Homework(3((((1. (5 points) In tomatoes, red fruit (A-) is dominant to yellow (aa), and a tall stem (B-) is dominant to dwarf stems (bb). A series of matings between dihybrid tomato plants yields the following offspring: 557 tall, red-fruited plants 187 tall, yellow-fruited plants 192 dwarf, red-fruited plants 64 dwarf, yellow-fruited plants. Are the fruit-color and stem length genes independently assorting? Perform a chi-square test to support your argument, and clearly state the degrees of freedom and interpretation of the p-value you obtain. Use the chi-square table below to obtain your p-value. (((((((((((((((( (2.(((12(points)(Three(of(the(many(recessive(mutations(in(Drosophila*melanogaster(that(affect(body(color,(wing(shape(or(bristle(morphology(are(black((b)(body(versus(the(dominant(WT(gray(body;(dumpy(wings((dp)(versus(dominant(long(wings(in(the(WT;(and(hooked(bristles((hk)(versus(dominant(straight((not(hooked)(bristles(in(the(WT.((From(a(cross(of(a(dumpy(female(with(a(black,(hooked(male,(all(the(F1(progeny(were(WT(for(all(three(characteristics.((One(F1(female(was(testcrossed(with(a(dumpy,(black,(hooked(male(to(give(the(progeny(in(the(following(table.((NOTE(that(only( the(mutant(phenotypes(are(listed.((If(no(mutant(phenotype(is(given,(the(phenotype(was(WT(for(that(trait.((For(example,(the(set(described(as(‘black’(have(black(bodies((a(mutant(phenotype)(and(are(WT(for(the(wing(and(bristle(traits.((WT 169 black 19 black, hooked 301 dumpy, hooked 21 hooked 8 hooked, dumpy, black 172 dumpy, black 6 dumpy 304 TOTAL PROGENY 1000 (a.(((2(points)(write(the(phenotype(pairs((in(the(table(below(( Number Phenotype Pair 1 Pair 2 Pair 3 Pair 4 (b.((2(points)(What(are(the(parental(classes?((order(is(not(important)(((((c.((2(points)(What(are(the(double(cross(over(classes?((order(is(not(important)(((((d.((2(points)(What(is(the(gene(order?((((e.((2(points)(Calculate(the(distance(between(the(leftMmost(gene(and(the(middle(gene.((Show(your(work.(((((f.((2(points)(Calculate(the(distance(between(the(middle(gene(and(the(rightMmost(gene.((Show(your(work.(((((3.((6(points)(In(the(diagram(shown(below,(LOD(tests(were(performed(for(a(marker((called(#1)(that(is(suspected(to(be(linked(to(a(human(genetic(disease.((Plotting(the(data(in(this(way(can(help(us(to(define(a(potential(range(of(map(distances(where(a(marker(may(reside(relative(to(our(gene(of(interest.(((a.((3(points)(How(far(is(Marker(#2(from(our(gene(of(interest((remember(this(will(be(a(range(of(distances)((((((((b.(((3(points)(Does(Marker(3(appear(to(be(linked(to(our(gene(of(interest?(Defend(your(answer(in(two(sentences(or(less.(((( (4.#(14#points)#As#we#have#discussed#in##class,#the#location#of#a#disease#locus#can#be#established#using#molecular#markers#to#map#its#the#location.##We#worked#through#the#process#of#establishing#a#genetic#map#using#molecular#markers.##For#this#assignment,#we#will#use#DNA#markers#to#determine#the#portion#of#an#affected#parent’s#chromosome#that#is#inherited#in#affected#children#and#the#portion#that#is#inherited#in#unaffected#children.##At#right#is#the#pedigree#for#an#autosomal(dominant#trait#that#we#wish#to#map.####Six#molecular#markers#were#used#for#mapping#in#the#family#shown#in#the#pedigree,#with#the#results#shown#below : a. (1 point) For markers A, B, and C, what alleles are present in the mother (individual 1 in the pedigree)? b. (1 point) For markers A, B, and C, what alleles are present in the father (individual 2 in the pedigree)?c. (2 points) For marker A, B, and C, what MATERNAL alleles were inherited by children (individuals 3-12 in the pedigree)? d. (2 points) For marker A, B, and C, what PATERNAL alleles were inherited by children (individuals 3-12 in the pedigree)? e.((4 points)(Using(the(hypothesis(that(marker(A(and(B(are(linked,(how(many(chromosomes(inherited(by(the(children(seem(to(be(recombinant?(((HINT:(the(ten(children(have(a(total(of(20(chromosomes(that(you(should(analyze.)(( (f.(((4(points)Now(test(the(hypothesis(that(marker(B(is(linked(to(the(autosomal(dominant(disease(shown(in(the(pedigree.((How(many(chromosomes(inherited(by(the(children(seem(to(be(recombinant?(((HINT:(only(the(maternally(inherited(chromosomes(are(useful(for(this(analysis.)(((((((((((((((( (5.(((13(points)(This(is(the(map(of(a(common(cloning(vector(called(pUC18.((Note(the(antibiotic(resistance(gene((AmpR),(the(origin(of(replication((ColE1(origin),(the(lacZ(alpha(fragment,(and(the(multiple(cloning(sites(adjacent(to(it.((The(AmpR(gene(confers(resistance(to(the(antibiotic(ampicillin.((((((Below(is(the(map(of(an(existing(clone(that(has(the(gene(encoding(the(fluorescent(protein(GFP.((Note(the(antibiotic(resistance(gene((CmR),(the(origin(of(replication((ColE1(origin),(and(the(GFP(gene.((The(CmR(gene(confers(resistance(to(the(antibiotic(chloramphenicol.((((Your(task(is(to(move(the(GFP(gene((labeled(EGFP)(from(the(clone(shown(below(into(the(pUC18((vector(shown(above.(((a. (3(points)(The(first(experiment(you(try(is(doomed%to%failure.((You(decide(to(digest(both(plasmids(with(EcoRI,(mix(them,(and(ligate.((You(perform(transformation,(and(plate(on(ampicillin.((You(get(lots(of(colonies.((You(pick(a(few(of(them,(prepare(plasmid(DNA(,(cut(it(with(EcoRI(and(check(the(results(on(a(gel.((Draw(what(you(expect(to(see(after(this(failed(experiment(in(lane(1(of(the(gel(below:(( (b. (1(point)(If(you(had(plated(the(transformation(from(part(a(on(plates(containing(XMgal,(what(color(would(the(colonies(be?((c. ((3(points)(In(your(next(try,(you(almost(get(it,(but(not(quite.(You(decide(to(digest(both(plasmids(with(EcoRI(and(HindIII,(mix(them,(and(ligate.((You(perform(transformation,(and(plate(on(chloramphenicol.((You(get(lots(of(colonies.((You(pick(a(few(of(them,(prepare(plasmid(DNA,(cut(it(with(HindIII(and(EcoRI(and(check(the(results(on(a(gel.((Draw(what(you(expect(to(see(after(this(failed(experiment(in(lane(2(of(the(gel(above.((d. ((3(points)(Third(time’s(the(charm(as(they(say.((This(time,(you(get(your(act(together(and(digest(both(plasmids(with(EcoRI(and(HindIII,(mix(them,(and(ligate.((You(perform(transformation,(and(plate(on(ampicillin.(You(plan(to(prepare(plasmid(DNA(from(several(colonies,(cut(it(with(HindIII(and(EcoRI,(and(view(the(result(on(a(gel.((What(do(you(expect(to(see(if(the(cloning(was(successful?((Draw(it(in(lane(3(of(the(gel( a bove.((e. (3(points)(Below(is(what(you(actually(see(after(doing(the(experiment(described(in(part(c.((Using(2M3(short(sentences,(explain(why(t here(