Linkage mapping CSS431 Plant Genetics Recitation

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Linkage mapping CSS431Plant Genetics
Recitation 42008Peter Szucs
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Mendelian Inheritance
waxy/non-waxy
hulled
2/6-row
naked
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Validation of Mendel's Laws

• Segregation two alleles for each characteristic
  segregate during gamete production
• Independent assortment one gene's inheritance is
  not affected by that of another
• An exception to independent assortment develops
  when genes appear near one another on the same
  chromosome

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Genetic Linkage

• Genetic linkage occurs when particular alleles
  are inherited jointly
• Because of crossing over, alleles on the same
  chromosome can be separated into different
  gametes
• When alleles are far apart on the chromosome it
  is more likely that a crossover will occur
  between them

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Map Distance

• The genetic map distance between two genes,
  usually measured in centi-Morgans (cM), is based
  on the number of crossovers that occur between
  paired homologous chromosomes
• We observe the frequency of recombinants
  (non-parental), not the frequency of crossing
  over
• An odd number of crossovers between two loci
  produces recombinant haplotypes, whereas an even
  number of crossovers between two loci produces
  non-recombinant haplotypes

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Mapping Functions

• Recombination frequency (r) and map distance (d)
  are equal in the absence of multiple crossovers
• Mapping functions are used to transform
  recombination frequencies into map distances to
  better estimate map distance by counting single
  crossover events once and double crossover events
  twice
• Some mapping functions Haldane (1919), Morgan
  (1928), Kosambi (1944), Felsenstein (1979),
  binomial (Karlin, 1984)

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Mapping Functions
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Exercise

• Using the given data calculate the
• recombination frequency r no. of non-parental
  plant / no. total offspring
• and Haldane map distance d -0.5ln(1-2r)
• for the
• waxy and nud markers
• waxy and vrs1 markers
• waxy and bPb-5494 markers
• bPb-5494 and nud markers

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Discussion

• Which markers are linked?
• Is the linkage strong?
• What is the chance for multiple crossovers
  between the linked marker pairs?
• What is the likely order of the linked markers?
• Please calculate a map using 275 markers

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Haldane Distance
r0.36 0.32 0.34
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Kosambi Distance
r0.36 0.32 0.34
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• Oregon Wolfe Barley Map
• 187 classical loci

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• Oregon Wolfe Barley Map
• 187 classical 555 pilot-OPA1 467 pilot-OPA2
  722 DArT 1931 loci