Question

You conduct a QTL experiment to find the loci controlling fruit size and sugar content starting from two parental varieties, “Sam’s Giant (SG)” and “Sweet Baby Red (SBR)”. Your cross “Sam’s Giant” and “Sweet Baby Red” and generate F1’s and then interbreed F1’s to generate a series of F2 individuals and measure size and sugar content in all of them. You determine the genotype at many individual SNP markers, 5 of which (each on a different chromosome) are shown below. The data are:

Type SNP A SNP B SNP C SNP D SNPE Fruit size (g) 740 AA CC SG SBR F1 F2#1 F2#2 F2#3 F2#4 F2#5 F2#6 F2#7 F2#8 320 540 670 650 590 570 550 530 500 460 Sugar content (mg/G tissue) 12 39 24 18 22 24 26 29 32 34 37 AC AC CC АА CC АА AC CC AC IT GG TG TT TT TG TG TG GG GG GG GG AA GA GA GG AA GA GA GG AA GA AA CC AC AC CC AA AC АА CC АА AC CC TT СТ CC CC СТ СТ TT TT TT TT

1. Which, if any, of the SNPs are associated with fruit size? Explain
2. Which, if any, of the SNPs are associated with sugar content? Explain
3. What do the results from parts a and b say about the two traits (fruit size and sugar content)?

Answer 1

a) Let us analyze which SNPs are present in the Type with the largest sizes, they are SG, F2 1 and F2 2, they have in common the genotypes for SNP B and SNP E. Then we can propose SNPs B and E are associatedd to fruit size, with the genotypes TT and CC respectively

b) Let us do the same but now for the Types with the highest sugar content, they are SBR, F2 8 and F2 6, theya have in common the genotypes for SNP B and SNP E too. Then we can propose SNPs B and E are associeted to sugar content, with the genotypes GG and TT respectively.

c) It says they are related to a single locus and are determined by different genotypes, that means we cannot achieve to have a single fruit with the largest size and the highest sugar content at the same time.