BIOB 375 1st Edition Lecture 29Outline of Last Lecture II. Practice of Genetic AnalysisOutline of Current Lecture III. Genomicsa. Genetic mapping and physical mappingb. CloningCurrent LectureGenomics- Genomics is the study of an organism’s entire genome, including the entire DNA sequence, fine-scale genetic mapping and gene cloningDNA template = mixes with a primer + DNA polymerase + regular dNTPs + one of the ddNTPsHow do we sequence a genome?- Approaches: o “Clone-by-clone” approacho “Whole-genome shotgun”“Clone-by-clone”“Whole-genome shotgun”Genetic maps and physical maps of an organism- Genetic maps (also called linkage maps) – show the locations of the genes in each chromosome and their genetic distances calculated based on recombination frequency- Physical maps – show the locations of the genes in each chromosome and their physical distance in base-pair based on DNA analysis (or sequencing)Fine-scale mapping:- Genetic mappingo Measured by recombination ratioo Map unit is cM- Physical mappingo Measured by physical distanceo Map unit is base pair or bpGenetic distance ≠ Physical distanceWhen the mapping population is not big enough, the orientation of the genes could be wrongWhy do we need fine-scale mapping? Identifying “the” geneGene cloning:- Map-based cloning- Homology-based cloningMap-based cloningStep 1: locate “the” gene to a chromosomeStep 2: locate “the” locus that did not recombine with the phenotype of the geneStep 3: Complementary study to confirm the geneWhat are required for mapping a gene?- The gene has different alleles that confer distinct phenotypes- A segregating population that the offspring have distinct phenotypesFor example, to clone a gene controlling flower color in petunia Petunia, 2n=2X=14How many linkage groups does Petunia have? – 7To find the gene that controls the flower color:1. Select at least one locus form each linkage group2. Test them on the parents3. If the two parents have different alleles, then test them on the offspring Genotype Phenotype #Observed RecombinantsAA Blue 20Aa Blue 18Aa White 27 Raa Blue 17 Raa White 6Total 88RI = (27+17)/88 = 50%RI= recombination frequency of B-flower color locus Gene control flower color is located on chromosome
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