CDCB Keeps Pace with Advancing Genomic Technology Through Integration of Genotyping-by-Sequencing

BOWIE, Md., June 5, 2025 — After receiving nearly 11 million genotypes into the National Cooperator Database, the Council on Dairy Cattle Breeding (CDCB) has certified the first sequencing-based laboratory for data submission. As a part of this certification process, CDCB validated the first single-nucleotide polymorphism (SNP) panel derived from sequencing data, destined for the national database. This achievement marks major progress in diversifying the genomic tools available for U.S. dairy cattle and is the first time the technology is to be utilized in a national dairy cattle genetic evaluation system anywhere in the world.

Since the introduction of genomic testing in 2008, the U.S. system has relied solely on SNP chip technology. This process identifies key genetic markers associated with traits of interest and utilizes imputation to complete the genetic information needed for genomic evaluations.

Genotyping-by-sequencing (GBS) technology represents the next frontier in genetic data. GBS enables the identification of SNPs directly from sequence data. This is an alternative to traditional genotyping chips and is a technology widely used in plant and other animal breeding programs. GBS is increasingly attractive for use with dairy animals due to its scalability, flexibility, and potential to provide deeper genomic insight.

“Integrating GBS marks a pivotal step forward for CDCB, enabling us to stay at the forefront of technological advancements and meet the evolving needs of our stakeholders,” shared José Carrillo, CDCB Chief Data Officer. “GBS allows us to include high-density genetic information that seamlessly aligns with our existing infrastructure, strengthening both comprehensive genetic evaluations and forward-looking research initiatives.”

GBS is not a single method but rather a suite of approaches. The first sequencing panel certified by CDCB for genomic evaluations uses a hybrid method that combines low-pass sequencing and targeted sequencing:

• Low-pass sequencing involves sequencing the entire genome at low coverage, enabling broad variant discovery at a lower cost.
• Targeted sequencing enriches the coverage of specific, high-priority SNPs — especially those that CDCB already uses in national evaluations — to ensure compatibility and reliability.

This approach offers both comprehensive data capture and consistency with the existing SNP-based evaluation system.

“This milestone not only reinforces our current genetic improvement efforts but also opens new opportunities to explore a range of GBS technologies,” Carrillo added. “By embracing these innovations, CDCB reaffirms its commitment to delivering advanced genomic tools and maintaining its leadership in the dynamic field of animal genetics.”

As the provider of national genetic evaluations and data services for the U.S. dairy industry, CDCB remains committed to integrating innovative technologies that enhance the value and accuracy of its offerings. Any new technology, data type, or genotyping platform goes through an intensive review and validation process before it can be accepted for use in genetic evaluations. This ensures the quality and reliability that dairy producers expect from CDCB remains uncompromised while still moving forward. Incorporating GBS into the existing pipeline required the development of a careful validation framework that protects the quality and integrity of the National Cooperator Database.