Jesse Hoff, Agrigenomics Product Manager - Jan 19, 2021

Gencove’s improved cattle low-pass sequencing solution

The new product supports more breeds and returns higher accuracy through an updated reference panel. We have also made it easier to use for industrial scale applications.

We are excited to announce an update to our cattle imputation reference panel, which now includes over 50 breeds and 1800 animals. This better supports the demand we’ve had for all the most important breeds being utilized by the cattle industry today. Since launching our original panel, we’ve been busy optimizing our pipeline and adding new features to make low-pass sequencing more powerful and easier to use. We believe this platform is now the best high-throughput solution for building genomic breeding programs.

Our new panel now returns over 50 million variants that you can genotype with over 99% accuracy. This includes over 98+% of the sites for the existing arrays in production today, from the Illumina BovineHD to the SNP50. We support “Final Report” backwards compatibility for any available array manifest so that the data you generate can be seamlessly integrated into existing workflows. It also now characterizes indels as well as SNPs and multiallelic sites. We have exact matches at 98% of the SNPs in the ICAR200 parentage panel.

The key to successful low-pass genotyping is making sure the common haplotypes from a population are included in the reference. Our panel now has 9 breeds with over 40 samples each. Due to the large amount of sharing of common genetics amongst different European cattle breeds, this combined breed panel improves performance across the whole dataset (see below). Huge thanks to all the public research partners who released sequence data.

Global cattle diversity captured within our new panel, dominated by Angus, Holstein and Indicine diversity. Indicine samples contributed far more diversity to the panel per animal.

Focusing on diversity within European cattle, distinct breed clusters exist, even in largely overlapping groups. This is why a combined breed panel provides improved imputation. However, there is also substantial variation that is difficult to capture without low-pass sequencing.

A great example of the impact of our expanded panel is the Jersey breed. In our V2 panel, there were only 15 public samples. But thanks to the inclusion of only an additional 27 samples, we were able to see a large improvement in genotyping accuracy, from 98% to 99%, as measured by concordance to a genotyping array. This performance is partially due to the small effective population size of Jersey. Despite the small population size, there are hundreds of thousands of unique variants that can now be captured with low-pass sequencing. Many thanks to Brian Kirkpatrick of University of Wisconsin for sequencing the additional Jersey samples and sharing them with us.

If your breed or variant of interest isn’t included in our current data, we can easily incorporate new animals into the reference panel to further extend this resource, on a proprietary or public basis.

Our goal with low-pass sequencing is to continue to deliver the affordable tool you need today to replace arrays, while building the future of genetic evaluations. We were excited to produce a validation of using low-pass to fit evaluations for beef cattle along with the USDA MARC and Warren Snelling.

With our partners we have started to see enormous potential for harnessing the millions of genetic variants to optimize the markers used in evaluation. Recent work by AgVictoria highlights the impact of customization of genomic selection marker sets with selected sequence data. Custom designing arrays has been popular in recent years, but is an expensive and cumbersome process. Rather than designing custom arrays, low-pass sequencing can be used to comprehensively include all potential causal variation segregating in a population.

We offer Gencove’s low-pass sequencing platform through different set ups:

  • End to end service from sample to data through our partner labs
  • In-house set up for users with sequencers. Our team can help you deploy a high throughput affordable sequencing workflow.
  • SaaS only for users that already have the FASTQs input

Low-pass sequencing, powered by the Gencove platform is trusted by our partners, such as Neogen and Genetic Visions-ST . We’re excited to help the industry make continuous improvements to genomic evaluations. The future of genotyping with sequencing starts now.

Reach out at to learn more!