Homework(3((((1. 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. (((((((((((((((( (#.((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.(((4(points)(write(the(phenotype(pairs((in(the(table(below(( Number Phenotype Pair 1 Pair 2 Pair 3 Pair 4 (b.((4(points)(What(are(the(parental(classes?((order(is(not(important)(((((c.((4(points)(What(are(the(double(cross(over(classes?((order(is(not(important)(((((d.((4(points)(What(is(the(gene(order?((((e.((4(points)(Calculate(the(distance(between(the(leftNmost(gene(and(the(middle(gene.((Show(your(work.(((((f.((4(points)(Calculate(the(distance(between(the(middle(gene(and(the(rightNmost(gene.((Show(your(work.(((((#.((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.((How(far(is(Marker(#2(from(our(gene(of(interest((remember(this(will(be(a(range(of(distances)((((((((b.((Does(Marker(3(appear(to(be(linked(to(our(gene(of(interest?(Defend(your(answer(in(two(sentences(or(less.(((( (#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.$$For$this$assignment,$we $w ill$use$D NA $m ark ers$to$determine$the$portion$of$an$affected$parent’s$chromosome$that$is$inherited$in$affected$children$and$the$portion$that$is$inherited$in$unaffected$children.$$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. For markers A, B, and C, what alleles are present in the mother (individual 1 in the pedigree)? b. For markers A, B, and C, what alleles are present in the father (individual 2 in the pedigree)?c. For marker A, B, and C, what MATERNAL alleles were inherited by children (individuals 3-12 in the pedigree)? d. For marker A, B, and C, what PATERNAL alleles were inherited by children (individuals 3-12 in the pedigree)? e.((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.((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.)(((((((((((((((EXTRA(CREDIT:(Use(a(chiNsquared(test(to(determine(whether(linkage(between(marker(A(and(marker(B(is(supported(by(the(data.(( (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!XHgal,!what!color!would!the!colonies!be?!!Blue—you!would!be!seeing!religated!pUC18.!!(Religated!EGFP!won’t!grow!on!ampicillin.!!Ligation!of!two!vectors!together!leads!to!problems!with!replication—mentioned!briefly!in!class—and!does!not!happen.)!!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.