Changes in genetic trends in US dairy cattle since the implementation of genomic selection.

Genetic trends measure the success or failure of a breeding program and are needed to justify the usefulness of genetic evaluations and, therefore, the rationale behind using new methodologies, such as genomics. The accepted advantage of genomic selection is increased accuracy and a decrease in the generation interval, thereby accelerating genetic changes in dairy populations. Since the implementation of genomic selection in the US, it has been shown that genetic trends have changed significantly for the Holstein breed. Milk, fat, and protein yields have increased remarkably alongside the uptake of genotyping. Apart from the Holstein, it is accepted that genetic changes for all other breeds (Ayrshire, Brown Swiss, Guernsey and Jersey) due to genomics improved, but there is little evidence and documentation of such improvement since the introduction of genomic evaluations.

Reviewing the assumptions of genetic progress since the introduction of genomics is crucial for advising breed associations and non-academic stakeholders on how to use this technology moving forward. Therefore, the main purpose of this study was to investigate genetic trends in the five breeds receiving genomic evaluations for production, fertility, longevity, and health traits. A further objective was to investigate changes in generation intervals and inbreeding levels of these breeds.

Breeds included Ayrshire, Brown Swiss, Guernsey, Holstein and Jersey, which were characterized by the evaluation breed the animal received. Mean genomic predicted breeding values (PBV) were analyzed per year to calculate genetic trends for bulls and cows. The data set contained in excess of 154 000 bulls and 33 million cows born since 1975. Generation intervals and inbreeding levels were also investigated since 1975. Milk, fat and protein yields, somatic cell score, productive life, daughter pregnancy rate, and livability PBV were documented.

Overall, production traits have increased steadily over time. The Holstein and Jersey breeds have benefited most from genomics, with up to 192% increase in genetic gain since 2009. Due to the low number of observations, trends for Ayrshire, Brown Swiss, and Guernsey were difficult to infer from. Trends in fertility are most substantial; particularly, most breeds are trending downwards and daughter pregnancy rate for Jerseys has been decreasing steadily since 1975 for bulls and cows. Levels of genomic inbreeding are increasing in Holstein bulls and cows. In 2017, genomic inbreeding levels were 12.7% for bulls and 7.9% for cows. For sires of bulls, the estimated generation intervals were 2.2 years in Holstein, 3.2 in Jersey, 4.4 in Brown Swiss, 5.1 in Ayrshire and 4.3 in Guernsey.

Comment: Whereas there was vast progress in production traits, some negatives were associated with that, particularly in fertility and inbreeding. This will have to be addressed or controlled. A suggestion to control inbreeding is to include the genomic inbreeding coefficient with a negative weight to the selection index of bulls with high future genomic inbreeding levels.