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2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
2008 PGSAS G-nomes
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2008 PGSAS G-nomes

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  • Transcript

    • 1. The Human Genome Project
      • June 26, 2000: Successful completion of the first ‘draft’ of the entire human genome!!!
      • The race between Celera and NIH is finished. The private company appears to have won.
    • 2. The Chicken Genome Project
      • An initiative begun by NIH in 2002
      • Completed in 2004
      • Other species considered:
        • Cats, cows, sheep, horses, dogs
          • Cow begun in 2004
          • Pig begun in 2005
          • Who's next?
        • Look here: Ensembl
      • But, What the heck is a ‘genome’? What did they/we win?
    • 3. The Genome (?)
      • G-nomes; Grumpy and Sleepy?
        • With apologies to Dr. Dean Snow
      • Not really.
      • A genome is a complete sequence of all the known genes of an organism; including their structure and function
    • 4. Maps and markers
      • What’s a genetic map?
      • With apologies to Dr. David Bottstein.
    • 5. One kind of map of Penn State
    • 6. Here’s a better view
    • 7. Now I know this will be helpful
    • 8. Perhaps we need a different kind of map?
    • 9. How about this?
    • 10. Or, this?
    • 11. Or, even this?
    • 12. The Genome (among friends)
      • Chromosomes
        • Each chromosome is one molecule of DNA.
        • 10 7 to 10 8 base pairs
        • A structural gene, coding for a polypeptide/protein, is between 10 3 to 10 4 bp.
        • Approximately 10% of the genome is coding.
      • DO THE MATH!!
        • A chromosome contains 1,000 to 10,000 genes.
        • Vertebrate genomes contain approximately 50,000 to 100,000 genes.
      • These are generalizations and are highly species specific.
      • Indeed, calculations from the human genome project suggest that there are approx. 35,000 genes
    • 13. Genes and Markers and Maps
      • Gene Mapping
        • The location of genes to specific positions (e.g., loci) on specific chromosomes.
    • 14. Structural Genes
      • Consider Hemoglobin!
      • Normal adult hemoglobin consists of 2 molecules each of 2 different polypeptides.
        • α (141 aa) and β (146 aa)
        • On chromosomes 16 and 11
      • Given 3 bp per aa
        • the β chain has 4 438 possible single bp variants
        • This number exceeds the total number of fundamental particles in the universe.
    • 15. Hemoglobin- β mutations
      • Non-sense
      • Nil-STOP
      • UAG
      • ATC
      • Mutant
      • Mis-sense
      • Valine
      • GUG
      • CAC
      • Mutant
      • Same-sense
      • Glutamate
      • GAA
      • CTT
      • Mutant
      • Wild-type
      • Glutamate
      • GAG
      • CTC
      • Normal
      • Type
      • Amino Acid
      • mRNA codon
      • DNA codon
      • Allele
    • 16. Mapping
      • Prior to the 1980’s all mapping was accomplished using major genes of obvious phenotypic effect.
      • The advent of RFLP’s, AFLP’s, microsatellites and other molecular markers, we can identify large numbers of segregating loci, simultaneously in the same cross.
      • Remember that these markers are not true genes and are really ‘framework maps’, since they provide the ‘road map’ to locate genes of interest.
        • Useful for locating and studying QTL / MAS.
        • Invaluable to investigating genomic organization across related species/genera.
    • 17.  
    • 18.  
    • 19.  
    • 20.  
    • 21.  
    • 22.  
    • 23.  
    • 24. Gene Order and Arrangements
      • Now that we’ve talked about structure and function …
      • How do we figure out their placement on the map?
      • We take advantage of a violation of the law.
      • Specifically, Mendel’s law of independent assortment .
    • 25. Consequences of crossing over (1) Chiasma A B A B A B a b a b a b
    • 26. Linkage between a mutant gene and a marker Meiosis Mutant gene DNA marker Wild-type gene Variant DNA marker
    • 27. Consequences of crossing over (2a)
    • 28. Consequences of crossing over (2b)
    • 29. Chiasma frequency and distance between loci
    • 30. Using the test-cross
      • 135
      • Total
      • 3
      • aB
      • aaBb
      • aB
      • 4
      • Ab
      • Aabb
      • Ab
      • Recombinants
      • 60
      • ab
      • Aabb
      • ab
      • 68
      • AB
      • AaBb
      • AB
      • Parentals
      • Number
      • Progeny Phenotype
      • Progeny Genotype
    • 31. Calculating Recombination Frequency
        • Number of ‘A’ individuals:
          • 68 + 4 = 72
        • Number of ‘a’ individuals:
          • 60 + 3 = 63
              • χ 2 =0.6; ns
        • Number of ‘B’ individuals:
          • 68 + 3 = 71
        • Number of ‘b’ individuals:
          • 60 + 4 = 64
              • χ 2=0.37; ns.
      • RF = (4+3)/135 = 0.0518 or 5.18%
    • 32. What if you had 3 genes of interest?
      • Start with an F 1 produced by 2 pureline parents (AABBCC x aabbcc).
      • Backcross the F 1 to the triple-recessive parent.
      • Check that all alleles are segregating in a 1:1 ratio in the backcross
        • Altered segregation will give a poor estimate of RF%.
          • differential survival
          • misclassification
    • 33. Here’s how to determine gene order
      • 400
      • TOTAL
      • 32
      • aBc
      • 24
      • AbC
      • 4
      • 7
      • aBC
      • 14
      • Abc
      • 3
      • 49
      • abC
      • 51
      • ABc
      • 2
      • 120
      • abc
      • 103
      • ABC
      • 1
      • F 1 gametes
      • Number of progeny
      • Progeny phenotypes
      • Class
    • 34. Calculate RF% as before
      • ALL χ 2 are non-significant.
      • A – B = (14+7+24+32)/400 = 0.1925 or 19.25%
      • A – C = (51+49+14+7)/400 = 0.3025 or 30.25%
      • B – C = (51+49+24+32)/400 = 0.3900 or 39.00%
    • 35. And the answer is: B A C Since B-C is the largest RF, genes B and C must be the furthest apart; while A is in between. 39.00% 19.25% 30.25%
    • 36. Genes and Markers and Maps
      • Gene Mapping
        • The location of genes to specific positions (e.g., loci) on specific chromosomes.
      • Linkage
        • Genes that are located on the same chromosome are ‘linked’.
    • 37. The Human Map 1 263 Mb 17 92 Mb 21 50 Mb X 164 Mb

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