Mixed Breed or Single Breed – Genomic Evaluation Results for the Entire Herd

Marj Faust, Data Driven Genetics

Marj Faust, Data Driven Genetics

The saying goes that you can’t manage something if you aren’t measuring it.  This concept is equally valid in dairy management and genetics.  With the dramatic growth in the use of genotyping for heifers and cows, new tools have been made available empowering dairies to better leverage their genetic investment.  For example, herd audits help dairies identify cows that should be bred to beef semen, heifers that should be culled, and donors and recipients for a herd in vitro fertilization (IVF) program.

Until recently, genomic information was available only for animals whose make-up was determined by genomics analyses to be of a single breed (i.e. at least 90% Holstein, Jersey, Brown Swiss, Guernsey, or Ayrshire).  However, new techniques developed by USDA and implemented by the Council on Dairy Cattle Breeding (CDCB) make it possible to obtain genomic evaluation results for mixed breed / crossbreds.  Dairies now have access to genomic information and decision-making tools for virtually all females in the herd.

What the genomic evaluation results represent for mixed breed and crossbred females.

The U.S. system to compute genomic evaluations for mixed breed animals is unique and relies on all-breed traditional evaluations, all-breed genomic evaluations, population and breed parameters, relatedness, and the Breed Base Representation (BBR).  The BBR information is determined for each animal using the animal’s genotype result to estimate the proportion of animals’ DNA from each breed.  Individual BBR information is used in trait blending calculations and in identifying the breed constituting the largest proportion of DNA and thus defining the animal’s evaluation base.

Animals whose ancestors trace to the five listed breeds and their crosses now are eligible to receive genomic evolution results through the CDCB.  In fact, animals that were genotyped and did not receive genomic evaluation results in the past because they were determined to be of mixed breed can have their genotypes resubmitted for inclusion using this new approach.

  • Holstein
  • Jersey
  • Brown Swiss
  • Guernsey
  • Ayrshire

Genomic evaluation results for individual animals are labeled “S” when they are from a single-breed evaluation and “M” when the results represent a multi-breed blended evaluation.

At the trait level for mixed breed and crossbred animals, breed specific differences for groups of traits mean that it is important to clarify what is being reported from this new approach when mixed breed and crossbred animals are genotyped.



  • Production and Management Traits

Mixed breed / crossbred animals receive genomic Predicted Transmitting Abilities (gPTA) accounting for the proportion of their individual DNA from each breed.  This fully integrated and blended approach is made possible in part because for this category the definitions of traits are consistent across breeds.

  • Conformation Traits and Type

Unlike production and management traits, breeds have adopted different definitions of type and individual conformation traits.  As a result of these trait differences where some conformation traits are comparable across breeds and other traits are not, the values reported for mixed breed animals include only the trait genomic data for the animal’s evaluation base breed.

  • Calving Difficulty and Calving Related Traits

By 2019, calving difficulty and calving related trait evaluations are run for the Holstein and Brown Swiss populations.  On the other hand, calving related trait results are not available for Jersey, Guernsey, and Ayrshire bulls or females.  As a result, for the mixed breed genomic evaluation blending procedures were deemed as inappropriate and are not being used.  Instead, mixed breed and crossbred animals with a Holstein or Brown Swiss evaluation base will receive genomic results for calving related traits derived solely from the respective base breed.



  • Health Traits

Genomic evaluations for health traits have been released by the CDCB for Holstein but are not yet available for other breeds.  As health trait evaluations for other breeds are implemented, these data will be used in genomic analyses for mixed breed and crossbred animals.  Today, mixed breed and crossbred animals with a Holstein evaluation base will receive Holstein-derived gPTAs for health traits.

  • Haplotypes Affecting Fertility

At this time, haplotypes affecting fertility will not be reported for mixed breed / crossbred animals.  However, work is continuing to develop methodology that overcomes technical challenges resulting from genetic breed differences in order to provide results with high reliability.

Making use of genomic results for mixed breed and crossbred cows and heifers

      • Use genomic evaluation results to assess and compare the relative genetic merit and value of all mixed breed, crossbred, and purebred / straight bred cows and heifers.For all animals regardless of breed make-up, DNA is passed from parents to progeny. Genetic merit and how individuals compare genetically to herdmates are important when deciding whether individuals should contribute to the herd’s next generation.
        • Identify heifers that should be culled
        • Find cows and heifers that should be bred to beef semen
        • Identify genetically high-ranking females as donors for a herd in vitro fertilization (IVF) program. Lower ranking cows and heifers may then be used as recipients.
      • In a herd with animals from diverse genetic backgrounds, use genomic results to refine grouping and management strategies.
        • Consider breed based maturity patterns when creating breeding pens for heifers
        • In close-up and transition cow pens, consider breed make-up and differences in risks for calving difficulty, milk fever and other transition cow disorders
        • Get an early jump on managing body condition score by incorporating genomic data and affiliated data about breed make-up for grouping and nutritional strategies
    • Incorporate information into mating programs.
    • Use genomic evaluation results to manage backcrossing and rotational crossbreeding programs.
      • Monitor progress across the herd when backcrossing
      • When managing rotational crossbreeding programs, use genomic data and affiliated data about breed make-up to identify service sire breeds for individual cows and heifers

    Genotyping and genomic evaluation results provide dairies with powerful information and decision-making tools for managing and leveraging their genetic investment.  On-going developments and improvements mean that much of the same information and many of the tools available for single breed cows and heifers now can be accessed for mixed breed and crossbred animals.

    Add these genomic tools to the dairy’s toolkit to better leverage and manage investments in genetics across the entire herd.

    Editor’s note: Dr. Marj Faust is a founder and principal of Agri Innova LLC and Data Driven Genetics, where she and her team partner with established and emerging organizations as well as farming businesses globally to build strategy and deliver innovation. She was an R&D executive at ABS Global and Genus plc, served on the faculty at Iowa State University, provided consulting services in regulatory sciences to Novartis/Syngenta Seeds and FASS, and has held leadership posts in several dairy organizations. Readers may contact her with questions or suggestions at [email protected].

You can see the video interview with Dr. Faust on this topic below:

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