Thursday, June 1, 2017

BIF 2017: Genetics of reproduction project

Alison Van Eenennaam
UC-Davis

The grant dubbed the "heifer fertility project" is really looking for embryonic lethal variants. These are DNA variants that if an embryo inherits two copies of the variant, that embryo is aborted. The DNA variant breaks a gene. If an animal inherits two copies, it can't live.

The project sequenced the entire genome of hundreds of cattle. This is not genotyping thousands of DNA variants, it is looking at all 2.6 billion base pairs of the genome. From sequencing these bulls, the team identified millions of DNA variants. They selected 200,000 of these DNA variants that are predicted to affect proteins encoded by genes to build a new SNP chip. This chip is called the GGP-F250.

They then genotyped 17,000 cattle with the GGP-F250 chip. Taylor then looked for DNA variants for which there are not observed in two copies. If a DNA variant is at high frequency, but is never seen as two copies, then we have evidence that this is a lethal DNA variant. There appears to be hundreds of these lethal variants in Angus cattle.

Van Eenannaam is working on the producer applications from this grant. If there are lots of DNA variants responsible for embryonic loss, we will have to strategically manage them. If we don't use animals that carry embryonic lethal variants, we will basically be practicing single trait selection. If you haven't heard, single trait selection is bad!

What is important is to never mate a carrier to another carrier of the same lethal variant. Mate selection tools allow us to do this in a sophisticated way.

For more information, see http://beefreproduction.org/.


MateSel is a software program for mate selection. MateSel works to increase genetic merit while limiting inbreeding. Van Eenannaam's graduate student showed simulations using MateSel.
There is a trade-off between never using a carrier and economic genetic progress.

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