2008 PGSAS G-nomes


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  • 2008 PGSAS G-nomes

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