ICB BREEDER TOOL
Tutorial
What is this?
Welcome to this introduction to the components of the ICB Breeder Tool. We’re going to walk you through the information it provides and how you can use it to guide your breeding decisions. The information for the tool can be produced either by a pedigree database or DNA data. The data in this tutorial use DNA data obtained from a study published by Embark.
Why do DNA analysis?
DNA is the secret code that contains the "instructions" for your dog. You can now obtain the genotype data for your dog, something that would have set you back tens of thousands of dollars only a few years ago.
Embark is the commercial lab that provides this service to breeders using the most up-to-date, research grade analysis platform, the Illumina HD (high density) Canine SNP (single-nucleotide polymorphism; pronounced "snip") chip. We just call it "the snip chip." It reads information from > 200,000 locations (loci) on the DNA of the dog. From this information, you can learn a lot about your dog - the genes it has for physical traits, health, behavior, and much more. These data can also tell you about your dog's ancestry, who its relatives are, and how inbred it is. A goldmine of information.
Embark sends you a report of the information about particular genes for mutations and traits in your dog, and they also allow you to download your actual data files. Those data are provided in an Excel table with one row for your dog and 200,000 columns of the letters A, C, T, and G. By itself, it won't tell you a thing about your dog. (In fact, special software is necessary to open the files.) But with the right software, and expertise in how to analyze SNP data, a huge amount of information can be extracted from all these letters.
Why do you need a breeder tool?
A breeder tool extracts information from this rubble of alphabet letters and presents it in a way that provides insight into individual dogs, groups of dogs, breeds, and dogs in general. DNA data are now available for hundreds of breeds and hundreds of thousands of dogs. The ICB Breeder Tool is designed to provide breeders with the basic information they need to make more informed choices about breeding options, and also - and perhaps more importantly - monitor and manage the genetics of their breed to insure protection of genetic diversity and health.
The ICB Breeder Tool is the first of its kind for dog breeders. It uses analyses that have been the basis of conservation genetics programs and animal breeding for decades, but have never been available to breeders.
Breeding involves a lot of luck (we call it "chance"), but if you have the right data and how it is interpreted, it certainly is not a "crap shoot". If we believe in genes (and we do!), there is much that is predictable if we have the information we need.
This version of the tool is most basic. New tools and information will be added as it is developed, with the goal of being the most comprehensive, most accurate tool for genetic analysis available to dog breeders.
We really can aspire to "precision breeding." Go through this online tutorial and get started!
Using the interactive tables
The tables in the breeder tool are interactive. You can sort by number or label, ascending or descending. You can also select specific individuals from a matrix of options. You can also sort or filter multiple columns, in any order; e.g., select all females without a specific mutation.
Welcome to this introduction to the components of the ICB Breeder Tool. We’re going to walk you through the information it provides and how you can use it to guide your breeding decisions. The information for the tool can be produced either by a pedigree database or DNA data. The data in this tutorial use DNA data obtained from a study published by Embark.
Why do DNA analysis?
DNA is the secret code that contains the "instructions" for your dog. You can now obtain the genotype data for your dog, something that would have set you back tens of thousands of dollars only a few years ago.
Embark is the commercial lab that provides this service to breeders using the most up-to-date, research grade analysis platform, the Illumina HD (high density) Canine SNP (single-nucleotide polymorphism; pronounced "snip") chip. We just call it "the snip chip." It reads information from > 200,000 locations (loci) on the DNA of the dog. From this information, you can learn a lot about your dog - the genes it has for physical traits, health, behavior, and much more. These data can also tell you about your dog's ancestry, who its relatives are, and how inbred it is. A goldmine of information.
Embark sends you a report of the information about particular genes for mutations and traits in your dog, and they also allow you to download your actual data files. Those data are provided in an Excel table with one row for your dog and 200,000 columns of the letters A, C, T, and G. By itself, it won't tell you a thing about your dog. (In fact, special software is necessary to open the files.) But with the right software, and expertise in how to analyze SNP data, a huge amount of information can be extracted from all these letters.
Why do you need a breeder tool?
A breeder tool extracts information from this rubble of alphabet letters and presents it in a way that provides insight into individual dogs, groups of dogs, breeds, and dogs in general. DNA data are now available for hundreds of breeds and hundreds of thousands of dogs. The ICB Breeder Tool is designed to provide breeders with the basic information they need to make more informed choices about breeding options, and also - and perhaps more importantly - monitor and manage the genetics of their breed to insure protection of genetic diversity and health.
The ICB Breeder Tool is the first of its kind for dog breeders. It uses analyses that have been the basis of conservation genetics programs and animal breeding for decades, but have never been available to breeders.
Breeding involves a lot of luck (we call it "chance"), but if you have the right data and how it is interpreted, it certainly is not a "crap shoot". If we believe in genes (and we do!), there is much that is predictable if we have the information we need.
This version of the tool is most basic. New tools and information will be added as it is developed, with the goal of being the most comprehensive, most accurate tool for genetic analysis available to dog breeders.
We really can aspire to "precision breeding." Go through this online tutorial and get started!
Using the interactive tables
The tables in the breeder tool are interactive. You can sort by number or label, ascending or descending. You can also select specific individuals from a matrix of options. You can also sort or filter multiple columns, in any order; e.g., select all females without a specific mutation.
ESSENTIAL CONCEPTS
Measures of diversity and relatedness
The ICB Breeder Tool uses standardized concepts and measures of genetic diversity and relatedness from population and conservation genetics. If you want more information about these analyses, you can find these terms in any population genetic textbook or review paper.
The purpose of the ICB Breeder Tool is two-fold: to help you breed healthy and genetically sound puppies, and to preserve the genetic diversity of your breed. It is based on four key genetic concepts in population and conservation genetics. You will become familiar with these as you use the Breeder Tool and learn more about the importance of genetics in breeding decisions.k here to edit.
The purpose of the ICB Breeder Tool is two-fold: to help you breed healthy and genetically sound puppies, and to preserve the genetic diversity of your breed. It is based on four key genetic concepts in population and conservation genetics. You will become familiar with these as you use the Breeder Tool and learn more about the importance of genetics in breeding decisions.k here to edit.
These essential concepts are:
1) Inbreeding (Coefficient of inbreeding; COI or F): Inbreeding is the probability of inheriting two copies of the same allele from an ancestor, which is called “homozygous”; it is also the fraction of genes that are homozygous. This measure of inbreeding is represented by the symbol F and is expressed either as a number between 0 and 1 (like 0.12), or as a percentage (like 12%).
1) Inbreeding (Coefficient of inbreeding; COI or F): Inbreeding is the probability of inheriting two copies of the same allele from an ancestor, which is called “homozygous”; it is also the fraction of genes that are homozygous. This measure of inbreeding is represented by the symbol F and is expressed either as a number between 0 and 1 (like 0.12), or as a percentage (like 12%).
2) Relative Inbreeding (Fixation index; Fis)
Another way to express inbreeding is relative to the population. This is also called the “fixation index”, which is abbreviated as Fis. In a randomly breeding population, the average Fis is zero. A breeding of two individuals that are more closely related than average reflects selection for inbreeding and will produce a positive Fis. Breeding two individuals that are less related than average is outbreeding, and Fis will be negative.
3) Heterozygosity (Observed heterozygosity; Ho)
In an individual, Ho the average proportion of loci for which the two alleles are different. In a population, the percentage of loci that are heterozygous is called the observed heterozygosity (Ho) and is determined for each locus. Consequently, Ho reflects the genetic diversity of the population.
4) Kinship (k)
Your relatives are your “kin”. In population genetics, we express the degree of relatedness between two individuals using the “kinship coefficient”, which is the fraction of genes that are the same between two individuals. The kinship coefficient of a male and female is the predicted inbreeding coefficient of their litter if they were bred.
Quantification of degree of relationship
We often express the level of inbreeding (COI) using comparisons with family members.
Another way to express inbreeding is relative to the population. This is also called the “fixation index”, which is abbreviated as Fis. In a randomly breeding population, the average Fis is zero. A breeding of two individuals that are more closely related than average reflects selection for inbreeding and will produce a positive Fis. Breeding two individuals that are less related than average is outbreeding, and Fis will be negative.
3) Heterozygosity (Observed heterozygosity; Ho)
In an individual, Ho the average proportion of loci for which the two alleles are different. In a population, the percentage of loci that are heterozygous is called the observed heterozygosity (Ho) and is determined for each locus. Consequently, Ho reflects the genetic diversity of the population.
4) Kinship (k)
Your relatives are your “kin”. In population genetics, we express the degree of relatedness between two individuals using the “kinship coefficient”, which is the fraction of genes that are the same between two individuals. The kinship coefficient of a male and female is the predicted inbreeding coefficient of their litter if they were bred.
Quantification of degree of relationship
We often express the level of inbreeding (COI) using comparisons with family members.
1) First Cousins
A cross of first cousins produces inbreeding of 6.25%; that is, the probability that one of their offspring will inherit two copies of the same allele at a locus that originated from the same ancestor is 6.25%. This also means that about 6.25% of the genes have two copies of the same alleles and are homozygous.
2) Half-siblings
This produces an average level of inbreeding of 12.5%.
3) Full-siblings
Full siblings from unrelated parents produce an average level of inbreeding of 25%
All of these assume that the parents are not related. If the parents are related, then all of these will be higher.
A cross of first cousins produces inbreeding of 6.25%; that is, the probability that one of their offspring will inherit two copies of the same allele at a locus that originated from the same ancestor is 6.25%. This also means that about 6.25% of the genes have two copies of the same alleles and are homozygous.
2) Half-siblings
This produces an average level of inbreeding of 12.5%.
3) Full-siblings
Full siblings from unrelated parents produce an average level of inbreeding of 25%
All of these assume that the parents are not related. If the parents are related, then all of these will be higher.
