Jesse Hoff, Agrigenomics Product Manager - Jul 06, 2022

Get the Utility of Sequencing at the Cost of a Microarray

Molecular breeding has made significant strides over the past decade and is driving key discoveries across many species. Funding for genomics and genetics-powered breeding programs in both plants and animals by the USDA alone is well into the tens of millions of dollars per year.

Drivers of the investment are the increased utility and the decreasing cost of sequencing technologies. Sequencing is the foundation of major milestones such as completing a complex genome from telomere to telomere and identifying genetic variation in dispensable genes of a pangenome. However, the cost of the gold standard 30X whole genome sequencing (WGS) coverage for variant detection projects prohibits its use as a routine, high-throughput genotyping tool.

On the other end of the spectrum, microarrays are inexpensive on a cost-per-sample basis after the initial time and financial investment is made to develop the chip. In breeding programs where known markers are used to power genomic selection and no updating or development of new markers is expected, a high-density microarray may provide enough information for breeding decisions.

However, if you’d prefer a pipeline that genotypes your known key markers and also provides genome-wide information for millions of other variants for future exploration, Gencove’s low-pass whole genome sequencing and analysis platform is a powerful, cost-effective, high-throughput, future-proofed solution.

Gencove’s low-pass sequencing, imputation and analysis platform is concordance (typically >99%) with both microarray and high-coverage WGS across a wide variety of plant and animal species.

Importantly, the ability to get millions of variants that are identified with the Gencove platform increases predictive power for GWAS studies, trait identification, and genomic selection.

Researchers at the USDA Meat Animal Research Center (MARC), in a paper published in MDPI Genes, showed that low-pass whole genome sequencing and genotyping via the Gencove platform accurately assays variants regularly captured by commercial genotyping arrays for beef cattle and provides comparable results in the genomic prediction of commercially relevant traits. Additionally, low-pass sequencing and imputation enable the reliable assaying of a vastly larger set of functionally relevant variants compared to genotyping arrays, plus provides accurate results across the allele frequency spectrum. The authors note, “imputation from low coverage sequence offers a viable, low-cost approach to obtain functional variant genotypes that could improve genomic prediction.”

Furthermore, it can be argued that the value of the sequencing data is higher than that of a fixed microarray. While microarrays can provide genotypes for up to 500,000 SNPs on a single chip, low-pass sequencing routinely looks at tens of millions of variants across the genome, opening many new lines of inquiry into additional variants. From this perspective, the cost per data point for sequencing data is significantly lower than that for microarrays and will continue to fuel discoveries in the future.

Want to find out how many data points and at what cost you can get them for your plant or animal species? Get in touch for a free pilot project consultation.