Question

Problem 3 You're a dog breeder looking to understand the genetic basis of adorable floppy ears. You perform a GWAS to identify the gene involved in the floppy ear trait. Your dataset of phenotypes and genotypes for two SNPs are below. dog Bailey ear typers289rs872 floppy CT Duke Bear Lucy Chopper straight CT Sadie floppy floppy straight TT AC AC AC AC CT CT straight TT AC RockystraightCT a) Is the dataset representing a binary or continuous trait? [2 points] b) Calculate genotype frequencies for SNP rs289 in floppy eared dogs, SNP rs289 in straight eared dogs, SNP rs872 in floppy eared dogs, and SNP rs872 in straight eared dogs. [12 points] c) Calculate allele frequencies for SNP rs289 in floppy eared dogs, SNP rs289 in straight eared dogs, SNP rs872 in floppy eared dogs, and SNP rs872 in straight eared dogs. [8 points] d) Based on the frequencies you calculated, which SNP (if either) is associated with the floppy ear trait? [2 points] e) What aspect of your frequency results lead you to that conclusion? [4 points]

Answer 1

"GWAS" stands for "Genome-Wide Association Studies." The genomes of thousands of unrelated individuals, with a disease are analysed. The results are compared with genomes of individuals without the disease. And then they are trying to find genetic variations that may confer risk of developing the disease. For example, in most of the cases, the environmental and genetic differences act as risk factors (a) Based on the given data, the data set represents a "binary trait." It is a complex trait, mutations could have been in more than one gene that has attributed to the phenotypic variation SO (b) The genotypic frequency of SNP rs289 (floppy eared dogs) is as follows: number of floppy eared dogs SNP rs289 (CT)= Total 3 4 0.75 number of floppy eared dogs SNP rs289 (CC)= Total 4 -0.25 The genotypic frequency of SNP rs289 (straight eared dogs) is as follows:

number of stright eared dogs SNP rs289 (TT) or (CT) Total 4 0.5 The genotypic frequency of SNP rs872 (floppy eared dogs) is as follows: number of floppy eared dogs SNP rs872(AC) Total 3 4 = 0.75 number of floppy eared dogs SNP rs872(AA)=| Total 4 -0.25 The genotypic frequency of SNP rs872 (straight eared dogs) is as follows: number of stright eared dogs SNP rs872(AC)= Total 2 4 0.55 number of stright eared dogs SNP rs872(AA)=| Total 4 -0.25

0.25 number of stright eared dogs SNP rs872 (CC) Total 1 4 -0.25 (c) The allelic frequency of SNP rs289 (floppy eared dogs) is as follows: number C alleles SNP rs289 (C) Total 8 -0.625 number T alleles SNP rs289 (T) =! Total 3 8. -0.375 The allelic frequency of SNP rs289 (straight eared dogs) is as follows:

number T alleles SNP rs289 (T)= Total =0.625 SNP rs289 (C)=/number C alleles Total 3 -0.375 The allelic frequency of SNP rs872 (floppy eared dogs) is as follows: number A alleles SNP rs872(A)= Total 5 = 0.625 - number C alleles SNP rs872 (C)= Total 3 0.375 The allelic frequency of SNP rs872 (straight eared dogs) is as follows: nco

number alleles SNP rs872(A) or (C)= Total 0.5 (d) The SNP rs289 is associated with floppy ear types