Genomics 2.0 – Collaboration Delivers Improvements for December 2018 Evaluations and More

Dr. Marj Faust Data Driven Genetics

Dr. Marj Faust Data Driven Genetics

The genomics 2.0 bovine map is here and while you will see some immediate changes, ultimately genomics 2.0 delivers a number of important improvements for dairy (and beef) genetics now and into the future.  Beginning with December 2018, the U.S. Council on Dairy Cattle Breeding (CDCB) evaluations (trait Predicted Transmitting Abilities – PTA, Net Merit $, haplotype results, etc.), female and bull genotyping results, breed Standardized Transmitting Abilities (STA) for conformation traits, and even Holstein USA TPI® and the Jersey Performance Index™ – JPI results rely on results derived using this new and improved second generation bovine genomics map.

The Bovine Reference Genome Map

The first-generation bovine reference genome map defined genomics 1.0.  This initial map was made available in 2004 and was a key accomplishment of a six-year international collaboration of ~300 scientists in 25 countries coupled with research investments totaling $53m.  The genomics 2.0 map is the first ground up revision of the bovine genomic map in nearly 14 years.  This second-generation map also results from a multi-country collaboration including scientists from several U.S. Department of Agriculture (USDA) laboratories, the U.S. National Institute of Health (NIH), the Universities of California-Davis and Missouri, and commercial companies on two continents.

Genomics 2.0 is a new and significantly more accurate map of the cattle genome.  In our current genomics era, the genome map is very important to dairy genetics because it underpins tools such as CDCB bull proofs, female and bull genotyping results, genomic parentage discovery, haplotype/gene testing, genomic mating programs, breed trait evaluations (STAs), and subsequently JPI™ and TPI® results.

Improvements Made Possible by the Genomics 2.0 Reference Map

By using the new genomics 2.0 reference map, USDA and CDCB scientists have expanded the number of SNP used  in routine genomic evaluations and other CDCB services from ~60,000 to approximately 80,000.  In addition, the SNP derived from the genomics 2.0 map are expected to provide more reliable results across time.  Using the new map, USDA and CDCB scientists also have refined testing for haplotypes/genes affecting fertility.

Outcomes for December 2018 Evaluation Results

What changes from using the new map can we expect for genomic results and related services?  Going forward, for individual bulls, cows, and heifers we can expect more accurate and stable CDCB genomic

evaluations, female and bull genotyping results, genomic parentage discovery, haplotype/gene testing, breed trait STAs, and index values such as NM$, JPI™, and TPI®.  For December 2018, some differences in results from August 2018 can be observed.

  • Bull proofs and cow and heifer evaluation results
    • Across traits, December 2018 results for young genomic bulls are lower on average than respective August results for all breeds.
    • For all breeds, correlations between December and August 2018 evaluation results are very high for animals with records and progeny.
    • Comparable correlations for young animals also are high, but as expected are slightly lower than correlations for males and females with phenotypic data.
    • Despite the high correlations, some re-ranking among elite high genomic bulls and heifers will occur.
    • On the whole, the impact and improvements from genomics 2.0 are greatest in Holstein and Jersey evaluations, both of which benefit from large genotyped reference populations.
  • Haplotype/gene status
    • In every breed and for essentially all haplotype/gene affecting fertility, a small number of animals will change status. For the vast majority of haplotypes/genes, more than 99% of animals will retain their original status.
    • For the ~1% to ~3% of animals of each haplotype/gene test which experienced status changes, most changes are from non-carrier to haplotype/gene carrier status.
  • Trait reliabilities (REL)
    • For Holsteins, trait REL will be more realistic and accurate.
    • A study of REL for Jerseys will be undertaken.

For the dairy industry, the improvements resulting from genomics 2.0 are analogous to the changes we all experience when using a new computer with much improved electronics and chips.  Initially some of the changes may seem difficult to manage, however over time the benefits of the improvements become more evident and continue to deliver value.

We all owe a big “Thank you,” for the public U.S. research funding and expert collaboration that have delivered this innovation in genomic for the dairy and beef industries!

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

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