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TraitSeq uses AI to optimise plant breeding

03 August 2023

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Researchers from the Earlham Institute at Norwich Research Park have set up a company that uses AI-based technology to help agrochemical, plant breeding and gene editing companies accelerate their product development and help protect global food production.

The researchers have successfully developed an innovative AI-based software capable of analysing RNA sequencing (RNA-Seq) data in organisms such as plants and livestock. They are now directing their efforts towards its commercialisation through a cloud-based technology platform called TraitSeq that will host their software.

The original idea for TraitSeq came from co-founder Joshua Colmer’s PhD study, which investigated how to apply AI techniques to RNA-Seq data in plants to predict, through gene sequencing analysis, complex traits such as the likelihood of them succumbing to a disease.

RNA is similar to DNA, but its principal role is to act as a messenger carrying instructions from DNA for the creation of proteins. It is essential for most biological functions. Unlike DNA, RNA-Seq data provides more comprehensive information about an organism, including the environmental factors in which that organism lives.

Until recently, DNA sequencing has been used as the main basis for plant and livestock analysis. But the ability to analyse RNA-Seq data quickly and cheaply could be a game-changer for discovering which genes in an organism could be impacted by disease.

TraitSeq offers a unique method for analysing RNA-Seq data that could provide new discoveries and more accurate results on a larger scale than was previously possible. The software is a sophisticated blend of bioinformatics and machine-learning algorithms.

Using bespoke, machine-learning methods, TraitSeq identifies predictive biomarkers – which are naturally occurring molecules, genes or characteristics – that help to identify pathological processes, physiological processes or diseases that can harm them.

Traditionally, plant breeding companies would spend a huge amount of time and money each year cross-breeding and testing tens of thousands of combinations of staple crops such as wheat, maize and rice in field trials to try to find the varieties that will be more resistant to disease or could offer higher yields. Once the best varieties are identified (a process that can take up to 10 years), these are then sold as seeds to farmers.

TraitSeq’s technology generates trait prediction models that transcend state-of-the-art accuracy levels and can incorporate environmental variations into its calculations. This can help agrochemical, crop breeding and gene editing companies to target the most appropriate varieties swiftly and more efficiently. TraitSeq enables the precise selection of varieties for specific locations and conditions that can lead to significant yield improvements and a much shorter product development timeline.

TraitSeq’s technology aims to help address many of the major challenges faced in agriculture.

Global food security is one such issue. TraitSeq’s predictive modelling will help the agricultural sector with breeding, gene editing and crop protection, improving the efficiency of crop development and increasing crop yields.

Water use efficiency is another. TraitSeq can identify biomarkers for traits associated with climate change, such as water use efficiency. It is becoming increasingly urgent for plant breeders to develop crop varieties that make better use of water.

TraitSeq’s technology offers breeders a cost-effective solution to predict water use efficiency and test genetically diverse plant material with greater accuracy predictions than ever before. The development of different varieties of crops can be accelerated – making them more robust to environmental variation and the environmental challenges of the future.

Another benefit is the early evaluation of the gene editing efficacy, where a targeted gene in a plant that is susceptible to disease is removed or silenced – thus improving resistance. TraitSeq’s complex trait prediction models could help to accelerate a more cost-effective path to improving crop traits by gene editing.

The plan is that TraitSeq will earn revenue from licence fees companies will pay to use its software.

Joshua Colmer of TraitSeq said: “We are tremendously excited about the potential impact that TraitSeq could have in empowering the agricultural sector to enhance complex traits in crops and livestock that ultimately end up in the food chain.

“Thanks to grant funding from the BBSRC’s ICURe programme and pre-seed funding from Anglia Innovation Partnership, we have been able to validate our predictive trait modelling and biomarker identification software with the agricultural industry and have received overwhelmingly favourable feedback that reinforces the demand and credibility of our propositions.”

Following the completion of many successful academic proof-of-concept projects, TraitSeq is now engaged in a number of industry pilot projects to demonstrate the impact and commercial potential its technology has in real-world scenarios.

Joshua continued: “The sequencing work we have conducted at the Earlham Institute has been invaluable in developing this new technology and coupled with the support of Anglia Innovation Partnership has meant we’ve got our company up and running much quicker than expected.

“Norwich Research Park provides us with a fantastic location to develop our ideas. Not only do we have world-class lab facilities and equipment, but also the important ability to collaborate with so many researchers from the institutions that are based on campus. Our primary objective now is to secure investment that will enable us to elevate our business to the next level of growth and development.”

Roz Bird, CEO of Anglia Innovation Partnership, the organisation that runs Norwich Research Park, said: “We are seeing more examples of world-leading science being translated into real-life business applications here at Norwich Research Park. TraitSeq is a great example of researchers recognising the impact their work can have on solving some the more serious challenges that the human race faces, in this case global food security and production.

“We are creating an eco-system here to unearth more potential companies to spin out of the institutes on the Park as well as attracting other businesses to relocate here. The aim is to attract more investment into companies like TraitSeq so that they can grow, employ more people and make a larger contribution to the Norfolk economy.”

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