Slide #1.

Summer 2013
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Slide #2.

Genetics and Markers  Measure aspects of an organisms structure and function How do genes and environment influence individual differences and fitness? What aspects should we measure? Morphological (measurements of the body of the organism) Behavioral Molecular
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Slide #3.

Genetic markers Phenotype is the result of genotype How much of a trait depends only on the genes? How much do differences in genes drive differences in appearance? How different are organisms in the same species from each other? How different are organisms in difference genus’ from each other?
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Slide #4.

Relatedness Whales to Hippos Even-toed, hoofed mammals are called artiodactyls. This is further broken down to Camels + llamas Cattle + deer Pigs + peccaries Hippopotamuses Cetaceans don’t have toes – ancestors had an even number of appendages.
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Slide #5.

What is a molecular marker? A piece of DNA on a chromosome May be part of or closely linked to a gene that makes a protein that affects cell survival May be part of controlling elements May be in the larger area of ‘non-coding’ DNA Markers have a known location What is being marked?
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Slide #6.

Human genome 23 pairs of chromosomes 3 X 109 base pairs of DNA Different families of repeated sequences Sex chromosomes (X and Y)
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Slide #7.

Chromosome banding occurs at reproducible positions, so the bands are another level of marker. Studies reveal that gene-rich and gene-poor regions correspond to banding patterns within the genome.
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Slide #8.

DNA can have very simple sequences, like CACACACACA, or sequences that are unique across a long distance. The simple ones are present at much higher concentration than the unique ones, so the recombine (‘reanneal’) quickly after separation.
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Slide #9.

Composition of the human genome Simple sequence repeats can expand quickly if in noncoding regions, and are a rich source of variation for individual
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Slide #10.

SSRs are common in the human genome Estimated 96,000 4 bp repeats in the human genome
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Slide #11.

Interspersed repeats in the human genome
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Slide #12.

SSRs and Length Polymorphisms Simple sequence repeats The number of units have a certain number of can vary if the units of the repeat: polymerase stutters (CA)13 has 13 of the CA (loses its place). units in a row. Two individuals differ by the number of repeats: CA 3 repeats vs 5 repeats  produces length differences.
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Slide #13.

Turning SSRs into markers You can use a restriction enzyme that recognizes a sequence just outside the boundaries. But it takes a lot of DNA and you will have a lot of other fragments cluttering up the gel CCATGG GGTACC AATT TTAA Fragment 1 Fragment 2 CCATGG GGTACC AATT TTAA
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Slide #14.

Turning SSRs into markers You can use PCR with primer sequences that lie just outside the boundaries. Primer 1 Primer 2 Primers match conserved sequence, lie just outside the repeated region and amplify across is, so most of the PCR product is the repeated region Fragment 1 Fragment 2
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Slide #15.

AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
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Slide #16.

Fragment Size Estimation 10,000 bp 7,000 bp 3,000 bp 600 bp
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