- EXAMPLES
- Trisomy-X 47, XXX (female)
- Double-Y 47, XYY (male)
- Klinefelter Syndrome 47, XXY (male, sterile)
- Turner Syndrome 45, X (female, sterile)
40- Chromosome Abnormalities
- Deletions/Duplications
- Inversions
- Translocations
41 Deletions Duplications
42- Inversions genetic rearrangements in which the
order of genes in a chromosome segment is
reversed - Inversions do not alter the genetic content but
change the linear sequence of genetic information - In an inversion heterozygote, chromosomes twist
into a loop in the region in which the gene order
is inverted
Chromosome Inversions
43- Paracentric inversion
- Does not include centromere
- Crossing-over produces one acentric (no
centromere) and one dicentric (two centromeres)
chromosome
- Pericentric inversion
- Includes centromere
- Crossing-over results in duplications and
deletions of genetic information
44Reciprocal Translocations
- Adjacent-2 segregation homologous centromeres
stay together at anaphase I gametes have a
segment duplication and deletion - Alternate segregation half the gametes receive
both parts of the reciprocal translocation and
the other half receive both normal chromosomes
all gametes are euploid, i.e have normal genetic
content, but half are translocation carriers
45Polyploidy
- Polyploid species have multiple complete sets of
chromosomes - The basic chromosome set, from which all the
other genomes are - formed, is called the monoploid set
- The haploid chromosome set is the
- set of chromosomes present in a gamete,
irrespective of the chromosome number in the
species. - Polyploids can arise from genome duplications
occurring before or after fertilization - Through the formation of unreduced gametes that
have double the normal complement of chromosomes
or - Through abortive mitotic division, called
endoreduplication.
46Polyploids can generate new species
47A seedless watermelon is a sterile hybrid which
is created by crossing male pollen for a
watermelon, containing 22 chromosomes per cell,
with a female watermelon flower with 44
chromosomes per cell.
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49The karyotype of the Chinook salmon has been
characterized as 2N 68, with 16 pairs of
metacentric chromosomes and 18 pairs of
acrocentric chromosomes (Simon 1963)
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