How does parent verification work?

The November issue of the Register contained a Down to the Genes article focused on parentage testing.  Here we republished a blog post with more in depth information on how the parentage analysis works and a hands-on example where readers can work through who is the correct sire.

By Jackie Atkins, Ph.D., Director of Science and Education

Originally published on the ASA Science blog, Mar 7, 2016.

Whether you use parent verification to confirm your breeding records, distinguish between AI and pasture bred calves, or to sort through progeny from a multi-sire pasture, parental validation is an important test for breeders.  Roughly 10% of pedigrees reported across all breed associations are inaccurate.  These are frequently honest mistakes but never-the-less, vital to fix and make informed breeding decisions.  The theory behind parental validation is to determine if an animal could have inherited specific DNA markers from their reported parents.  If the animal could not inherit a specific DNA Marker from the sire or dam, then the parent is excluded.  With enough qualified markers, an animal is confirmed as the sire or dam of the offspring.

In the past, 15 microsatellite markers (also called Short Tandem Repeats or STRs) were used to confirm parentage but these were costly and not always reliable tests.  Most new parental validation is completed with single nucleotide polymorphisms or SNPs (pronounced “snips”).  The SNPs are locations in the DNA that vary from one animal to another.  The SNP parentage test uses over 100 SNP markers to either qualify or exclude an individual as a parent.  Each animal has two markers at each SNP location (one on each pair of chromosomes representing one from each parent).

Let’s work through a hypothetical example using SNPs for parental validation.  We have test results for SNPs on a calf, two possible sires, and the likely dam.  We look at each SNP and see if the calf could have inherited that SNP from the possible parents and also if the mating (the parents analyzed together) could have passed along those SNPs.  The following diagram and table show four SNP markers for the individuals and the conclusions drawn.


Example of 4 SNP markers for a calf and his potential parents.  See the table and text for explanation of the analysis.


Hypothetical SNP markers at 4 locations for a calf and his potential parents.  See text for further explanation for the conclusions drawn.

Working through each SNP marker, we look if the calf could have inherited his DNA markers (genotype; options are A, T, C, or G) from the potential parents.  At SNP 1, the calf has a genotype of A/T.  This means the calf inherited an “A” from one parent and a “T” from the other parent.  Both the Dam and Sire 1 are homozygous T and SNP1.  This means they could only have passed along a T at this location.  The potential dam and Sire 1 could not have conceived the calf together as neither could have passed along an “A” at this location.  However, we can’t exclude either the dam or Sire 1 based on this information, we just know that they can’t be confirmed as the parents together.

Continuing through our analysis, we cannot exclude any of the parents with SNPs 2 and 3 because the pairing of both sires with the dam could pass on the calf’s SNP markers.  Looking at SNP 4 is helpful.  The calf has two “T”s at SNP 4, one from his dam and one from his sire.  Sire 1 has two “A”s at SNP 4 so he could not have passed along a T at this location.  Sire 1 is excluded based on this comparison.  If Sire 1 is excluded, then the potential Dam and Sire 2 work for the remaining SNP locations.  The parental validation at the lab uses the same logical progression as this simple example except it uses approximately 100 SNP markers for the analysis.


Spring 2019 THE is Now OPEN!

We’re not sure about the weather in your neck of the woods, but the snow is already flying here in Montana and that can only mean one thing…Total Herd Enrollment (THE) season has arrived! It’s time to enroll your spring calving females. As of Monday, October 15, Spring 2019 THE enrollment is OPEN.


Any females of calving age that will calve between January 1, 2019 to June 30, 2019 will need to be enrolled by December 15, 2018 to take advantage of the lowest enrollment fees.  ALL members previously enrolled in Total Herd Enrollment MUST submit an inventory even if there are not any changes/updates to enrolled females. If you submit an enrollment today, you will be able to adjust your inventory online through Herdbook Services up until the deadline of December 15 as many times as you wish. There’s absolutely no reason not to go ahead, fill out an inventory today and submit it well before the deadline.

Our THE motto is: don’t delay, enroll today! To download step-by-step enrollment instructions click here. For a refresher on the four THE enrollment Options offered click here.

Need a quick refresher on how to get a job started? Look no further!

Quick Instructions

  1. Select Herdbook Online Services

  2. Log In by entering

  • 6-digit member number (zero filled example: 000317)

  • Password

  1. Under Data Entry select Online

  2. On the inventory tab make sure the year selected is 2019 and the season is Spring

  3. Choose Update 2019 – Spring THE Cow Inventory button

– This will load your preliminary inventory into the spreadsheet with a row for each female

  1. At the top right hand corner, select Options, Auto Fill
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  2. Under Column 1 select THE-A/B/C/N and in the blank box to the right fill in the Option you are enrolling in, for example A

  3. Under Column 2 select THE-Bill Code and in the blank box to the right fill in either an H for half of the fees or an F to pay the full amount now
    Screenshot from 2018-04-27 10-11-23

  4. Select Auto Fill

  5. Now go down your inventory and for the dams being removed place a removal code in the primary code column and change the A/B/C/N column to an N

  6. For dams being enrolled, enter in an enrollment code in the primary code column or leave blank if no special code is needed. Keep in mind if the dam is a commercial female or registered with another breed association you can enroll them in any option, regardless of how the registered Simmental females are enrolled.
    Screenshot from 2018-04-27 10-23-00

  7. Add any additional females at the bottom of the job on a blank row by their ASA registration numbers. If a blank row is not available, click the cursor in to the last row and hit your enter key a few times to create blank rows

  8. Please see numbers 15-16 below for instructions on how to submit your job through completion

Detailed Instructions (use 1-5 listed above)

  1. Update Inventory

  • If the dam is remaining in your herd, enter appropriate Enrollment code in Primary Code column or leave blank if no special code is needed

  • If the dam has been removed from your herd, enter a Removal Code in the Primary Code column. To designate a second reason for removal (optional), you may enter a Removal Code in the Addtnl Code column as well.

  • A/B/C/N Enrollment Type If you are enrolling in Option Aplace an A in this column. For Option Bplace a B in the column. For Option C place a C in this column. For Option D place a D in this column. If the cow is being removed from the herd place an N in the column.

  • Remarks You may use this column if you wish to have additional remarks on a dam. This column is for member use only, ASA will not adjust enrollment based on this column.

  • Bill Code This column is to be used by members to indicate how you would like to be billed for your enrollment. A “H” in this column indicates you wish to pay half the enrollment fee at time of submission. The other half of the fees will be billed in the second half of the same year. An “F” indicates to pay the full THE fee at the time of submission. If nothing is entered or column is left blank, a “F” is assumed.

  • To add cows: (Scroll down to a blank row. If you do not have a blank row, click on your last dam and hit your enter key. This will create a blank row.)

      • Cows on file with ASA*, enter ASA number in AnmRegNbr column

      • Cows not on file with ASA*, enter tattoo in the AnmTatt column, enter birthdate in BirthDt and breed(s) in Brdcds column.

*Please note: If your dam has had a calf reported to her or has been enrolled in THE previously, she will have a number in ASA’s system. Please enter that number into the AnmRegNbr column so that a new dam record does not get created.

  1. If there are Errors and/or Warnings

  • Errors (indicated in red at beginning of row) or Warnings (indicated in purple at beginning of row)

  • Move cursor to the top of spreadsheet and select tab labeled Errors or Warnings

      • Screen will display each error or warning

      • Errors must be corrected before submitting data to ASA

      • Warnings may need to be corrected before submitting to ASA

      • Jobs may be submitted to ASA with warnings, but not errors

Once all cows have been given an enrollment or at least one removal code and
there are not any errors, select Submit Data

  •  A new page will display; if there are no errors, a Proceed to Billing link will
    be available
  • Select the Proceed to Billing link to display a billing summary. THE is billed
    at the time of submission, so you will have an invoice amount due if you are
    enrolling in Option A or C (after the first deadline all options (A, B or C) will
    have a balance due).
  • Choose one of the following to complete your job:
    • If you wish to complete payment with a credit card select Add
      Payment. Enter in your credit card information and select confirm.
      You will then need to select the button Final Submit (Only click
      once). A screen will then show an invoice that you can print and store
      in your records. It should also say Invoice Status : Complete.
    • If you would rather mail a check to ASA or make payment later, select
      Final Submit. A screen will then show an invoice with the current
      amount due that you can print and store in your records.
  1. To save job and return later, select Save and Exit. The job will remain in an incomplete status under your account. Please be aware that billing will work off the submission date, not the date the job was initiated.

***Please double check to make sure your inventory job is complete. If you go to Data Entry, select Online and on the left hand side choose Incomplete Jobs. If your

Inventory Dam 2019 S job is listed with a button that says Resume, it is at an incomplete status. Select Resume and submit your job through completion.

  1. Submit your inventory by June 15, 2018 to ensure the lowest possible THE

enrollment fees. All rates are listed below.

Option A (TR) Option B (SR) Option C

On/Before December 15    $15.00     FREE      $7.50

After December 15      $16.00      $1.00      $8.50

*If you miss the December 15, 2018 deadline and were enrolled for Spring 2018:

  • All of your dams on the preliminary inventory generated by ASA will be enrolled in Option A at $16.00 each.

  • Members will have until February 1, 2019 to make adjustments to their inventory (the same way as enrolling) including a choice to change from Option A to Option B or C. (THE fees will be adjusted if you change to Option B or C within the 30 days).

Note: If adjustments are not made by February 1,2019 your preliminary inventory will be accepted as is (including enrolled in Option A, regardless of previous year’s option). There is a $1.00 late-enrollment fee that will not be refunded.

**Remember, you cannot delete females from your job, if the female is listed she needs to be updated as enrolled or removed.

If you would prefer to submit an inventory either by email or paper submission contact our office, and we can make the necessary arrangements. If you have specific enrollment questions or need assistance cleaning up errors, please email or call our office at 406.587.4531 and ask to be connected to THE department.

Posted in THE

Top Tips for Taking Blood and TSU Samples

Sample failure can often be prevented by ensuring the sample collection process is correct.

With mail time, DNA testing can take around 2 months. FedEx’ing kits from ASA to members, and from members to the lab, can cut down this time. However, if a sample fails this time is doubled.

Below are tips for taking blood and TSU samples.

Please find the Down to the Genes article, “Common Reasons for Delays in DNA testing”, in the October issue of the Register for more information.


DNA Updates: Pricing, Kits Sent FedEx, and More

DNA and genomic testing provides valuable insights to animals in a relatively short period of time.  By using genomics, breeders can have EPDs as accurate as cattle with 20 or more progeny records (depending on the trait).  All this can be accomplished while the calves are still nursing. The DNA services at the the ASA have grown and the ASA is putting in measures to continue to make our customer services more efficient and more accurate. 

Here are some recent changes to the DNA services:

    1. Billing at the time of kit or DNA test request started Sept.1.  In order to more efficiently and accurately bill for DNA tests, the ASA is now billing at the time of the kit or DNA test request. Keep in mind, this means members may be billed twice if kits are ordered twice for the same animal.  Billing up front gives members a chance to correct any mistakes prior to the test being ran. Billing up front is also more efficient allowing for more ASA staff time spent uploading results or on other customer service needs.
    2. New DNA pricing:  To cover the ASA’s cost, members will be charged $1.00 per blood card, $2.00 per sample pull, and research fees ($1/minute) associated with DNA work outside the regular procedures, for instance misidentified samples or samples showing up to the laboratory without proper paperwork.  A sample pull refers to the process where a DNA sample that was previously tested needs to be pulled from the archive for a newly requested test. Many DNA results are available as “add on” content from genomic tests (for instance coat color). These “add-on” results would not be subject to the sample pull charge.
    3. Automatic 3-day FedEx shipping for kits.  Due to delays in transit times, the ASA will now automatically ship kits via 3-day FedEx, charged to the member account.  Members can request to use US Postal service but the default will be for FedEx 3-day shipments starting Monday, October 1. 
    4. Genomic data schedule and review.  With the IGS Multi-breed Genetic Evaluation powered by BOLT, all genotypes available by Monday will enter into the evaluation which is completed and published that weekend.  If genomic data is completed on a Wednesday, the parentage results may be uploaded into Herdbook that week but the genomically enhanced EPDs will not be available until the following week’s evaluation (9 to 10 days later).  Also, the genomic data goes through a quality control process prior to entering the genetic evaluation. Some of the genotypes will be removed as they do not meet the requirements for the evaluation. If breeders notice animals that are missing genotypes, please notify the ASA ( for next steps to resolve these cases. This schedule and QC process are more reasons to start testing as early as possible.   
    5. New staffing.  Robin Marston recently joined the DNA department and will help with DNA customer support.  Marston has previous experience working in another breed association’s DNA department and is very familiar with seedstock breeders, DNA services, and working with genotyping companies.  Marston joins Lilly Platts and Riley Foster to provide ASA members with timely and quality DNA services.

Please email or call 406-587-4531 with any questions.


DNA Timeline, Requirements, and Top Tips

By Lilly Platts, Jackie Atkins, Riley Foster, and Leoma Wells

Everything you need to know about ASA’s DNA Services & more. This is an extended version of the first installment of ‘Down to the Genes’ published in the September 2018 issue of the Register.  This article covers frequently asked questions and offers tips for a smooth DNA process. For additional FAQ’s and information, see the September issue of the Register.

When do I have to DNA test an animal?

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I purchased semen, are those selling semen monitored by ASA to ensure HD/150K testing?

No. Breeders are responsible for completing ASA’s testing requirements. It is strongly suggested that buyers of semen ensure a bull has all required testing prior to purchasing semen and breeding cows.

Do ASA’s genetic defect testing requirements match those put in place by sales management and bull tests?

Not always. Sales managers and bull tests may require additional testing depending on their requirements. It is always best to follow up with the specific sales manager or bull test on the testing requirements prior to ordering DNA kits from ASA to ensure the animal can be sold through that venue.

Do other associations require the same testing?

Each association has different requirements. If a sire/dam is registered with ASA from another breed certificate, additional testing may be required to register progeny. Make sure to contact ASA with any questions prior to progeny being born to avoid delays at registration time.


Take home message:  Do not delay your DNA testing – order your kits today!

Ten things you can do to ensure a smooth DNA testing process:

  1. Familiarize yourself with ASA’s DNA testing requirements.
  2. First contact the sale, bull test, show, etc., you may participate in to be clear of their DNA requirements.
  3. Order kits early (at least two months before you need results) by contacting the ASA – or 406-587-4531. Please follow instructions and have all required information before calling.
  4. Use a blood card, TSU, or hair card for collection. NEVER send vials of blood, bags of hair, etc. to the lab.
  5. Follow the instructions for collection included with your kits. Failure to collect the samples properly may result in samples failing testing – watch for more information in the October issue.
  6. If you make a mistake, i.e. collect sample from the wrong animal, etc., do NOT send the sample to the lab. If you do, contact ASA immediately.
  7. Never send kits to the lab without either ordering them for specific animals, or if you have blank kits, always complete paperwork with the DNA department first.
  8. Send samples to the lab as soon as they are ready. Getting them out the door ensures faster processing and less time for paperwork to get mixed up.
  9. Check your email for results.
  10. If you have a question, ASA is happy to help. Please have your membership number and information on the animal you are inquiring about (ASA number, tattoo, etc.).


Fall 2017 – Calf Data Reporting and Compliance

Fall 2017 compliance reporting is now in effect. What does this mean? It means that each dam enrolled on your Fall 2017 THE inventory needs to either have a calf reported or a productivity code (the reason why she did not calve). If the reporting requirement has not been met, your account is considered to be in non-compliance and you will not be able to process any registrations/transfers until the data has been turned in. There are three ways to submit the compliance information: online, spreadsheet or by paper submission.


Log-in to Herdbook Services
Go to Data Entry, select Online
There are four tabs on the left, select the bottom one, Manual Job
Under Job Type, leave it as selected in Animal Data Reporting
Enter in a Job Title, i.e., Last of 2017 calf data
From the right under default groups, select the last one, Dams Not in Compliance
Click the black dot into As Dams
Select Start New Job
This will start an online job that lists all of the dams lacking data for the 2017 fall calving season or any *prior seasons. If the dam had a 2017 born calf you will enter the calf information. If she did not calve, report a productivity code and the productivity year as 2017.
*If you are out of compliance for more than one year please contact ASA for assistance.
Screenshot from 2018-04-02 09-20-13

Keep in mind, if you are not reporting a 2017 calf record, you will need to record a productivity code for the female indicating why she did not calve in the calendar year 2017.  The productivity columns are located under the BrthDam tab.  Click on the Productivity column header for a help box that displays the 11 different codes you can choose from.  Next, you will need to fill in the productivity year, which in this case would be 2017.  By reporting a productivity code, you are informing the database that this dam did not have a calf in the calendar year 2017.  There will not be any calf data information listed under the Animal tab for this female, just a productivity code and year under the BrthDam tab. Note: A productivity code should only be used if there is not any calf data to report for the given year and cannot be used in addition to calf data, it’s either a calf is being reported or a productivity code, not both.

Dam Prod (Dam Productivity) – Use if there is no calf to report
1 = Calf/Calves Stillborn
2 = Aborted
3 = Not Exposed to calve in given season/year
5 = ET Donor
6 = ET Recipient
7 = Exposed and Failed to Conceive—Moved to Next Season
8 = Exposed and Failed to Conceive—Moved to Next Year
9 = Exposed and Failed to Conceive—Removed from Herd
10 = Calving Interval Overlaps Season (Dec-Jan) (Jun-Jul)
11 = Bred—but Sold, Removed or Died Prior to Calving
12 = Cow Calved—Calf Not Found Intact or at All
Productivity Reporting

If you prefer to work on your data reporting offline(in an excel spreadsheet) follow these steps to download the non-compliance females in to a working template.

Download/Upload Spreadsheet

Log-in to Herdbook Services
Go to Data Entry, select Download
From the left under default groups, select the last one, Dams Not in Compliance
On the right under Animal Entry, select Standard File
Under Download File, select As Dams
Select Document type, i.e., MS Excel
Select Download
This will open a spreadsheet that lists all of the dams lacking data for 2017 fall calving season.  If the dam had a 2017 born calf you will go ahead and enter the information.  If she did not calve, report a productivity code and the productivity year as 2017.  After you have filled in the spreadsheet with the necessary information you can either go back to Herdbook Services and upload your file or email to and we can process it for you.
Screenshot from 2016-04-08 10:08:00
If you refer to submit the information on paper submission forms, contact ASA and request a non-compliance packet be mailed out to you.  You will receive a form containing all of your dams that need data reported for 2017 along with any other years your herd is missing data.
Once the non-compliance information has been entered, your account will immediately be considered to be in compliance with THE reporting requirements and you will be able to submit registration/transfers requests at will.
If you have any questions or concerns about THE and compliance reporting please email or contact our office at 406.587.4531 and ask to be connected to THE department.

Fall 2018 THE – Late Enrollment

If ASA did not receive a completed inventory submission for Fall 2018 THE by the deadline of June 15, 2018, and you participated in Fall 2017 THE, your herd was late enrolled on July 5, 2018. Your account was invoiced $16.00/dam for each dam listed on your preliminary inventory. The good news is you have 30 days to adjust your inventory for credit. Continue reading for instructions on what needs to be done.

IMPORTANT: You have until August 15, 2018, to adjust your inventory for credit.  An inventory update can be submitted online, or by email, fax or mail.

If you submit an adjusted inventory prior to August 15, 2018, here’s what you can expect to happen.

Option A: Enrolled dams will be invoiced $16.00/dam. Removed females will be credited the full $16.00 fee that was charged initially.

Option B: Enrolled dams will be invoiced $1.00/dam. Removed females will be credited the full $16.00 fee that was charged initially.

Option C: Enrolled dams will be invoiced $8.50/dam. Removed females will be credited the full $16.00 fee that was charged initially.

To get started, log-in to Herdbook Services and submit an adjusted enrollment today by following these steps.

Go to Data Entry, select Online
There are 4 tabs on the left, you should be on Inventory
Below the calf reporting graph there is a blue button that says
Update 2018 – Fall THE Cow Inventory
Screenshot from 2018-07-06 09-17-48

This will start an online job that lists each female enrolled from your preliminary inventory. You will need to update each female on the list with a primary code. If the dam needs to remain on enrollment, assign her a code between 0-6. If the dam needs to be removed, assign her a code between 60-82. Remember, if you remove a female from enrollment(code 60-82) and at a later point need to report a calf to the female, there is a $35.00 re-enroll fee that will apply. Make sure to only remove females that have physically left the herd. For a list of enrollment/removal codes, click on the blue column header for Primary Code and a help box will come up. You may need to scroll down to view all the codes.

Since your dams were late enrolled, each of them loads with a T in the A/B/C/N column.  If the female is remaining on enrollment, you will update the T to either an A, B, or C, depending on which option you’re enrolling in for 2018.  To review the different enrollment options, click here. If the female is being removed from inventory, update the T to an NN stands for not enrolling, removed from the herd. If the female needs to be be moved back to Spring 2018(calved January 1-June 30) please email her ASA number to and ask for us to move her. We will respond once she has been moved to Spring 2018. If you wish to pay half the enrollment fee that is due now and be invoiced for the other half in March 2019, make sure to place an H in the BillCode column on at least one female you are enrolling.  If you leave the BillCode column blank it will default to invoice the full amount due. Once you have updated each female on the list, go to the top right-hand corner of your screen and select Submit Data.  It will run through error checks and one of the following two things will happen.

1) A button that says Proceed to Billing will appear. Click on it, which takes you to the invoicing screen where you will be issued the credit of $16.00/dam and then charged according to how many dams/which option they’re being enrolled in.  Either select Add Payment(enter in debit/credit card for payment) or Final Submit so the job finishes through completion.
2) A button that says *Edit Job appears, this means there are errors in your job that need to be corrected before it can be submitted.  Click on Edit Job, which takes you back to your spreadsheet so you can fix the errors.  If you need assistance cleaning up errors please contact our office at 406.587.4531 and press the number 5 to be connected to THE department. *It is possible the edit job button appears because your account is not in compliance with 2017 spring calf data reporting or previous years. If that happens, click here to view examples on how to clean up compliance.

If you prefer to complete your adjustment via paper submission THE packets will be mailed out on July 10, 2018.  Fill out the paper enrollment and postmark to ASA by August 15, 2018.