Jesse Hoff, Agrigenomics Product Manager - Jan 30, 2024

A vision for the future of the cattle industry

At Gencove, we’ve long talked about Moo-res law, the trend of increasing genotype adoption in the cattle breeding world, with global genotyping in the cattle industry likely to hit 5 million samples annually by mid-decade. The successes of genomic selection are well known, led by the US dairy evaluation’s pioneering efforts over 15 years ago, with adoption following in many cattle breeding programs globally.

It looks to be another busy 15 years to come. At Gencove, we can envisage a world in which nearly all of the 40 million cows born in the US annually will be genotyped, following the terrific example pioneered by the Irish Cattle Breeding Foundation. So how do we get there?

Three key ideas:

  • We will need a massive scale of data generation and compute to deliver these solutions.

  • Novel applications will mean novel business models for data collection and utilization in the cattle industry.

  • Our analytical focus will transition from breeding to precision management of genomic data.

Sequencing will be the foundation of this transition, offering the most affordable and scalable future technology path. Merely 10 years ago, genome sequencing cost upwards of $10,000 per cow. Whole genomes now cost ~$100. We have been consistently providing low-pass whole genome sequencing for prices in the order of magnitude of 10's of dollars, and the path to solutions well under $5 is clear.

For scale, Illumina has shipped over 400 NovaSeq machines, each capable of processing 25 million low-pass cow genomes a year. A national lab network with less than $4 million in equipment could process all the cattle born in the US every year.

The clear trajectory to single-dollar genomes is a fantastic fit for the cattle industry, where individual animals have a lifetime value across the supply chain in the thousands of dollars.

To date, the benefits of genomic data have directly benefited the breeding segment and indirectly benefited our downstream partners. Business model innovation is required to unlock the value of genomics at the scale of the herd.

What will this mean technologically? For one, cattle breeding and management programs will become some of the largest genomic data programs in the world. And there are several key opportunities to leverage genomic data at that scale:

  • Prediction of genetic merit that can scale to incorporate 100 million genomic records, totally turning the n/p problem on its head and allowing us to estimate SNP-level genetic effects.

  • Prediction of phenotypes for precision management.

  • Prediction of the effect of alleles and genes.
  • Across this data set, we will see every gene knocked out several times, and hundreds of millions of de novo variants. Perhaps we don’t need gene editing in cattle with this resource if we can figure out how to use this natural variation (each cow has ~50 novel snp mutations).

Solving disjointed supply chain and information-sharing issues has long been challenging for the cattle industry, but genomics can make it a strength. Gencove is focused on helping partners build flexible, affordable solutions to generate and process this data. Scalable compute is a critical part of this, and our goal is to be the industry's leading provider in building genomics analysis solutions in the cloud. We are confident that cattle breeding will generate one of the world's largest genomic resources, and we’re excited to solve the problems needed to achieve that future.