Genetics PCB 3063

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Genetics - PCB 3063

• The Test will be next Tues, 10 Feb 2004
• Turn in your homework
• Todays focus
• Linkage and Mapping
• We will continue to focus on a single major
  question
• How are genetic maps generated?

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The Map Unit The Centimorgan

• A. H. Sturtevant named the map unit the
  centimorgan. to honor his mentor, T. H. Morgan.
• 1 centimorgan is defined as 1 recombinant
  progeny in a testcross.
• Thus, one can calculate the map distance as
• Three-point crosses represent the preferred
  method of mapping genes.
• This involved the use of three linked genes (we
  can call them A, B, and C).
• These genes have to have alleles that can be
  distinguished (e.g., A and a).

R (recombinants/total) x 100 distance in cM
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The Map Unit The Centimorgan

• A. H. Sturtevant named the map unit the
  centimorgan. to honor his mentor, T. H. Morgan.
• 1 centimorgan is defined as 1 recombinant
  progeny in a testcross.
• Thus, one can calculate the map distance as
• Three-point crosses represent the preferred
  method of mapping genes.
• This can establish the frequencies of single
  crossover events between two of the three genes
  and double crossover events reflecting
  recombination between each of the three genes.
• However, the frequency of two close crossovers is
  often less than expected based upon numbers of
  recombinants observed between two loci (H. J.
  Mullers results).
• Muller called this phenomenon INTERFERENCE.

R (recombinants/total) x 100 distance in cM
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Genetic Maps are Assembled Like Puzzles

• Data from multiple test crosses can be used to
  arrange sets of genes into linkage groups.
• If the data are extensive enough, the linkage
  groups should correspond to chromosomes.
• Since three point crosses provide the order of
  three genes relative to each other, they provide
  more useful information.
• Imagine we have five genes (a, b, c, d, and e).
• We do several three point cross and find
• Taken together, these data support a map like
  this

31.4
1.9
4.2
10.4
C
B
A
D
E
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How Do We Use Three-Point Mapping?

• Imagine three genes (A, B, and C) that we can
  score in a testcross

• Note Since all crosses are testcrosses only a
  single parent is shown.
• Obviously, the class of progeny arising from
  double crossovers will be rare, and there will a
  weaker bias against the single crossover progeny.

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How Do We Use Three-Point Mapping?

• Now examine the data

• For recombinants between A and B, we find
  (31129824)615 of 8535 total.
• So A and B are (615 / 8535)x1007.2 cM apart.
• For recombinants between B and C, we find
  (51159024)1170 of 8535 total.
• So B and C are (1170 / 8535)x10013.0 cM apart.

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Distances between Distant Loci are Difficult to
Estimate

• In the three-point testcross I described, it is
  important to note that we would have seen and
  apparent map distance between A and C of
• This is fairly close to the sum of the A to B and
  the B to C distances
• but it is a little lower. Why is this?
• We would only have counted the double crossovers
  once if we had only considered A and C,
  independently of B. We know from the three-point
  cross that they should count twice. - Can you
  see another problem with this?
• In general, map distances between more loosely
  linked genes will be underestimates of the actual
  distance, if one only considers genes two at a
  time.
• This can be corrected using a MAPPING FUNCTION,
  which corrects for multiple crossover events (but
  these estimates will be imperfect).

(31151129859024)1716/8535 (x100)20.1 cM
7.2 cM (A-B) 13.0 cM (B-C) 20.2 cM
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Tetrad Analysis can beused for Mapping

• Some organisms, such as ascomycete fungi, allow
  recovery of all four progeny from a meiotic
  division.
• Imagine a diploid yeast heterozygous at two loci
  (called a and b)
• The distance in cM between a and b can be
  estimated using

Parental Ditype (PD)
Tetratype (TT)
Nonparental Ditype (NPD)
R ( NPD 1/2 TT / total ) x 100 cM
Note Equation in book presents the parentheses
incorrectly
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Ordered Tetrads in Neurospora Allow Mapping
Relative to the Centromere

• The meiotic progeny of N. crassa form in a sac,
  like the other ascomycetes, but they are present
  in a linear order that reflects meiotic division.
• N. crassa spores are formed by a single mitotic
  division after the completion of meiosis.

• Remember that the duplicated chromosomes that are
  held together by the centromere segregate during
  the first meiotic division.
• Thus, a locus that is close to the centromere
  would often segregate during the first meiotic
  division.
• Recombination between the gene of interest and
  the centromere would produce second division
  segregation tetrads.

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Mapping Neurospora Genes Relative to the
Centromere

• Tetrads produced by second division segregation
  are related to the distance from the centromere
  by this equation

R (1/2 second-divison / total ) x 100 cM
Both patterns reflect second division segregation
of the A and a alleles. What would first
division segregation look like?

• How would double crossovers alter this estimate?

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Additional Methods for Genetic Mapping

• Mitotic (rather than meiotic) crossover does
  occur and can be used to map genes.
• This can be done by examining patches of cells
  derived from a clone that has undergone mitotic
  crossover.
• Mitotic crossover much less common than meiotic
  crossover, and the distances estimated can be
  very different.

Mitotic map
Meiotic map
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Additional Methods for Genetic Mapping

• Deficiency mapping, based upon complementation of
  large deletions involving multiple genes, can be
  used to map genes.
• In Drosophila, chromosomes in the salivary gland
  replicate multiple times without cell division,
  forming large structures called polytene
  chromosomes.
• These chromosomes are visible with a light
  microscope, so it is possible to note the regions
  that have been deleted.
• If a recessive mutant is crossed to a deficiency
  line that has a deletion in the region containing
  the gene, the recessive mutation will not be
  complemented.

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Somatic Cell Hybrids

• Somatic cell hybrids contain some but not all
  human chromosomes.
• These cell lines are generated by fusing human
  cells with rodent cells using agents such as
  polyethylene glycol or Sendai virus.
• After fusion, a subset of the human chromosomes
  will be lost.
• If one has the ability to detect the presence of
  specific human gene products (e.g., antibodies,
  enzyme assays, PCR of sequences) one can ask
  which chromosome the gene is on.

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Physical Mapping and Sequencing

• Physical maps can be produced by cloning segments
  of an organisms genome into bacteria.
• It is possible to find how these segments
  overlap, potentially covering the whole genome.
• If we have a DNA segment corresponding to a gene
  of interest, it is possible to find the segment
  of the genome that corresponds to the gene of
  interest.
• Finally, the highest resolution map is a complete
  genome sequence
• However, the sequence still has to be anchored to
  the genetic map by finding markers that have been
  mapped genetically.