Invited review: The future of selection decisions and breeding programs: What are we breeding for, and who decides?

Authors: Cole, John; DURR, JOAO - Council On Dairy Cattle Breeding; NICOLAZZI, EZEQUIEL - Council On Dairy Cattle Breeding

Submitted to: Journal of Dairy Science
Publication Type: Review Article
Publication Acceptance Date: 1/3/2021
Publication Date: 5/1/2021
Citation: Cole, J.B., Durr, J.W., Nicolazzi, E.L. 2021. Invited review: The future of selection decisions and breeding programs: What are we breeding for, and who decides? Journal of Dairy Science. 104(5):5111–5124. https://doi.org/10.3168/jds.2020-19777.
DOI: https://doi.org/10.3168/jds.2020-19777

Interpretive Summary: Genetic selection has been a very successful tool for the long-term improvement of livestock populations, and the adoption of genomic selection doubled the rate of gain in dairy cattle. Data collected through the national dairy herd improvement (DHI) program are used to compute genomic evaluations for comparing and ranking animals for selection. Over time, the majority of the emphasis in the index has shifted from yield traits to fertility, health, and fitness traits. This work will describe how U.S. selection objectives are developed, as well as discuss opportunities and challenges associated with new technologies for recording animal performance.

Technical Abstract: Genetic selection has been a very successful tool for the long-term improvement of livestock populations, and the rapid adoption of genomic selection over the last decade has doubled the rate of gain in some populations. Breeding programs seek to identify genetically superior parents of the next generation, typically as a function of an index which combines information about many economically important traits into a single number. In the U.S., the data that drive this system are collected through the national dairy herd improvement (DHI) program that began more than a century ago. The resulting information about animal performance, pedigree, and genotype is used to compute genomic evaluations for comparing and ranking animals for selection. However, the full expression of genetic potential requires that animals are placed in environments which can support such performance. The Agricultural Research Service (ARS) of the U.S. Department of Agriculture (USDA) and the Council on Dairy Cattle Breeding (CDCB), a non-profit, producer-based organization, collaborate to deliver state-of-the-art genomic evaluations to the dairy industry. Today, most breeding stock is selected and marketed using the Net Merit Dollars (NM$) selection index, which evolved from two traits in 1926 (milk and fat yields) to a combination of 36 individual traits following the last NM$ update in 2018. Updates to NM$ require the estimation of many different parameters, and it can be difficult to achieve consensus from ARS, CDCB, industry, and university experts on what should be added to, or removed from, the index at each review. Over time the majority of the emphasis in the index has shifted from yield traits to fertility, health, and fitness traits, mirroring changes in production economics. Phenotypes for many of these new traits are difficult or expensive to measure, or both. This is driving interest in sensor-based systems that provide continuous measurements of the farm environment, individual animal performance, and detailed milk composition. There is also a need to capture more detailed data about the environment in which animals perform, including information about feeding, housing, and milking systems. However, many challenges accompany these new technologies, including a lack of standardization or validation, need for high-speed Internet connections, increased computational requirements, and interpretations that are often not backed by direct observations of biological phenomena. This work will describe how U.S. selection objectives are developed, as well as discuss opportunities and challenges associated with new technologies for recording animal performance.