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Note for instructors: Please see the notes field for answers. Teaching Genetic Linkage and Recombination through Mapping with Molecular Markers Lisa McDonnell & Jennifer Klenz Gels to analyze as part of In-Class Lesson (see Supplemental Material S1 Lesson Slides, slides 42-45) Note for instructors: Please see the notes field for answers.

MARKER A 50 RESISTANT F2 PLANTS F1 self-fertilized Note to instructors: we are only listing the molecular marker genotypes for the parent and F1 plants. Students could fill in the resistant and susceptible genotypes (or draw chromosomes labelled with alleles for the parent plants and F1) to help them identify parental and recombinant genotypes. F1, susceptible 200/400 F1 self-fertilized Resistant 200/200 X Susceptible 400/400 MARKER A 50 RESISTANT F2 PLANTS Resistant. Susceptible F1 (parent)) (parent) #1 #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12 #13 #14 #15 #16 #17 #18 #19 #20 #21 Resistant F2 plants CONTROLS #22 #23 #24 #25 #26 #27 #28 #29 #30 #31 #32 #33 #34 #35 #36 #37 #38 #39 #40 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 Linked. Count the number of recombinant bands/total bands. Recombinant band is the 400 band. 14 high bands/100 bands total *100% = 14% recombinants, 14 map units. Resistant F2 plants

MARKER B 50 RESISTANT F2 PLANTS F1 self-fertilized F1, susceptible X Susceptible 100/100 F1, susceptible 350/100 F1 self-fertilized MARKER B 50 RESISTANT F2 PLANTS Resistant 350/350 Resistant. Susceptible F1 (parent)) (parent) #1 #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12 #13 #14 #15 #16 #17 #18 #19 #20 #21 CONTROLS Resistant F2 plants #22 #23 #24 #25 #26 #27 #28 #29 #30 #31 #32 #33 #34 #35 #36 #37 #38 #39 #40 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 Linked Count the number of recombinant bands/total bands. Recombinant band is 100. 6 recombinant bands/100 bands total *100% = 6%, or 6 map units. Resistant F2 plants

MARKER C 50 RESISTANT F2 PLANTS F1 self-fertilized F1, susceptible 90/550 F1 self-fertilized Resistant 90/90 X Susceptible 550/500 MARKER C 50 RESISTANT F2 PLANTS Resistant. Susceptible F1 (parent)) (parent) #1 #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12 #13 #14 #15 #16 #17 #18 #19 #20 #21 CONTROLS Resistant F2 plants #22 #23 #24 #25 #26 #27 #28 #29 #30 #31 #32 #33 #34 #35 #36 #37 #38 #39 #40 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 Independent assortment 550 is the recombinant band 50 recombinant bands/100 total *100% = 50%  independent assortment. Resistnat F2 plants

MARKER D 50 RESISTANT F2 PLANTS F1 self-fertilized F1, susceptible 50/75 F1 self-fertilized MARKER D 50 RESISTANT F2 PLANTS Resistant 50/50 X Susceptible 75/75 Resistant. Susceptible F1 (parent)) (parent) #1 #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12 #13 #14 #15 #16 #17 #18 #19 #20 #21 CONTROLS Resistant F2 plants #22 #23 #24 #25 #26 #27 #28 #29 #30 #31 #32 #33 #34 #35 #36 #37 #38 #39 #40 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 Likely independent assortment 75 is the recombinant band 49 recombinant bands/100 total *100% = 49%  independent assortment. Because we already have linkage between the BR locus and two markers on chromosome 1 it is likely that the locus assorts independently from this marker, on chromosome 3. If we screened more plants the percentage recombinants would probably be 50% (or even slightly higher). Resistant F2 plants

MARKER E 50 RESISTANT F2 PLANTS F1 self-fertilized F1, susceptible 675/600 Resistant 675/675 X Susceptible 600/600 Resistant. Susceptible F1 (parent)) (parent) #1 #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12 #13 #14 #15 #16 #17 #18 #19 #20 #21 CONTROLS Resistant F2 plants #22 #23 #24 #25 #26 #27 #28 #29 #30 #31 #32 #33 #34 #35 #36 #37 #38 #39 #40 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 Independent assortment 600 is the recombinant band 52 recombinant bands/100 total *100% = 52%  independent assortment. Resistant F2 plants

MARKER F 50 RESISTANT F2 PLANTS F1, susceptible 220/410 F1 self-fertilized Resistant 220/220 X Susceptible 410/410 MARKER F 50 RESISTANT F2 PLANTS Resistant. Susceptible F1 (parent)) (parent) #1 #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12 #13 #14 #15 #16 #17 #18 #19 #20 #21 CONTROLS Resistant F2 plants #22 #23 #24 #25 #26 #27 #28 #29 #30 #31 #32 #33 #34 #35 #36 #37 #38 #39 #40 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 Independent assortment 410 is the recombinant band 51 recombinant bands/100 total *100% = 51%  independent assortment. Resistant F2 plants