Gene Linkage and Genetic Mapping

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4 Gene Linkage and Genetic Mapping
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If two genes are on different chromosomes
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If 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
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Now 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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Gene 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)

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Fig. 4.6
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Gene 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

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Mapping 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

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Mapping (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----
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So 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----
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• 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
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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.

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Genetic 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)

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RFLPs

• 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

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Fig. 4.18
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RFLPs

• 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
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SNPs

• 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

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SSRs

• 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

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Mapping 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.

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Mapping 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

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A 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
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A 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
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Tetrad 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

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Tetrad 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

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Tetrad 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

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Neurospora 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

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Tetrad 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

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• 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

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Gene 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

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• 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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5 Human Chromosomes and Chromosome Behavior
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Karyotype stained and photographed preparation
of metaphase chromosomes arranged according to
their size and position of centromeres
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Human 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.

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Centromeres

• 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

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Abnormal 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

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An 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)

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• Chromosome Abnormalities
• Deletions/Duplications
• Inversions
• Translocations

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Deletions Duplications
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• 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
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• 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

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Reciprocal 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

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Polyploidy

• 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.

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Polyploids can generate new species
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A 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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The 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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