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When it comes to choosing a genotyping platform to support breeding programs, discussions of technical ability to drive genomic prediction and cost per sample tend to dominate the conversation. And while they are important, the ability to implement a new pipeline quickly and that platform’s adaptability to discoveries and future advancements should also be considered. In this respect, Gencove's low-pass sequencing and imputation platform offers several valuable advantages.

Backward compatibility and flexibility

All the genotyping pipelines that are built on the Gencove platform are backward compatible. Therefore, if you want to include new markers in your reference panel or update the reference genome used for genotyping, you can do so and re-run your previously genotyped samples without generating new data for those samples. In species where new populations are continually being explored for valuable traits, an easily updatable platform that is backward compatible helps to futureproof your investment in genomics.

For example, the soybean reference panel that is readily available to Gencove users can be used with the public v2 or v4 reference genome, providing a path to answer your research questions in a more specific way.

Genotyping and Additional Analyses

Another consideration for evaluating genomic technologies is how flexible and adaptable it is to emerging knowledge. At Gencove, we are your scientific partners to leverage data for additional analyses such as trait scores, breed analysis, parentage, and more.

As an example, in collaboration with the J. R. Simplot Company, Gencove scientists helped develop a robust prediction model and a novel EPD for bovine congestive heart failure (BCHF). After low-pass sequencing of 5,000 individuals for training the predictive model, the approach demonstrated a heritability estimate of 34% for BCHF, indicating a significant genetic component similar in magnitude to important heritable carcass traits. The use of an extensive database of phenotypes and low-pass sequencing genotypes to create this genomic EPD drives a prediction of the proportion of a bull’s calves that will be at risk for developing congestive heart failure.

Continued innovation

Gencove is continually innovating to bring genomic information to the forefront of advancing global health and sustainability. The combination of low-pass sequencing and target capture is an exciting Gencove offering that can be used in any species. In a single, reliable molecular reaction, low-pass sequencing plus target capture enables a cost-effective solution for direct observation of the known and unknown genetic variation across the whole genome.

In addition to genome-wide information, hybrid capture probes designed for 774 sites to look at the important traits in the cattle industry, such as those associated with diagnostics and parentage, were tested and validated in 340 animals. The results show 100% genotype match to microarrays, providing an exciting avenue for fast, cost-effective, adaptable genomic information with the breadth of genome-wide sequencing and the depth of deep sequencing at key loci.

The Gencove platform: high-quality data and actionable analytics to drive new insights

Gencove’s low-pass whole genome sequencing and analysis platform powers critical decision-making now while preparing you for the future of sequencing-based molecular breeding.

If you’d like to learn more about low-pass sequencing and the Gencove analysis platform, please contact us.