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Flashcards in Y chromosome Deck (27)

How many base pairs does the haploid autosomal nuclear DNA have?

3,2 billion bp (giga bp)


How many bases does the mtDNA have?

16 569 base pairs


What determines sex?

  • 7-8 weeks embryo - development of reproductive duct system
  • SRY gene (testis determination factor) - undifferentiated gonad --> testis
  • testis development - secretion of testosterone - external male genitalia
  • Müllerian inhibiting hormone (MIH) = a hormone produced by testis --> breakdown of Müllerian (female) ducts in embryo


why does the Y chromosome look the way it does?

It occured in four evolutionary steps, each involving a failure or recombination:

  1. from nascent to as in monotremes: recombination failure leading to deneration and shrinkage of the affected Y chromosome part; the affected area is no longer able to recombine with the X chromosome
  2. from as in monotremes to as in marsupials: recombination failure triggering more decay of Y chromosome
  3. from marsupials to as in monkeys: recombination failure, further shortening
  4. from as in monkeys to as in humans: further shrinkage
  5. SRY moved to short arm at unkown time point


Name some characteristics of the Y chromosome

  • haploid
  • is acrocentric (one short and one longer arm)
  • contains many repetitive DNA seqences
  • 60MB long
  • unique for men
  • paternally unchanged inherited
  • mutations may cause changes
  • 95% do not undergo recombination
  • pseudoautosomal PAR region
    • PAR1 and 2 undergo recombination during meiosis


How many genes does the Y chromosome contain?

78 genes, whereof:

  • SRY gene
  • 8 other genes specific for Y chromosome
  • 27 Y-specific protein coding genes
  • 16 housekeeping genes
  • MSY - male specific regions on the Y chromosome


Why is there such a low number of genes on the Y chromosome?

Because there is no recombination


Why can mutations easily be passed on to the next generation?

Because there is no correction of genes since there is no chromosome cross-linking


How does the Y chromosome get rid of mutations?

  • 8 genetic palindromes
  • forward or reversed order
  • 1/4 euchromatic DNA in the male genes
  • a sort of back up



  • most found on the q arm
  • approximately 300 Y-STRs
  • 200 billalic Y SNPs
  • 1 minisatellite MSY1


what is the Y chromosome used for?

  • tracing male migration patterns
  • evolutionary studies
  • population structure
  • human identification
  • forensic applications


How many markers should be used according to SWGDAM?


(9 minimal plus two more)


Name some Y-STRs

  • DYS19
  • DYS389I
  • DYS389II
  • DYS390
  • DYS391
  • DYS392
  • DYS393
  • DYS438
  • DYS439
  • DYS385a/b


What are the advantages of using a multiplex of several markers?

  • several markers are amplified simutaneously --> one standard
  • cross border comarison possible
  • smaller amounts of DNA are used --> saving of sample material


Name two commercial kits

PowerPlex Y and AmpflSTR Yfiler


How is the Y chromosome used in forensic analysis?

  • male DNA can be detected in samples containing both male and female DNA
  • DNA from several men
  • Sex determination (amelogenin)


How is the Y chromosome used in paternal kinship?

  • paternity testing
  • kinship testing
  • missing person cases


Which male:female DNA ratio can still be handled by kits in terms of efficiency and sensitivity?



What is the average mutation rate for Y-STRs?

1 in 10^3


What is the mutation rate of Y-SNPs?

1 in 10^9


Why are Y-SNPs suitable for haplogroup classification?

Because the very seldom mutate at the same position

Because they have a slower mutation rate



How are Y haplogroups determined?

  1. Y-SNPs - are more accurate than STRs
  2. Y-STRs - a statistical estimation is done


What is a haplotype?

A haplotype is a set of genetic markers, inherited simultaneously


What are haplogroups?

Haplogroups are groups of haplotypes with certain specific common mutations


The amelogenin gene

  • deletion of six base pairs in X chromosome
  • different number of base pairs
  • reveals the sex of the specimen


Why do we use the Y chromosome in forensic genetics?

  • most violent crimes are commited by males
  • mixtures of male DNA with high levels of female DNA - differential extraction not necessary
  • lower discrimination capacity. Diversity only derived from mutations due to lack of recombination
  • paternal lineages


How can you distinguish between male relatives?

There are rapid mutating Y-STRs (RM Y-STRs) that increase the power of discrimination to 60%