Step 1The branch of Biological Sciences that deals with the study of genome is known as Genomics. Thegenome 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 isrequested to upload the remaining questions separately.Step 2Question 1:GWAS or Genome-wide Association Study is a method for identifying the genes that are responsible forgiving an organism its phenotype. This method is very useful because -• It provides information on the SNPs that need our attention in order to know about the genetic riskfor a particular condition in an organism.• The SNP identification makes it possible to understand the mechanisms that might cause thegenetic risk and also might provide a scope to clarify the differences between the 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 entire genome of an individual.Understanding the underlying mechanisms of disease in a better way, from genetic point of view.Question 2:The three combinations of alleles (C and A) that a dog could have for the SNP shown in Fig.2 are -i) CC, ii) AA and iii) CA.Question 3:SNPs are referred to as "markers" or "signposts" because they are majorly used as Biological Markers.Biological markers are those which help detect a biologic state. The SNPs work very efficiently to locateor detect the genes that are supposedly associated with a particular disease, that the scientist is tryingto understand. The SNPs are present throughout the genome, and in a stable state. This makes themfunction as excellent biomarkers. Besides, SNPs are capable of tracking the inheritance of disease-associated genetic variants that flow within different families. Due to these reasons, SNPs are referred toas "markers" or "signposts".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 twogroups: dogs with black fur and dogs with white fur. We would then determine which SNPs are significantlymore common in dogs with black fur compared to dogs with white fur. These SNPs are "markers" for regionsof 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 genethat causes the trait or in a regulatory area for that gene. If so, the SNP could directly affect the gene's functionand the resulting trait. However, some SNPs in or near a gene may have no effect on the gene or its trait.www.Biolnteractive.orghhmi BiolnteractiveMapping Genes to Traits in Dogs Using SNPsAssociated SNPsoutside of geneno effect on proteinproduction or functionTGAssociated SNPswithin geneno effect on proteinproduction or functionRegulatory sequencesACoding regionCNoncoding SNP:changes amount ofprotein producedCausative SNPswithin geneUnassociated SNPfar from geneon same chromosome. Tor different chromosomeProteinCoding SNP:changes aminoacid sequenceb. Which types of SNPs might be identified in a GWAS?Updated November 2020Page 2 of 7ActivityStudent HandoutFigure 3. A diagramshowing various waysin which a SNP could beassociated with acertain gene and itstrait.4. Consider the different types of SNPs shown in Figure 3: associated, unassociated, and causative (includingboth noncoding and coding).a. Which types of SNPs affect protein production or function for the gene of interest?GWAS in the NewsRead the following news release, which describes a GWAS study with dogs. Note that a dog's coat refers to itsfur or hair.Variants in Three Genes Account for Most Dog Coat DifferencesVariants in just three genes acting in different combinations account for the wide range of coat textures seen indogs from the poodle's tight curls to the beagle's stick-straight fur. A team led by researchers from theNational Human Genome Research Institute (NHGRI), part of the National Institutes of Health, reports thesefindings today in the advance oniine issue of the journal Science."This study is an elegant example of using genomic techniques to unravel the genetic basis of biologicaldiversity," said NHGRI Scientific Director Eric Green, M.D., Ph.D. "Genomics continues to gain new insights fromthe amazing morphological differences seen across the canine species, including many that give clues abouthuman biology and disease."Until now, relatively little was known about the genes influencing the length, growth pattern and texture of thecoats of dogs. The researchers performed a genome-wide scan of specific signposts of DNA variation, calledsingle nucleotide polymorphisms, in 1,000 individual dogs representing 80 breeds. These data were comparedwith 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 7. Why do you think it is important to analyze the DNA of many dogs when doing this research?8. Humans have SNPs too. In general, how might GWAS studies with dogs benefit humans?PART 2: Applying GWAS to Dog Fur ColorLet's explore how a GWAS works using a simple example that compares two groups of dogs: dogs with black furand dogs with white fur. Table 1 shows the dogs' SNP alleles at 17 specific locations in the genome. Thesespecific locations in the genome are called loci (singular: locus). The SNP alleles at each locus are represented bytwo 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 17CC AT CC GG AA TCTT CC GG AA TT GT AG AA CC GG AT*3:3CC AT AC GG GG TT TT CC GG AG TT GG AG AG CC GG ATwww.Biolnteractive.org3:3CC AA AC CG GG TT TT CT GG AA TT GT AG AG CC TT AT3:3CC AA AC GG AG TT TT CT GG GG TT GG AG AG CC GT AThhmi BiolnteractiveMapping Genes to Traits in Dogs Using SNPsCC AT CC CG AATTAA CT GG AA TTGT AA AA CC GT ATUpdated November 2020Page 4 of 7ActivityStudent HandoutCC AT CC GG AATTAA TC GG AA TT GG AG AA CC GG TTCC AT CC GG AATTAA CC GG AA TT GG AA AA CC GT ATCC AA CC GG AG TTAA TC GG GG TT GG AA AA CC TT ATIf a SNP is found much more frequently in dogs with white fur than in dogs with black fur, the SNP is associatedwith the white fur color.9. Give two possible reasons for why a SNP would be associated with a trait like fur color.To determine whether any of the SNPs in Table 1 are associated with fur color, you can compare the SNPs of thedogs with black fur to those of the dogs with white fur. A SNP is completely associated with fur color if alldogs with white fur share the same alleles at that position, and all dogs with black fur share different allelesat that position. A SNP that is completely associated with a trait is likely located within or close to a generesponsible for that trait.10. Which SNP in Table 1 do you think is completely associated with fur color? Explain the reasoning for yourchoice.A SNP is completely unassociated with fur color if its alleles occur with equal frequency in dogs with black furand dogs with white fur. A SNP that is completely unassociated with a trait is unlikely to be located within ornear the gene responsible for that trait.11. Which SNPs in Table 1 do you think are completely unassociated with fur color? Explain the reasoning foryour choices. (Hint: There are five in total.)The other SNPs in Table 1 have varying strengths of association with fur color. You'll learn more about how toevaluate the strength of an association in the next part of this activity. For the question below, make your bestguess based on what you've learned so far.

Question

Step 1The branch of Biological Sciences that deals with the study of genome is known as Genomics. Thegenome 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 isrequested to upload the remaining questions separately.Step 2Question 1:GWAS or Genome-wide Association Study is a method for identifying the genes that are responsible forgiving an organism its phenotype. This method is very useful because -• It provides information on the SNPs that need our attention in order to know about the genetic riskfor a particular condition in an organism.• The SNP identification makes it possible to understand the mechanisms that might cause thegenetic risk and also might provide a scope to clarify the differences between the 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 entire genome of an individual.Understanding the underlying mechanisms of disease in a better way, from genetic point of view.Question 2:The three combinations of alleles (C and A) that a dog could have for the SNP shown in Fig.2 are -i) CC, ii) AA and iii) CA.Question 3:SNPs are referred to as &#34;markers&#34; or &#34;signposts&#34; because they are majorly used as Biological Markers.Biological markers are those which help detect a biologic state. The SNPs work very efficiently to locateor detect the genes that are supposedly associated with a particular disease, that the scientist is tryingto understand. The SNPs are present throughout the genome, and in a stable state. This makes themfunction as excellent biomarkers. Besides, SNPs are capable of tracking the inheritance of disease-associated genetic variants that flow within different families. Due to these reasons, SNPs are referred toas &#34;markers&#34; or &#34;signposts&#34;.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 twogroups: dogs with black fur and dogs with white fur. We would then determine which SNPs are significantlymore common in dogs with black fur compared to dogs with white fur. These SNPs are &#34;markers&#34; for regionsof the dog genome that contain genes affecting fur color.3. Why do you think SNPs are referred to as &#34;markers&#34; or &#34;signposts&#34;?Figure 3 shows several possibilities for why a SNP is associated with a certain trait. The SNP may be in the genethat causes the trait or in a regulatory area for that gene. If so, the SNP could directly affect the gene's functionand the resulting trait. However, some SNPs in or near a gene may have no effect on the gene or its trait.www.Biolnteractive.orghhmi BiolnteractiveMapping Genes to Traits in Dogs Using SNPsAssociated SNPsoutside of geneno effect on proteinproduction or functionTGAssociated SNPswithin geneno effect on proteinproduction or functionRegulatory sequencesACoding regionCNoncoding SNP:changes amount ofprotein producedCausative SNPswithin geneUnassociated SNPfar from geneon same chromosome. Tor different chromosomeProteinCoding SNP:changes aminoacid sequenceb. Which types of SNPs might be identified in a GWAS?Updated November 2020Page 2 of 7ActivityStudent HandoutFigure 3. A diagramshowing various waysin which a SNP could beassociated with acertain gene and itstrait.4. Consider the different types of SNPs shown in Figure 3: associated, unassociated, and causative (includingboth noncoding and coding).a. Which types of SNPs affect protein production or function for the gene of interest?GWAS in the NewsRead the following news release, which describes a GWAS study with dogs. Note that a dog's coat refers to itsfur or hair.Variants in Three Genes Account for Most Dog Coat DifferencesVariants in just three genes acting in different combinations account for the wide range of coat textures seen indogs from the poodle's tight curls to the beagle's stick-straight fur. A team led by researchers from theNational Human Genome Research Institute (NHGRI), part of the National Institutes of Health, reports thesefindings today in the advance oniine issue of the journal Science.&#34;This study is an elegant example of using genomic techniques to unravel the genetic basis of biologicaldiversity,&#34; said NHGRI Scientific Director Eric Green, M.D., Ph.D. &#34;Genomics continues to gain new insights fromthe amazing morphological differences seen across the canine species, including many that give clues abouthuman biology and disease.&#34;Until now, relatively little was known about the genes influencing the length, growth pattern and texture of thecoats of dogs. The researchers performed a genome-wide scan of specific signposts of DNA variation, calledsingle nucleotide polymorphisms, in 1,000 individual dogs representing 80 breeds. These data were comparedwith descriptions of various coat types. Three distinct genetic variants emerged to explain, in combination,virtually all dog hair types.&#34;What's important for human health is the way we found the genes involved in dog coats and figured out how 7. Why do you think it is important to analyze the DNA of many dogs when doing this research?8. Humans have SNPs too. In general, how might GWAS studies with dogs benefit humans?PART 2: Applying GWAS to Dog Fur ColorLet's explore how a GWAS works using a simple example that compares two groups of dogs: dogs with black furand dogs with white fur. Table 1 shows the dogs' SNP alleles at 17 specific locations in the genome. Thesespecific locations in the genome are called loci (singular: locus). The SNP alleles at each locus are represented bytwo 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 17CC AT CC GG AA TCTT CC GG AA TT GT AG AA CC GG AT*3:3CC AT AC GG GG TT TT CC GG AG TT GG AG AG CC GG ATwww.Biolnteractive.org3:3CC AA AC CG GG TT TT CT GG AA TT GT AG AG CC TT AT3:3CC AA AC GG AG TT TT CT GG GG TT GG AG AG CC GT AThhmi BiolnteractiveMapping Genes to Traits in Dogs Using SNPsCC AT CC CG AATTAA CT GG AA TTGT AA AA CC GT ATUpdated November 2020Page 4 of 7ActivityStudent HandoutCC AT CC GG AATTAA TC GG AA TT GG AG AA CC GG TTCC AT CC GG AATTAA CC GG AA TT GG AA AA CC GT ATCC AA CC GG AG TTAA TC GG GG TT GG AA AA CC TT ATIf a SNP is found much more frequently in dogs with white fur than in dogs with black fur, the SNP is associatedwith the white fur color.9. Give two possible reasons for why a SNP would be associated with a trait like fur color.To determine whether any of the SNPs in Table 1 are associated with fur color, you can compare the SNPs of thedogs with black fur to those of the dogs with white fur. A SNP is completely associated with fur color if alldogs with white fur share the same alleles at that position, and all dogs with black fur share different allelesat that position. A SNP that is completely associated with a trait is likely located within or close to a generesponsible for that trait.10. Which SNP in Table 1 do you think is completely associated with fur color? Explain the reasoning for yourchoice.A SNP is completely unassociated with fur color if its alleles occur with equal frequency in dogs with black furand dogs with white fur. A SNP that is completely unassociated with a trait is unlikely to be located within ornear the gene responsible for that trait.11. Which SNPs in Table 1 do you think are completely unassociated with fur color? Explain the reasoning foryour choices. (Hint: There are five in total.)The other SNPs in Table 1 have varying strengths of association with fur color. You'll learn more about how toevaluate the strength of an association in the next part of this activity. For the question below, make your bestguess based on what you've learned so far.

Accepted Answer

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