If a SNP is found much more frequently in dogs with white fur than in dogs with black fur, the SNP is associated with 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 the dogs with black fur to those of the dogs with white fur. A SNP is completely associated with fur color if all dogs with white fur share the same alleles at that position, and all dogs with black fur share different alleles at that position. A SNP that is completely associated with a trait is likely located within or close to a gene responsible for that trait. 10. Which SNP in Table 1 do you think is completely associated with fur color? Explain the reasoning for your choice. A SNP is completely unassociated with fur color if its alleles occur with equal frequency in dogs with black fur and dogs with white fur. A SNP that is completely unassociated with a trait is unlikely to be located within or near the gene responsible for that trait. 11. Which SNPs in Table 1 do you think are completely unassociated with fur color? Explain the reasoning for your choices. (Hint: There are five in total.)

Human Anatomy & Physiology (11th Edition)
11th Edition
ISBN:9780134580999
Author:Elaine N. Marieb, Katja N. Hoehn
Publisher:Elaine N. Marieb, Katja N. Hoehn
Chapter1: The Human Body: An Orientation
Section: Chapter Questions
Problem 1RQ: The correct sequence of levels forming the structural hierarchy is A. (a) organ, organ system,...
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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 Color
Let's explore how a GWAS 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 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
CC AT CC GG AA TCTT CC GG AA TT GT AG AA CC GG AT
*
3:3
CC AT AC GG GG TT TT CC GG AG TT GG AG AG CC GG AT
www.Biolnteractive.org
3:3
CC AA AC CG GG TT TT CT GG AA TT GT AG AG CC TT AT
3:3
CC AA AC GG AG TT TT CT GG GG TT GG AG AG CC GT AT
hhmi Biolnteractive
Mapping Genes to Traits in Dogs Using SNPs
CC AT CC CG AATTAA CT GG AA TTGT AA AA CC GT AT
Updated November 2020
Page 4 of 7
Activity
Student Handout
CC AT CC GG AATTAA TC GG AA TT GG AG AA CC GG TT
CC AT CC GG AATTAA CC GG AA TT GG AA AA CC GT AT
CC AA CC GG AG TTAA TC GG GG TT GG AA AA CC TT AT
If a SNP is found much more frequently in dogs with white fur than in dogs with black fur, the SNP is associated
with 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 the
dogs with black fur to those of the dogs with white fur. A SNP is completely associated with fur color if all
dogs with white fur share the same alleles at that position, and all dogs with black fur share different alleles
at that position. A SNP that is completely associated with a trait is likely located within or close to a gene
responsible for that trait.
10. Which SNP in Table 1 do you think is completely associated with fur color? Explain the reasoning for your
choice.
A SNP is completely unassociated with fur color if its alleles occur with equal frequency in dogs with black fur
and dogs with white fur. A SNP that is completely unassociated with a trait is unlikely to be located within or
near the gene responsible for that trait.
11. Which SNPs in Table 1 do you think are completely unassociated with fur color? Explain the reasoning for
your 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 to
evaluate the strength of an association in the next part of this activity. For the question below, make your best
guess based on what you've learned so far.
Transcribed Image Text: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 Color Let's explore how a GWAS 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 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 CC AT CC GG AA TCTT CC GG AA TT GT AG AA CC GG AT * 3:3 CC AT AC GG GG TT TT CC GG AG TT GG AG AG CC GG AT www.Biolnteractive.org 3:3 CC AA AC CG GG TT TT CT GG AA TT GT AG AG CC TT AT 3:3 CC AA AC GG AG TT TT CT GG GG TT GG AG AG CC GT AT hhmi Biolnteractive Mapping Genes to Traits in Dogs Using SNPs CC AT CC CG AATTAA CT GG AA TTGT AA AA CC GT AT Updated November 2020 Page 4 of 7 Activity Student Handout CC AT CC GG AATTAA TC GG AA TT GG AG AA CC GG TT CC AT CC GG AATTAA CC GG AA TT GG AA AA CC GT AT CC AA CC GG AG TTAA TC GG GG TT GG AA AA CC TT AT If a SNP is found much more frequently in dogs with white fur than in dogs with black fur, the SNP is associated with 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 the dogs with black fur to those of the dogs with white fur. A SNP is completely associated with fur color if all dogs with white fur share the same alleles at that position, and all dogs with black fur share different alleles at that position. A SNP that is completely associated with a trait is likely located within or close to a gene responsible for that trait. 10. Which SNP in Table 1 do you think is completely associated with fur color? Explain the reasoning for your choice. A SNP is completely unassociated with fur color if its alleles occur with equal frequency in dogs with black fur and dogs with white fur. A SNP that is completely unassociated with a trait is unlikely to be located within or near the gene responsible for that trait. 11. Which SNPs in Table 1 do you think are completely unassociated with fur color? Explain the reasoning for your 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 to evaluate the strength of an association in the next part of this activity. For the question below, make your best guess based on what you've learned so far.
Associated SNPs
outside of gene
no effect on protein
production or function.
T
G
Associated SNPs
within gene
no effect on protein
production or function
Regulatory sequences
A
Coding region
с
T
Noncoding SNP:
changes amount of
protein produced
www.Biolnteractive.org
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?
4. Consider the different types of SNPs shown in Figure 3: associated, unassociated, and causative (including
both noncoding and coding).
a. 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."
Until now, relatively little was known about the genes influencing the length, growth pattern and texture of the
coats of dogs. The researchers performed a genome-wide scan of specific signposts of DNA variation, 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
they work together, rather than the genes themselves," said Elaine A. Ostrander, Ph.D., chief of the Cancer
Genetics Branch in NHGRI's Division of Intramural Research. "We think this approach will help pinpoint multiple
genes involved in complex human conditions, such as cancer, heart disease, diabetes and obesity."
6. In two or three sentences, describe how scientists identified these genes.
Updated November 2020
Page 3 of 7
hhmi Biolnteractive
Mapping Genes to Traits in Dogs Using SNPs
Artificial selection, at the heart of breeding for desirable traits in domesticated animals, has
yielded rapid change in a short span of canine history. While researchers estimate that modern dog breeds
diverged from wolves some 15,000 years ago, the genetic changes in the dog genome that create multiple coat
types are more likely to have been pursued by breeders in just the past 200 years. In fact, short-haired breeds,
such as the beagle, display the original, more wolf-like versions of the three genes identified in the study.
Activity
Student Handout
Modern dog breeds are part of a unique population structure, having been selectively bred for many years.
Based on this structure, the researchers were able to break down a complex phenotype-coat - into possible
genetic variations. "When we put these genetic variants back together in different combinations, we found that
we could create most of the coat varieties seen in what is among the most diverse species in the world the
dog," Dr. Ostrander said. "If we can decipher the genetic basis for a complex trait such as the dog's coat, we
believe that we can do it as well with complex diseases."
-Excerpt from a National Institutes of Health (NIH) News Release published August 27, 2009
Answer the following questions to check your understanding of the reading.
5. How many genes account for the wide variety of coat types in dogs?
7. Why do you think it is important to analyze the DNA of many dogs when doing this research?
Transcribed Image Text:Associated SNPs outside of gene no effect on protein production or function. T G Associated SNPs within gene no effect on protein production or function Regulatory sequences A Coding region с T Noncoding SNP: changes amount of protein produced www.Biolnteractive.org 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? 4. Consider the different types of SNPs shown in Figure 3: associated, unassociated, and causative (including both noncoding and coding). a. 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." Until now, relatively little was known about the genes influencing the length, growth pattern and texture of the coats of dogs. The researchers performed a genome-wide scan of specific signposts of DNA variation, 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 they work together, rather than the genes themselves," said Elaine A. Ostrander, Ph.D., chief of the Cancer Genetics Branch in NHGRI's Division of Intramural Research. "We think this approach will help pinpoint multiple genes involved in complex human conditions, such as cancer, heart disease, diabetes and obesity." 6. In two or three sentences, describe how scientists identified these genes. Updated November 2020 Page 3 of 7 hhmi Biolnteractive Mapping Genes to Traits in Dogs Using SNPs Artificial selection, at the heart of breeding for desirable traits in domesticated animals, has yielded rapid change in a short span of canine history. While researchers estimate that modern dog breeds diverged from wolves some 15,000 years ago, the genetic changes in the dog genome that create multiple coat types are more likely to have been pursued by breeders in just the past 200 years. In fact, short-haired breeds, such as the beagle, display the original, more wolf-like versions of the three genes identified in the study. Activity Student Handout Modern dog breeds are part of a unique population structure, having been selectively bred for many years. Based on this structure, the researchers were able to break down a complex phenotype-coat - into possible genetic variations. "When we put these genetic variants back together in different combinations, we found that we could create most of the coat varieties seen in what is among the most diverse species in the world the dog," Dr. Ostrander said. "If we can decipher the genetic basis for a complex trait such as the dog's coat, we believe that we can do it as well with complex diseases." -Excerpt from a National Institutes of Health (NIH) News Release published August 27, 2009 Answer the following questions to check your understanding of the reading. 5. How many genes account for the wide variety of coat types in dogs? 7. Why do you think it is important to analyze the DNA of many dogs when doing this research?
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