BIOB 375 1st EditionExam # 3 Study Guide Lectures: 23-30Lecture 23 (March 23)Genetic Analysis – one gene locus (for organisms that are sexually reproduced)What do we analyzie?1. How many locus is different between the two different individuals with different phenotypes?2. Which phenotype is dominant?3. What is the relationship of one gene locus to a known gene locus (belongs to the same linkage group or not)? One gene locus  one characteristic and multiple characteristis- Phiotropic effects on genesOne gene locus can have more than two alleles in the species, but each diploid individual has only two alleles at one locus What do we want to know form genetic analysis?How many locus is responsible for the phenotype?How many alleles at the locus among the individuals?Which phenotypes or allele is dominant, what type of dominance? ( complete, incomplete, or co-dominance)?Genotype predict PhenotypePhenotype deduce GenotypeChlorophyll biosynthesis pathway- 7 enzymes required- 7 genes requiredHow to determine which phenotypes is dominant when two phenotypes are observed?- Make a cross between the two individuals of different phenotypes- If a uniform phenotype observed in F1 generationIf we designate a letter G for the locus that is different between the two P1 and P2 plants, based on the experiment green is dominant, so G represents green and g represents albino When self pollinating, if next generation is heterozygous, the phenotype of that plant is dominant. One gene locus  one characteristicA segregating population, in which the individuals were sexually reproduced and have different phenotypes on the characteristic studied, is required for genetic analysisREMEMBER:There are only 4 possible ratios for one gene locusTwo pheotypes when AA and Aa are the same phenotypeAa x Aa 3:1 ratioAa x aa 1:1 ratioUse chi-square test too test if the data fits 3:1 ratioLecture 24 (March 25)Genetic analysis – one gene locus (for organisms that are sexually reproduced) One gene locus One characteristic  Multiple characteristics (pleiotropic effects of a geneOne allele can associate with multiple phenotypes- Pleiotropic effects of a geneOne gene:- Yellow color -- The suppressor is yellow color- Suppresses Raly expression in the early embryo  Embryo abortionOther gene:- Light non-yellow color – The activator is light non-yellow color- Activated Raly overexpression in the early embryoWhen the cell has both activator and suppressor, activator winsThe Lr34 locus in wheat- Has pleiotropic effects- Conferring resistance to rust diseases ( lr34lr34)- Leaf tip necrosis (Lr34Lr34)How do we know that a gene has pleiotropic effects?If in a segregating population for Lr34, 1200 plants were tested to see the response to a fungal pathogenYou should see at least 4 different phenotypesIf you observed two different phenotypes that are always together, its called co-segregating, then it’s possible that the two phenotypes are controlled by the same geneGenetic analysis – two gene loci (for organisms that are sexually reproduced)Two gene loci One characteristic Two characteristicsLecture 25 (March 27)Genetic Analysis-two gene lociTwo gene loci: one characteristic  two characteristics How do we know when the same phenotype is controlled by two different loci?When a population resulted from self-pollination, if the phenotype is uniform (termed no segregation) suggesting the locus controlling the phenotype is homozygous (can be dominant homozygous or recessive homozygous)When a population resulted from a cross between two individuals with different phenotypes, if the phenotype of the population is uniform (termed no segregation) suggesting the locus or loci controlling the phenotype in both parents is homozygous, one is dominant homozygous the other is recessive homozygous If we designate the A locus is segregating in P1 and the B locus is segregating in P2Ratio = 3:1Lecture 26 (March 30)Epistasis- The effect of gene interaction that one gene masks the effect of another gene at a different locusWhat is different from dominance?At least on locus is homozygous recessive in the offspring, ratio = 9:7Recessive epistasis- Bombay phenotype- Genotypes at both the H locus in the example and the ABO locus determine the ABO blood typeDominant epistasis- The color of summer squash is controlled by two loci: the W locus and the Y locus- White:Yellow:Green= (9+3):3:1 = 12:3:1Duplicate dominant epistasis- Resistant: susceptible ~ 15:1Two loci determine a single characteristic, interaction between genes produces new phenotypes9 red: 3 peach: 3 orange: 1 creamImportant to REMEMBER!!! Lecture 27 (April 1)Linkage and gene mapping- Linkage group is used to describe the genes that locate on the same chromosome- Since homologous chromosomes have the same gene in the same order, they belong to the same linkage group- How many linkage groups for a man? For a women?o Man = 24, Women = 23- How many linkage groups for a species of AABB, 2n=4X=28?o 14 linkage groups- AAAA, 2n=4X=28?o 7 linkage groups Gene Mapping1. Linkage group2. Genetic distance between genes3. Orientation of genesHow do we know if two genes are linked or unlinked?Ab:aB:ab:AB= 1:1:1:1Rf= (Recombined/Total) = 0.5If A and B are on the same chromosome, they can arrange in two configurations F1 (AaBb)- Based on the genotype of F1, do we know if this is coupling or repulsion?o No- Based on the genotype of F1, do we know gene A and gene B are linked?o No- SO we need to know the genotypes of the parents- Nonrecombinant gametes (parental gametes)o Ab and ab- Recombinant gameteso AB and ab- Total of the parental genotype gametes are more than the non-parental onesGenetic Distance- Genetic distance is measured by recombination frequency- Rf= (10/100) = 0.1 = 10%- 10% recombination frequency = map distance of 10 map units (cM)A Three-Point Test Cross- ExamplesLecture 28 (April 6)Practice on Genetic AnalysisAaBb X AaBb = AaBbA_B_ 9/16aaB_ 3/16A_bb 3/16aabb 1/16Total 16/16Two gene loci are segregating- Means two gene loci are heterozygous – AaBbWhen two gene loci are involved- No segregationo AABB, AAbb, aaBB, aabb- One loci is segregatingo AaBB, Aabb, aaBb, aaBb- Two loci are segregating o AaBbLecture 29 (April 8)Genomics- 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