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Sustainably feeding the wor...

Sustainably feeding the world with genomics-driven agriculture

5 Mar 2023

As cell meat manufacture develops in the lab, science is increasingly impacting arable farming in the field. Agrigenomics seeks to transition production to counter climate and population pressures, outlines Neil Ward.

The world’s population is set to grow by two billion in the next 30 years. Meanwhile, the impact of climate change on global ecosystems means many crops no longer have the specific environment they need to thrive. The impact of pest species, which already contribute to the loss of 40 per cent of global crops, is also worsening. In short, discussions on how to sustain and protect the world’s food supply have become critical.

Many governments and scientists are now turning to agrigenomics to tackle food sustainability and security. Agrigenomics involves the genome sequencing of plants and their microbiomes to provide a foundation of genetic resources to produce higher yielding, more nutritious, pest and disease-resistant foods faster than traditional breeding.

New legislation is reflecting this drive. In the UK, the Genetic Technology (Precision Breeding) Bill is expected to become law this year; permitting the use of technologies such as gene editing to produce more nutritious and weather-resistant foods. Similar conversations are happening in the EU, where decisions on gene editing are also expected this year. Yet, historically, embedding genomics into agricultural research has been constrained by limitations in sequencing technology.

Now, thanks to advances in the affordability, accuracy and speed of sequencing systems, the potential of agrigenomics is starting to be realised.

Unravelling plant complexity

Of the two main approaches to sequencing employed today – long and short-read – each has applications for different agrigenomics scenarios. Long-read sequencing gives insight into the whole genome. This is essential as plant genomes can be extremely complex; some wheat varieties have more than five times as much DMA as the human genome. Long-reads enable researchers to build reference pangenomes for crops of interest – collections of 20-30 whole genomes that give insight into the genetic diversity of a population. But to fully harness the evolutionary process for selective breeding also requires assembling genomic information for all organisms that interact with the crop, including microbes in the soil.

At the same time, the depth and length of longreads are needed to identify structural variations and genes that correspond to favourable traits, which cuts years off selective breeding timelines. For example, novel genes responsible for traits like immunity, metabolic detoxification and pesticide resistance are typically hard to find and are explained by a combination of genes and structural variants. These are too large to reliably discover with short-reads, which only examine fragments of DNA. Short-reads are suited to applications where high specificity is vital, but the length of long reads isn’t necessary. For example, validating DNA edits to prevent unintended side effects to the crop and giving researchers confidence in their modifications.

To date, long-read sequencing has had lower throughput, making it challenging to incorporate into studies where many seeds and microbe species must be sequenced. However, without sequencing at scale, researchers cannot unravel the complexity of plant genomes or discover biological information that will inform the production of more nutritious food, protect livestock health and increase agricultural yield. But this is changing. The good news for scientists is that advances in sequencing technologies mean machines are now faster, more affordable, have high capacity and are more accurate than ever before, reducing the barriers to wide-scale application of genomic insights in agriculture.

Appliance of science

Corteva Agriscience has been collaborating with PacBio to advance its agrigenomics programmes with highly accurate sequencing technology. The project focuses on establishing more efficient workflows and library preparation for use in Corteva’s laboratories. The goal is to enable the sequencing of tens of thousands of samples annually for its seed and crop protection research.

PacBio’s newest long-read sequencing system, Revio, has scaled the number of DNA samples that can be processed per day, driving high-throughput sequencing of plant genomes and ultra-high throughput sequencing of microbial genomes. The high-throughput workflows use a 96-well plate-based method rather than the more common single-tube protocol. Revio also makes it possible to load a subsequent run of samples while the current run is in progress, providing increased schedule flexibility for the lab. The machine also requires 50 per cent fewer consumables than previous models, meaning it is less resource-intensive for laboratories. For example, it no longer requires pure nitrogen, which can be difficult to source.

Thanks to advances in the affordability, accuracy and speed of sequencing systems, the potential of agrigenomics is starting to be realised

In the short read space, progress in the sensitivity and specificity of technology means there are fewer errors in read data. Therefore, scientists have higher confidence in each edited base, so modified crops can be shared with regulators sooner. Corteva Agriscience is a beta testing site for PacBio’s short-read sequencing system Onso, and is interested in using the platform for applications such as gene editing specificity analysis.

A new era

We are entering a new phase of agrigenomics. Rapid development in the affordability and speed of sequencing technology is making genomics increasingly accessible. This will make molecularlevel insight into crop complexity available to a wider pool of researchers, in addition to large companies currently paving the way. Moreover, the increased adoption of highly accurate sequencing technology will power exciting new discoveries and drive agrigenomics forwards, unlocking the complex biology of crops to sustainably feed our world.