## Step 1The branch of Biological Sciences that deals with the study of genomes is known as Genomics. The genome is the complete set of genetic information present in an organism.As per the guidelines, the answers for the first 3 questions are being provided here. The student is requested to upload the remaining questions separately.## Step 2### Question 1:GWAS or Genome-wide Association Study is a method for identifying the genes responsible for giving an organism its phenotype. This method is very useful because:- It provides information on the SNPs that need attention to understand the genetic risk for a condition in an organism.- SNP identification helps to understand the mechanisms causing genetic risk, providing clarity on differences between alleles.- This method can find genomic variants that cause a particular trait or disease in an individual.GWAS can solve problems such as:- Finding out genes associated with a particular complex disease.- Screening a large number of SNPs from the genome of an individual.- Understanding the genetic mechanisms of disease better.### Question 2:The combinations of alleles (C and A) that a dog could have for the SNP shown in Fig. 2 are:i) CCii) AAiii) CA### Question 3:SNPs are referred to as "markers" or "signposts" because they are majorly used as Biological Markers that help detect a biological state. SNPs efficiently locate or detect genes associated with particular diseases. Present throughout the genome, SNPs act as excellent biomarkers and can track the inheritance of disease-associated genetic variants within families.One way to find SNPs associated with a trait is by comparing groups with different versions of that trait. For example, in dogs, comparing black coats to white coats reveals informative SNPs associated with color. These SNPs are "markers" for regions containing genes affecting fur color.3. Why do you think SNPs are referred to as “markers” or “signposts”?### Diagram Analysis (Figure 3)**Figure 3 Description:**- The diagram shows various ways an SNP could associate with a gene and its trait.- It illustrates SNPs: - **Associated & Outside of Gene:** No effect on protein function. - **Associated & Within Gene:** No effect or it may change protein production/function. - **Unassociated & Far from Gene or Within Gene:** No effect. - **Causative SNPs Within Gene:** Affect **PART 2: Applying GWAS to Dog Fur Color**Let's explore how a GWAS (Genome-Wide Association Study) works using a simple example that compares two groups of dogs: dogs with black fur and dogs with white fur. Table 1 shows the dogs’ SNP (Single Nucleotide Polymorphism) alleles at 17 specific locations in the genome. These specific locations in the genome are called loci (singular: locus). The SNP alleles at each locus are represented by two nucleotides, one from each parental chromosome.**Table 1.** SNP alleles at 17 different loci in dogs with black fur (first four rows) and dogs with white fur (last four rows).| | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 ||---|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----||

By studying linkage, we can conclude about allele identity between loci is associated or not; allele…

One way to find SNPs associated with a certain trait is by comparing groups with different versions of that trait. In a GWAS looking for genes that affect dog fur color, for example, we could compare the SNPs of two groups: dogs with black fur and dogs with white fur. We would then determine which SNPs are significantly more common in dogs with black fur compared to dogs with white fur. These SNPs are "markers" for regions of the dog genome that contain genes affecting fur color. 3. Why do you think SNPs are referred to as "markers" or "signposts"? Figure 3 shows several possibilities for why a SNP is associated with a certain trait. The SNP may be in the gene that causes the trait or in a regulatory area for that gene. If so, the SNP could directly affect the gene's function and the resulting trait. However, some SNPs in or near a gene may have no effect on the gene or its trait. www.Biolnteractive.org hhmi BioInteractive Mapping Genes to Traits in Dogs Using SNPs Associated SNPs outside of gene a. no effect on protein production or function Associated SNPs within gene no effect on protein production or function Regulatory sequences Coding region с Noncoding SNP: changes amount of protein produced T Causative SNPs within gene Unassociated SNP far from gene on same chromosome or different chromosome Protein Coding SNP: changes amino acid sequence b. Which types of SNPs might be identified in a GWAS? T Updated November 2020 Page 2 of 7 Activity Student Handout 4. Consider the different types of SNPs shown in Figure 3: associated, unassociated, and causative (including both noncoding and coding). Which types of SNPs affect protein production or function for the gene of interest? Figure 3. A diagram showing various ways in which a SNP could be associated with a certain gene and its trait. GWAS in the News Read the following news release, which describes a GWAS study with dogs. Note that a dog's coat refers to its fur or hair. Variants in Three Genes Account for Most Dog Coat Differences Variants in just three genes acting in different combinations account for the wide range of coat textures seen in dogs from the poodle's tight curls to the beagle's stick-straight fur. A team led by researchers from the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health, reports these findings today in the advance online issue of the journal Science. "This study is an elegant example of using genomic techniques to unravel the genetic basis of biological diversity," said NHGRI Scientific Director Eric Green, M.D., Ph.D. "Genomics continues to gain new insights from the amazing morphological differences seen across the canine species, including many that give clues about human biology and disease." coats of Until now, relatively little was known about the genes influencing the length, growth pattern and texture of the . The researchers performed a genome-wide scan of ecific signposts of DNA called single nucleotide polymorphisms, in 1,000 individual dogs representing 80 breeds. These data were compared with descriptions of various coat types. Three distinct genetic variants emerged to explain, in combination, virtually all dog hair types. "What's important for human health is the way we found the genes involved in dog coats and figured out how