Partnership is said to have demonstrated the efficacy of the Annogen SuRE platform to identify gain-of-function in new variants of crops
In 2021, Annogen, the Amsterdam-based biotech company behind the SuRE technology for the functional annotation of the non-coding part of the genome, and KeyGene, the Wageningen-based research company developing innovative technologies for crop improvement, started a collaboration to systematically screen for variants that result in important crop traits.
The companies have now revealed that the project has led to the identification of sequence variants that upregulate important traits in plants.
More generally the results demonstrated the efficacy of SuRE-based sequence variant screening in plants for the improvement of crop traits such as higher yields and resistance to drought and pathogens, they said.
In the project, KeyGene provided Annogen with several hundred candidate sequence variants occurring in promoter or enhancer regions of trait-relevant genes, natural variants coming from diverse tomato types.
SuRE libraries for these variants were generated by Annogen and analysed in tomato protoplasts.
This allowed for the identification of several candidate variants which positively change the expression of trait-relevant genes, the companies outlined.
Two of these candidates were subsequently tested in planta in a homozygous setting.
The first variant was predicted to increase the expression of a gene that plays a critical role in biotic resistance, and indeed a roughly five-fold increase could be confirmed by qPCR after infection.
For the second variant, this was expected to increase expression of a gene involved in response to wounding. Indeed, a roughly two-fold upregulation after leaf damage of this gene was observed.
“The experiments demonstrate the value of SuRE in identifying promising gain-of-function sequence variants in a massively parallel setting, without the need to grow individual plants,” said Paul Bundock, senior scientist at KeyGene.
According to Annogen, SuRE can be applied to any crop and trait and is being further optimised at the company for in vivo applications using Agrobacterium.
“We are very excited that our SuRE approach identified sequence variants that in plants led to increased expression of trait-relevant genes,” said Joris van Arensbergen, Annogen’s founder and CEO.
”These results even exceed what we hoped for when we started this project three years ago.”
