Twist Bioscience

Mark Dupal

DNA sequencing is a technology that is renowned for its impact in molecular research and health fields. However, in recent years, the decreasing cost of sequencing has fueled a growing interest in applying this technology beyond its traditional sectors. One such application is in the agricultural space, where next-generation sequencing (NGS) is modernizing an ancient form of crop production.

An Evolving MAStery of Selective Breeding

Gregor Johann Mendel was a university-educated monk who lived in Brno, Moravia—or modern-day Czech Republic—in the 1800s. Working in a small garden on the monastery grounds, Mendel discovered that he could grow pea plants with specific traits (such as pea color and shape) through selective breeding. In essence, all he had to do was allow the plants with desirable traits to breed, and he would eventually get offspring with predictable features. This work was foundational not only to modern genetics but to modern agriculture.

From strawberries to rubber plants, modern farmers and seed producers carefully select their plants in an effort to produce tastier fruits, pest-resistant crops, or more environmentally friendly growth conditions. Unlike Mendel's peas, though, selecting for these complex traits is exceedingly difficult, not least of all because it may take years before you can measure phenotypes in a fruit-bearing plant. This means it may be years before you know if you've actually enriched your crops for the desired trait, and you've spent considerable resources just to get to this point.

Put simply, selective breeding in the modern era is a slow, challenging, and costly endeavor. Because of this, many growers have evolved their breeding techniques to adopt a process known as marker assisted selection (MAS).

MAS is the process of using molecular tools to search for telling genetic markers in an organism’s genome, specifically markers that can forecast desired phenotypes. This allows cultivars to rapidly sort and selectively breed a population of organisms based on whether they’ve inherited a set of markers. Such an approach has several advantages as it:

• Allows for the selection of subtle traits that are either difficult to observe or poorly heritable;

• Can be done early in an organism’s life cycle before significant resources have been committed to its growth;

• Enables simultaneous selection of multiple desired traits.

However, to carry out MAS, agriculturalists need tools that are capable of rapid, efficient, and large-scale marker screening. For that, many have turned their attention to NGS technology.

The Technology behind MAS

At the core of MAS is technology. In the early 2000s, MAS efforts were dominated by PCR or amplicon-based technologies which have slowly given way to microarrays. Briefly, microarrays are designed with oligonucleotide probes that are fixed onto a solid surface. When mixed with a DNA sample from an organism, the probes will hybridize to their complementary sequence and produce a recordable signal. Microarray probes can thus be designed to be complementary to DNA sequences containing genetic markers. If a signal is observed when these probes are mixed with an individual’s DNA, you know the genetic marker is present.

NGS Technology allows for Hypothesis-Free Interrogation

While useful, microarrays are limited by their hypothesis-driven nature: they can only answer the questions you know to ask, and will only provide a binary yes or no answer (“yes, marker is present,” or “no, marker is not present”).

Many issues stem from this, but in general, the limited data produced by microarrays means that users will struggle to update their breeding programs as new genetic markers are discovered, or as new species are introgressed into the breeding population.

Because of these limitations, many in the agricultural space have looked eagerly to the adoption of NGS technology as a means to improve MAS efforts.

NGS and Skim Sequencing

Unlike the binary readouts produced by microarrays, NGS technology allows for a hypothesis-free interrogation of DNA samples. The resulting information-rich data can be used for myriad purposes, including both the identification of known phenotype-associated markers and the discovery of new ones. As new markers are discovered, NGS data can be re-evaluated and assays can be easily updated, making NGS a more nimble and informative tool for MAS.

The benefits of NGS in MAS go beyond information density. NGS technology is designed to allow for multiplexing, meaning many hundreds of samples can be pooled and simultaneously sequenced. Not only does this allow for MAS on a large scale, but it opens the door to population-scale genetic diversity assessments—which can be critical for both protecting desired traits and the overall stability of the breeding population. In this way, NGS allows breeders to better cultivate a genetically diverse population which helps to protect farms from catastrophic losses that may stem from disease.

However, until very recently, the benefits of NGS came at a cost—both the infrastructure needed to carry out NGS, and the process of collecting sequencing data was prohibitively expensive. Fortunately, recent methodological and technological advances have considerably lowered the cost of NGS, making it a viable option for MAS.

One such advancement is the development of low-pass sequencing, also known as skim sequencing or simply skim-seq. Rather than providing deep and mostly contiguous coverage of the genome (as might be needed for clinical sequencing applications), skim-seq works by only sequencing specific portions of the genome, and only reading each section one or fewer times. Because each location is only covered once, the reliability of each individual sequencing read is decreased. But, with an understanding of the physical linkage between markers, the patterns revealed by skim-seq can generate an accurate and robust readout of an organism’s genome. Skim-seq thus represents a quick and efficient approach to MAS.

Modern Agriculture with Ancient Roots

In many ways, NGS is a natural extension of the way agriculture has been practiced for centuries; it allows us to selectively breed crops based on desirable traits. Skim-seq, and the tools that enable it, carry on the tradition of selective breeding, only with greater efficiency, accuracy, and scalability.

To this end, Twist Bioscience has recently developed a high throughput, no fragmentation library preparation kit that cultivars can use to perform whole genome skim sequencing on as many as 960 samples simultaneously. The kit is purpose-built for use in industrial seed selection and cattle breeding, among many other high-throughput applications.