Beyond Arrays: How a Blended Low Pass + Targeted GBS Strategy Is Reshaping AgBio Genotyping

For many years, microarrays have been central to applied genomics in agriculture. They enabled genomic selection, trait mapping, and population-scale studies by offering a standardized and cost-effective way to genotype large numbers of samples. For stable populations and well-characterized traits, arrays continue to deliver value.

However, the demands placed on modern breeding and genetics programs have evolved. Today’s crop and livestock programs operate across more diverse populations, pursue rapidly changing trait priorities, and require deeper biological insight without proportionally increasing cost. In this environment, the limitations of an arrays-only strategy are becoming increasingly apparent.

Microarrays: Efficient But Fixed

Microarrays are inherently fixed. Their marker content reflects historical discovery panels and assumes long-term relevance to specific populations. As breeding goals shift or new populations are introduced, arrays struggle to capture novel variation, rare alleles, structural variants, and emerging haplotypes. While arrays scale efficiently in volume, they are less adaptable to new biological questions.

Genome-wide Exploration With Low Pass

Low-pass whole-genome sequencing (lpWGS) offers a fundamentally different approach. Rather than interrogating a predefined set of markers, lpWGS examines variation across the entire genome, enabling more complete representation of genetic diversity. This genome-wide perspective improves imputation accuracy, enhances haplotype reconstruction, and performs more robustly across diverse or admixed populations commonly encountered in both crop and livestock systems.

With AgriPrep, seqWell’s one-step library preparation solution for lpWGS, this shift is now practical at population scale. AgriPrep is designed to simplify lpWGS workflows by reducing hands-on time, auto-normalizing over a broad range DNA input, enabling high multiplexing, and integrating seamlessly with automated laboratory environments. As a result, lpWGS can be scaled and deployed affordably, rather than reserved for specialized projects.

Confident Decision Making

Targeted genotyping-by-sequencing (tGBS) complements lpWGS by providing high-confidence genotypes at loci of known importance. For breeding programs and service providers alike, tGBS preserves continuity with historical datasets while delivering consistent coverage for traits under active selection. In a blended workflow, lpWGS expands discovery and genome-wide insight, while tGBS anchors decision-making at priority regions.

The Blended Approach: Critical Answers For Today, Powerful Insights For Tomorrow

Together, lpWGS and tGBS offer a flexible, future-proof alternative to microarrays alone. This blended strategy increases the amount of usable genetic information per sample, reduces bias introduced by fixed marker panels, and adapts readily as traits, populations, and markets evolve. For crop breeders, livestock geneticists, and AgBio service providers, it represents a smarter, more resilient foundation for modern genomics.

Microarrays remain useful tools, but relying on them alone increasingly limits what breeding and genetics programs can see—and therefore what they can decide. By integrating lpWGS with targeted GBS, organizations gain a more complete, adaptable view of their populations without sacrificing scale or continuity. It is a pragmatic step toward genotyping strategies that keep pace with real-world breeding challenges.