Genetic Screening for Beef and Dairy Herds

PLOS ONE - Didier Boichard; Hoyoung Chung; Romain Dassonneville; Xavier David; Andre´ Eggen; Se´bastien Fritz; Kimberly J. Gietzen; Ben J. Hayes; Cynthia T. Lawley; Tad S. Sonstegard; Curtis P. Van Tassell; Paul M. VanRaden; Karine A. Viaud-Martinez; George R. Wiggans

Type: Research Paper
Knowledge level: Advanced

Farm Table says:

Genetic screening has come a long way, with this study reporting low-density testing giving highly accurate results allowing for greater gains in each generation of your herd.

Design of a Bovine Low Density SNP Array optimized for Imputation

What is the problem?

There is an increasing use of genetic markers to select and breed cattle with. This can be costly to screen each sire at a high “resolution”. Low density screening is cheaper to complete as computer algorithms assume some of the information based off other genetic screening of similar bovine breeds.

This research was the effort of universities and institutes from multiple countries, with lead research from the National Institute for Agricultural Research (INRA), France. Through chemistry assay development, they improved the accuracy of imputations, or assumptions, made by the algorithms.

What did the research involve?

The researchers collated a wide collection of currently available data from both high- and low-density bovine chips. They also developed a chemistry assay that only relied on a single hybridization event, vs the double hybridisation event required in previous LD chips. Combining and overlapping data sources with the new assay technique led to increased imputation accuracy at low densities.

What were the key findings?

  • Accuracy of 99.94% for dairy breeds
  • Accuracy of 99.90% for beef breeds
  • Accuracy of 99.93% for total breeds

The varying levels of accuracy for differing breeds could be a result of less genetic data available, dairy breeds are currently the most genetically screened bovines.

Final comment

This paper only directly refers to other Illumina branded products as examples and comparisons to previous methods. It does not state how the Illumina BovineLD Beadchip compares against other current LD bovine imputation products, but still offers an option for cheaper screening.


This paper was summarised by Mia Courtney (Agricultural Sciences Student – La Trobe University) and reviewed by Nickala Best (PhD Student – La Trobe University). Learn more about Mia and Nickala here.

2012 - France - PLOS ONE - Didier Boichard; Hoyoung Chung; Romain Dassonneville; Xavier David; Andre´ Eggen; Se´bastien Fritz; Kimberly J. Gietzen; Ben J. Hayes; Cynthia T. Lawley; Tad S. Sonstegard; Curtis P. Van Tassell; Paul M. VanRaden; Karine A. Viaud-Martinez; George R. Wiggans
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