Lecture 4: Linkage Mapping Jan 29, 2013: Tracking recombination: Parents are pure lines.

Parent 2 is making the wild type alleles. The F1 will be wild type. The alleles are vestigial and purple. The ratiosa are if the genes are independently assorted. + is wild type. The parental games are We did a test cross with the homozagous recessive parent. With the phenotypes of the progenoies we would know the genotype of the F1 generation. If this was independent the ratio would have been 1:1:1:1. Parental gamees are high in frequency. When A is linked to B: the parental gametes are higly frequenct and it is not 1:1:1:1. The combination of the gametes dont matter. What matters is the gametes present. The crossing over happens in the prophase. This produces different combinations of the alleles. Two Chromosome Stage: If the recombination happened in the interphase the crossing over would have had the top pic. but Now we know that it happens in 4chromatid stage (the bottom pic). During cross over two moleculs of DNA are chnges. It happens between chromatids, not chromosomes. Tetrad Analysis: There are 2 cross over. The cross over happends between the two non-sister chromatids. There are more than two chromatids that are involved in recombination. Using recombination to map mutations: This helps us understand how far the mutations happen from each other depending on the frequency. Only 305 had the different phenotypes that allowed us to calculate it. Map units are also called ceni Morgans. Three point test cross: The capital letters are the F1 gamete and the small letters are from the tester. We always start these with pure populations. The unit maps dont add up. The double recombination event is the reason why they dont add up. When we are mapping, we overestimate the numbers since we ignore double recombination (two recombinations-two steps). When we divide the number we assume that the bottom number is larger and so we get a lower number for the each unit map. We dont know the actual length of the double recombinant until we ma it We would only know about the recombinant games only if we know the gametes of the parents. Double recombinant gamete is the one that has parental on the outside and recombinant in the middle. We dont account for them and this is where error is.

Lecture 4: Linkage Mapping Jan 31, 2013 Last question: 2 chromatids were crossed over Correcrting: The markers tehat are closer t each other there is a smaller chance of recombination and we would have more accurate results. The estimates of the two points that are far from each other there is more error. Understtimating double recombination when the two points are far from each other. The formula in the book are correcting the errorsof double recombinations that occur in far distances. 0.84% chance of double cross over. We expected 12 but we only see 8. The recombination between two loci interferes to have recombination between the cross over between the loci and another loci nearby. This has interference. Significance of linkage: There is 1:1:1:1 ratio, since there is a 25% chance of getting each of genotype. There is 0.5 chance of getting each gamete. If these are predetermined there is a df=4-1=3. The ratio comes from a theory. There are two ways of calculating this. Equal segregation and independent assortment are calculated. 1. Chi square test right away from the independent assortment. 2. The second way is more accurate. We can see that the B and b are equally segregated but we can see a higher difference between the existence of A and a. The reason the second way is more accurate is that we also corrected for the viability and we considered viability. Here the expected are from our calculations and we calculated them ourselves. df= (total rows-1)-2. We should use this since this is more accurate. Constructing a Genetic Map: the values are in centi Morgan When making map start by looking at the one that are the closest (C-D). The next is step is the addition of the smallest piece after (B-D). In reality the numbers are enderestimated so in reality the B-C would have been 0.14. Three ways: PCR, Satellite, Sequecing Microsatellite: tandem repeats. There is a high chance of mutation by RNA polymerase by adding or skipping some of these, since they are the same (repeats of the same thing). Florescence at the gels will give more accurate results. The graphs show heterozygous alleles for the gene. Sequencing: there is a fluorescence tag in the end. ddNTP are the terminating sequences.

Lecture 4: Linkage Mapping

Feb 7, 2013 The project: If all were german or all Italian it was parental. If they were mix of both, they are recombinant. 11cM means 11% of recombination between either two poinrs. When the Italian and and the mom are mating they are getting recombinnats. Example: mom is CC and the dad is T. In the F1 we will have CT and we will back cross with either male. CT X C will give CT/CC and CTXT will give TT/CT. we know whih allele came from the mom and which came from the dad. Another example is the combinations. RAtio 0 50 50 0 SNP1 T T C C SNP2 A G A G

Genetic mapping tells you how big the chromosomes are and where they are located. If we know which chromosmes the gene is located on, we can know whre it is located (the fraction ratios). We can then sequence it. Genetic and physical: Genetis tells us the mutation happens and where the mutations are located comared to each oher. We can then compare the recombination between the different organisms. Te recombination rate is higher in bees. If we compare the 1Mb the ceni morgan is higher in honey bees. 30 percent chance of recombination happeneinng in the bees that are 1mb away but there is 1.3 percent chance than humans. Yeast has the highest recombination rate.