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Explaining the Difference Between Genomic Panels

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Recently, ASA shared tips to determine which genomic panel is right in various situations, which can be found here.  The following article explains how the different density genomics tests work and why some animals should be tested on higher density platforms. 

When an animal is tested with any genomic test, the result is known DNA markers on a portion of the full genome of that animal. If an animal is tested with a low-density assay (with fewer DNA markers), we can impute (infer) DNA markers up to a higher density if that animal is related to other cattle with high-density DNA marker tests.  

For simplicity, let’s consider an example of a calf tested on a low-density panel with parents tested on a high-density panel.  We can infer some of the DNA markers on the calf based on the markers the parents had.  Think of this as a word bank.  The words would be used to make a sentence, which would correspond with the offspring of that mated pair.

Below you will find the sire and dam’s “word bank” if they had either the ultra-Low Density (33,000 markers), Low Density (47,000 markers), or High Density (150,000 markers). The High Density will give you the most words, the Low Density fewer, and the ultra-Low Density, even fewer. For the sake of keeping this simple, we will not type out 150,000, 47,000 or 33,000 different words, but the following will give you the same idea. 

When the calves of these animals would be tested the lab, we would be able to use these word banks of the sire and dam (if they had been tested)  to figure out what word goes where to form a sentence. At the very end of this, you can see the benefit of the different test, and how the higher tests on parents are very beneficial. When the sire and dam both have a high genomic test this allows you to use lower tests on the offspring while still providing accurate results, which is referred to as “inference”. 

Read through the following lists of words containing the “markers” available for each test:

 

ultra-Low Density

Sire's "markers Dam's "markers"
   
Small Bear
Girl Snake
Noticed Fish
Young Log
Boy  

 

Low Density

Sire's "markers Dam's "markers"
   
Up Bear
Over Snake
Across Log
Rocks Mountain
Sticks Throwing
Large Skipping
Small  
   

High Density

Sire's "markers Dam's "markers"
   
Down By
Boy A
River Side
Ocean The
Up Small
Over Gigantic
Across Tiny
Rocks Bear
Sticks Snake
Large Log
Small Mountain
Noticed Skipping
Young Saw

The following sentences can be “inferred” from the above lists, which is comparable to the process of genomic testing:

ultra-Low Density

_e yo_ _was do_ by _ __ ___in ___s _en he____ the ___ _sh 

 

Low Density

T e you g _y was do_n by _ __e_ _ing rocks _en he ____the __ _sh

 

High Density

T_e yo ng boy was do__ by a ri er sk _ ing rocks when he not ed the large f sh

 

The full sentence, or "genotype" is;

The young boy was down by a river skipping rocks when he noticed the large fish.

 

As you can see, the High Density gives the most complete genotype, as demonstrated by the more complete sentence. The Low Density is next, and the ultra-Low Density gives the least information. This is the reason all AI sires and Donor Dams must have a High Density test, because as high-impact animals we need to be able to infer as much as possible from their genotypes. That isn’t to say all animals need to just have a High Density–many were likely able to construct a sentence from the Low Density example sentence.

As with many things, the above example is over-simplified to make a point.  For genetic evaluation, the genomic markers might be inferred from a population rather than the parents.  In order for low density genomic tests to work well for wide spread use, high impact animals need to have higher density testing completed.  

 

 

 

 

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Down to the Genes Series

Photo credit: Southern Cattle Company

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