NSRDNA

What is the history behind breed composition testing?

Breed composition testing, or breed integrity testing has been in existence for many years. Hampshire, Landrace, and Yorkshire members were once required to perform a physical test mating with their sires to ensure the boar carried no non-breed color. This process took 3 months, 3 weeks, and 3 days for the test litter to be born to verify a sire was free from non-breed color. DNA testing for Halothane 1843 testing, often referred to as the Stress Gene, has been utilized to maintain breed integrity as well, with the NSR Stress Policy dating back to the early 2000’s. In 2004, the Hampshire Swine Registry changed from a physical test mating requirement to a DNA test developed by PIC to ensure no non-Hampshire color existed in AI sires. This policy was amended in 2014 whereby all Hampshire sires had to be tested and pass the DNA Hampshire Color Test. Transitioning to a DNA based-test shortened the time required from ~16 weeks to ~6 weeks.

The DNA Breed Profile Test concept began as a collaboration between Michigan State University, the American Yorkshire Club, the National Swine Registry, and USDA Meat Animal Research Center, conducting multiple genotyping projects with varying goals. One such project had a simple goal: Can DNA technology be utilized to eliminate the need for physical test matings for Yorkshire sires just as the PIC Hampshire Color DNA Test eliminated the need to perform physical test matings on Hampshire sires.

Initial results showed that not only could DNA technology eliminate the need to perform physical test matings on Yorkshire sires, it could also be used as a tool to cluster animals of the same breed into groups and determine breed composition. Below is a graph that shows visually how animals cluster together when DNA information is analyzed with a statistical model:

The processes and procedures utilized in DNA Breed Profile Testing have been well documented in peer- reviewed scientific journal articles.

Badke, Y. M., Bates, R. O., Ernst, C. W., Schwab, C., Fix, J., Van Tassell, C. P., & Steibel, J. P. (2013). Methods of tagSNP selection and other variables affecting imputation accuracy in swine. BMC genetics, 14(1), 8.

Funkhouser, S. A., Bates, R. O., Ernst, C. W., Newcom, D., & Steibel, J. P. (2017). Estimation of genome-wide and locus- specific breed composition in pigs. Translational Animal Science, 1(1), 36-44.

Huang, Y., Bates, R. O., Ernst, C. W., Fix, J. S., & Steibel, J. P. (2014). Estimation of US Yorkshire breed composition using genomic data. Journal of animal science, 92(4), 1395-1404.

Ramos, A. M., Crooijmans, R. P., Affara, N. A., Amaral, A. J., Archibald, A. L., Beever, J. E., ... & Hansen, M. S. (2009). Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PloS one, 4(8), e6524.

Is this a new test?

Development of the DNA Breed Profile Test began in 2009. Development of the Reference Panel and validation from multiple sources of genotyping data led to the American Yorkshire Club Board of Directors voting to implement the technology in 2016.

What boars are being tested?

All Duroc sires born on or after November 1, 2017 must pass the Duroc Breed Profile Test. Sires born prior to November 1, 2017 are grandfathered into the system.

All Hampshire litters born on or after June 1, 2019 must be sired by a boar that has passed their Hampshire Breed Profile Test

All Landrace litters born on or after March 1, 2018 must be sired by a boar that has passed their Landrace Breed Profile Test. Sires meeting previous color requirements (physical test mating) were permitted to sire litters until February 28, 2018.

All Yorkshire sires tested on or after July 1, 2016 must pass the Yorkshire Breed Profile test. Boars meeting previous color requirements (physical test mating) were grandfathered into the system.

What is the criteria for animals to Pass versus Fail?

Yorkshire, Landrace, and Hampshire sires are required to pass both a Breed Composition component and Color component. Duroc sires are required to pass a Breed Composition component. The Breed Composition component is reported as the Whole-Genome Breed Composition (WGBC), which is the percentage purebred an animal is based on its 10K gene marker genotype. The Color component is based on probability of non-breed color at gene locations known to control color: for Yorkshire and Landrace the area of note are genes around KIT and for Hampshires the area of note are genes around MC1R.

Will the Whole-Genome Breed Composition (WGBC) percentages of animals be shared?

Breeders of animals that have passed the Hampshire Composition test will be informed of results and then the results will posted online for the membership. Breeders of animals that have failed will be informed of the results and the percentage at which the animal has failed. Duroc, Landrace and Yorkshire results are reported as Pass/Fail.

Are junior hogs required to be tested for exhibition?

No. Juniors are not required to test their animals before exhibiting their animals. Champions and reserve champions, including Bred and Owned, will however, be tested for parentage, stress, and Hampshire color. All junior champions and reserve champions, including Bred and Owned, will be required to pass their respective breeds’ Breed Profile test effective January 1, 2021.

What is a “Reference Panel”?

A Reference Panel, Reference Population, or as some describe as the “Breed Standard”, is a group of registered purebred animals, as unrelated as possible, and representative of the entire population, that future test samples are compared against.

How was the Reference Panel developed for the NSR Breed Profile Test?

The NSR Reference Panel was developed as part of a larger research project conducted by Michigan State University to determine Linkage Disequilibrium in swine. Linkage Disequilibrium is the non-random association of gametes at different genetic locations, or more simply stated, how genes closer to each other in the genome move from generation to generation.

The initial NSR Reference Population consisted of 25 – 30 Sire-Dam-Offspring Trios for each NSR breed (Duroc, Hampshire, Landrace, Yorkshire). The trios were selected to be as unrelated as possible, where possible sharing no ancestry two generations back in the pedigree and as representative of each breed as possible. An effort was made to have representation from different “lines” or segments of each breed: show-oriented, commercially-oriented, “Old-line”, etc. In total, 117 trios across the four breeds were evaluated. Key to note, the NSR Reference Panel is built around representative animals from all four breeds. From the NSR Reference Panel, the probability that a particular gene marker is associated with a particular breed was determined – combining each of these probabilities across all ~10,000 gene markers to develop the algorithm used to calculate the breed composition of future samples.

The reference panel is updated annually with animals that have passed the test in the past year.

How was the test validated?

Initial validation was carried out utilizing sires from each NSR breed (already genotyped for a different research project) that had been selected for having large numbers of daughter records, thereby being influential in their respective breed. In addition, crossbred and non-registered Yorkshire animals that were known to be crossbreds or had failed a physical test mating were also evaluated. Also, a large number of Yorkshire sires genotyped in conjunction with a genomic selection project were also utilized. Results of this validation are available from:

Huang, Y., Bates, R. O., Ernst, C. W., Fix, J. S., & Steibel, J. P. (2014). Estimation of US Yorkshire breed composition using genomic data. Journal of animal science, 92(4), 1395-1404.

How did the Breed Boards decide to implement the test?

Prior to presenting results to each breed board for implementation, Michigan State researchers determined there was sufficient coverage of the diversity within the breed from all the animals genotyped. Each breed Board of Directors was presented background information regarding the science behind the technology, development of the Reference Panel, and validation results from the test.

For each breed, a Validation group of animals was selected to determine if the test could detect both purebred and crossbred animals. Purebred animals, influential sires, known (by pedigree) and unknown (look-a-lines) crossbreds, and animals that had failed previous tests (physical test mating, Stress, Hampshire Color Test) were genotyped and evaluated using the DNA Breed Profile Test procedure. Results from these validation tests were presented to each breed board, recommendations for Pass/Fail criteria were made, and the requirements for implementation were voted upon.

The pedigrees from each breed were adequately represented in the reference population to a degree that the Michigan State researchers determined that the test for each breed was reliable as confirmed by the validation testing. 

Can two animals which pass the DNA Breed Profile Test produce offspring that fail?

Yes, two parents which both pass the DNA Breed Profile Test may produce offspring which fail. Except in the case of identical twins, no two siblings (full-sibs or littermates) receive the exact same 50% of genes from their sire and dam. Genes segregate randomly when sperm and eggs are developed, so siblings may receive more or less non-breed genes.

This situation is similar to two parents, both with 6-6 underlines, producing an offspring with a 5-5 or 6-5 underline – both of which are ineligible to exhibit as a breeding animal (and results in pedigree cancellation in the Yorkshire and Landrace breeds). In addition, two perfectly belted Hampshire parents can produce offspring with broken/off-belted appearance or too much white color, both of which make an animal ineligible to be exhibited as a breeding animal.

How long does it take to receive results from testing?

Conservatively it takes 6 – 8 weeks to receive results. However, depending on timing the process can take as few as 4 weeks. NSR ships samples to the lab each Friday; stress testing is completed the following week. Samples are then grouped into batches of 24 for genotyping and the genotyping process takes 10 business day turnaround time. Factors that affect timing are mail schedule, holidays, sample quality, and how long it takes to group 24 samples for genotyping.

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As a result of the United Duroc Swine Registry Board of Directors decision, all Duroc boars farrowed on or after November 1, 2017 must pass the Duroc DNA Breed Profile Test in order to be used as the sire of a registered litter.  This is in addition to HAL-Stress testing requirement. Please keep in mind, results from this test can take approximately six to eight weeks from the date the sample is received at the lab.  Please plan your litter registrations accordingly and submit DNA samples for Duroc boars early.

Animals submitted for testing MUST have an NSR registration number.  For pricing on registration and DNA testing please click here.

For any other questions, please contact the Vice President of Genetics & Technology, Dr. Doug Newcom (newcom@nationalswine.com) or DNA Secretary, Whitney Webb (whitney@nationalswine.com). 

As a result of the Hampshire Swine Registry Board of Directors decision, use of the Geneseek Hampshire DNA Color Test procedure has been discontinued and replaced by the Hampshire DNA Breed Profile Testing procedure as a requirement for a Hampshire boar to sire a registered litter. All litters born on or after June 1, 2019 must be sired by a boar that has passed the Hampshire Breed Profile Test. Please keep in mind, results from this test can take approximately six to eight weeks from the date the sample is received at the lab.  Please plan your litter registrations accordingly and submit DNA samples for Hampshire boars early.

Animals submitted for testing MUST have an NSR registration number.  For pricing on registration and DNA testing please click here.

For any other questions, please contact the Vice President of Genetics & Technology, Dr. Doug Newcom (newcom@nationalswine.com) or DNA Secretary, Whitney Webb (whitney@nationalswine.com).

As the result of an American Landrace Association Board of Directors decision on March 28, 2017, ALL Landrace sires must pass the DNA Breed Profile Test before any litters can be recorded, effective with litters farrowed on or after March 1, 2018 (breeding date ~November 1, 2017). No sires with litters previously recorded, or passing the previous stress or physical test mating requirements are exempt. Sires passing previous requirements, but failing the current requirement will not have their pedigrees cancelled – however, their progeny farrowed on or after March 1, 2018 will NOT be eligible for registration.

The same blotter card used for Stress testing and DNA banking will fulfill this requirement. The card currently banked for sires previously stress tested can be utilized for this DNA Breed Profile test. Please keep in mind, results from this test can take approximately six weeks from the date the sample is received at the lab. Please submit DNA samples for Landrace boars early. Please contact DNA Secretary Whitney Webb (whitney@nationalswine.com) to order your previously banked sire sample tested as soon as possible to meet the new requirement.

Animals submitted for testing MUST have an NSR registration number. For pricing on registration and DNA testing please click here.

This new requirement replaces the current physical test mating requirement. Stress testing will still be required under the updated Sire Eligibility Requirements

For any other questions, please contact the Vice President of Genetics & Technology, Dr. Doug Newcom (newcom@nationalswine.com) or DNA Secretary, Whitney Webb (whitney@nationalswine.com).  

As the result of an American Yorkshire Club Board of Directors decision, ALL Yorkshire sires must pass the DNA Breed Profile Test before any litters can be recorded, effective with all DNA samples submitted on or after July 1, 2016. All current Yorkshire sires with a completed Physical Test Mating form on file, or have had previous litters recorded, are exempt.  This new requirement replaces the previous statute that only A.I. Service sires were required to have a completed Physical Test Mating.  The same blotter card used for Stress testing and DNA banking will fulfill this requirement.  Please keep in mind, results from this test can take approximately six weeks from the date the sample is received at the lab.  Please plan your litter registrations accordingly and submit DNA samples for Yorkshire boars early.

Animals submitted for testing MUST have an NSR registration number.  For pricing on registration and DNA testing please click here.

For any other questions, please contact the Vice President of Genetics & Technology, Dr. Doug Newcom (newcom@nationalswine.com) or DNA Secretary, Whitney Webb (whitney@nationalswine.com).  

During the National Swine Registry Executive Committee Meeting in March 2019, two innovative and exciting services were proposed and approved. Effective July 1, 2019 the NSR will offer crossbred boar DNA banking and crossbred litter recording services to its members. These services will be completely voluntary and are an opportunity to provide NSR members with increasingly high demand resources. Additionally, these services are an integral part of the NSR’s Long Range Strategic Plan.

MORE INFORMATION

NSR has updated policy on sire DNA requirements for recorded litters, effective Jan. 1, 2010. This change applies primarily to situations where a sire has died or was culled before DNA was collected, but also to instances where the DNA lab is unable to obtain a test result due to poor DNA quality. This can also apply to frozen semen from a sire that may not have a DNA sample on file, or it is too degraded to obtain quality DNA for genotyping. Since Jan. 1, the following must be met to satisfy the sire DNA requirement in instances where a quality sire DNA sample is not available:

1. A minimum of four (4) pigs from the litter must be DNA banked and tested according to the breed’s current DNA requirements. If there are less than five (5) head in the litter, 100 percent of the litter must be tested.
2. OR, if the dam of the dead boar is available, a sample from her may be tested.

Tests cannot be done overnight, so plan accordingly for registrations and show or sale deadlines.

As a requirement for registration of litters that are farrowed on or after July 1, 2004, all sires (Duroc, Hampshire, Landrace and Yorkshire) must have a negative stress status on file (by DNA test) before the litter can be registered. No animals will be grandfathered in with this policy.

1. As of April 1, 1998, no known stress positive or stress carrier animals will be allowed to be exhibited or sold at any NSR-sponsored event. (If an exhibitor places this information on his pen card or states that this animal is a stress positive or a stress carrier, he will be asked to remove this animal from the barn, and he will not be allowed to exhibit or sell this animal.) If any animal sold at a NSR-sponsored event is found to be stress-gene positive or a carrier of the stress gene, the purchaser has the right to receive a full refund of the purchase price.
2. DNA testing for the stress gene must be done within 90 days of the sale, and all cost associated with this test must be paid by the purchaser. The seller has the right to review the test results and the right to re-test the animal at a laboratory of his choice. Cost associated with the re-test by the seller is at the seller’s expense. There will be no refund of NSR commission from stress-positive or stress-carrier animals. * As of Jan. 1, 2000, the NSR requires the DNA stress gene status of A.I. sires to be declared on all A.I. Certificates issued for the registration of litters. All A.I. certificates issued after Jan. 1, 2000, must include the HAL 1843 test status of the sire, regardless of when the boar was placed in service. Test results must be reported as one of the following: 1) nm=normal, 2) mm=carrier, or 3) dm=homozygous positive. The NSR also recommends that owners of A.I. sires make this information available in their promotional literature.

In addition to the previous steps, the following policy was adopted by the Board of Directors of the American Yorkshire Club, the American Landrace Association, the United Duroc Swine Registry and the Hampshire Swine Registry with the effective dates indicated.

1. Any Yorkshire or Landrace that is farrowed on or after Jan. 1, 2000, that is proven to be a stress positive or stress carrier by a documented DNA test from a certified lab, will have its pedigree cancelled. Any Duroc farrowed on or after Jan. 1, 2001, that is proven to be a stress positive or stress carrier by a documented DNA test from a certified lab, will have its pedigree cancelled. Any Hampshire farrowed on or after Jan. 1, 2002, that is proven to be a stress positive or stress carrier by a documented DNA test from a certified lab, will have its pedigree cancelled. The purchaser has the right to receive a full refund of the purchase price. DNA testing for the stress gene must be done within 90 days of the sale, and all cost associated with this test must be paid by the purchaser. The seller has the right to review the test results and the right to re-test the animal at a laboratory of his choice. Cost associated with the re-test by the seller is at the seller’s expense.

Any warranty regarding the stress gene status of the animal is solely that of the seller and not that of the American Yorkshire Club, American Landrace Association, Hampshire Swine Registry or the United Duroc Swine Registry. The American Yorkshire Club, American Landrace Association, Hampshire Swine Registry and United Duroc Swine Registry assume no liability in connection with such warranty by the seller.

As the result of a NSR Executive Committee decision, all sires must be DNA banked before any litters can be recorded, effective with all litters farrowed after July 1, 2002. This new requirement will provide for the establishment of an incredible DNA data bank for the four NSR breeds, as well as help us in our effort to maintain breed purity.

This decision was made after much discussion, and was the result of a recommendation from the NSR Shows and Services Advisory Board, where it passed unanimously. All segments of our industry have weighed in on this issue, and it appears to be helpful for all members in the long run. Through the establishment of this DNA resource bank, Yorkshire, Duroc, Hampshire and Landrace breeders will have access to the largest and most-diverse DNA parentage bank in the industry.

As we continue to uncover more information about the genetic make-up of our hogs, and as the genetic map is more clearly defined, NSR members will be in a position to take advantage of any new discoveries that may impact genetic selection in the future. Whether it might be in the area of pork quality, disease resistance or production traits, the development of new genetic markers can quickly be matched to our existing genetic lines. It will position our breeds to once again be the leader in genetic improvement.

In addition to the selection opportunities it provides, this DNA data bank will also help maintain the purity and integrity of our breeds. This data bank might be utilized to verify the parentage of a pedigreed barrow that was named champion at a major show. On the other hand, it might be used to help a breeder, who after losing his breeding records, needs to use the DNA genotypes to match up offspring on some matings. Regardless, this DNA information will be a valuable resource to all of our breeds and members.

In an effort to minimize the expense and time required for this new regulation, your NSR Executive Committee has approved the use of “blotter cards” for the collection of this DNA material. Rather than contacting your veterinarian to draw blood from each of your sires, you will simply prick the ear of your animal and dab a small amount of blood on a blotter card, and submit to the NSR office for storage. There will be a nominal fee for each sample submitted to help defray the costs of the blotter card and storage records.

Please contact the NSR office to request the blotter cards for your boars that need to be DNA banked.

These instructions are intended to assist National Swine Registry breeders in collecting samples for submission to the NSR office and meet DNA requirements for sires when registering purebred Duroc, Hampshire, Yorkshire and Landrace litters. If using a blotter card, only OFFICIAL NSR Blotter Cards will be accepted. Cards must be purchased from the NSR office.

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