Enhancements to U.S. genetic and genomic evaluations in 2018 and 2019

  • Ezequiel Luis Nicolazzi Council on Dairy Cattle Breeding https://orcid.org/0000-0001-9680-5054
  • Lillian R. Bacheller
  • Gary C. Fok
  • Kristen L. Parker Gaddis
  • Laura Jensen
  • Joel H. Megonigal Jr.
  • H.D. Norman
  • Daniel J. Null
  • Leigh W. Walton
  • George R. Wiggans
  • John B. Cole
  • Joao W. Durr
  • Paul M. VanRaden

Abstract

In 2013, the Council on Dairy Cattle Breeding (CDCB) started calculating and releasing U.S. genetic and genomic evaluations, which historically had been totally managed by USDA. The role of USDA in the U.S. dairy genetics industry is still extremely important because USDA’s Animal Genomic and Improvement Laboratory conducts most of the research for developing the cutting-edge methodologies applied by CDCB. This presentation reviews the latest enhancements to U.S. evaluations during 2018 and 2019, all of them result of the interaction between public service and private U.S. industry. In April 2018, CDCB introduced six new health traits for Holsteins; these traits were included in lifetime net merit in August 2018. Early first calving, another new trait, was introduced in April 2019. In April 2018, CDCB also extended genomic evaluation to an all-breed system, which had been used for traditional evaluations since 2007. This, together with further methodology developments to determine an animal’s breed composition (breed base representation, or BBR), resulted in the first release of a multi-breed genomic evaluation for crossbred animals in April 2019. In December 2018, the reference genome assembly was updated from the UMD3 version to the latest ARS-UCD1 version. At the same time, the number of markers used in genomic evaluations was increased from 60k to 80k. The new set of markers included more exact gene tests, removed poorer performers, added new variants with larger effects on traits, and changed the marker order based on the new assembly. The latest discovered recessive haplotype in Holsteins (HH6, BTAU-16) also was released in December 2018, and haplotypes BH1 (Brown Swiss) and JH2 (Jersey) were discontinued. Further enhancements were applied to productive life and fertility traits in 2018. Future projects include the release of evaluations for Jersey health traits, further improvements to the marker set, and enhancements of crossbred evaluation.

Published
2019-10-17