Annogen – KeyGene collaboration demonstrates efficacy of the 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. This project has now led to the identification of sequence variants that upregulate important traits in plants. More generally the results demonstrate 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.
In the project, KeyGene provided Annogen with several hundred candidate sequence variants occurring in promoter or enhancer regions of trait-relevant genes. These variants came from EMS-generated tomato seedbanks or from variation found in diverse tomato lines. SuRE™ libraries for these variants were generated by Annogen and analyzed in tomato protoplasts. This allowed for the identification of several candidate new variants which positively change the expression of trait-relevant genes. Two of these candidates were subsequently tested in planta in a homozygous setting.
The first variant was predicted to increase expression of a gene that plays a critical role in biotic resistance, and indeed a ~5-fold increase could be confirmed by qPCR in the new variants after infection. For the second variant, this was expected to increase expression of a gene involved in response to wounding and we did indeed observe a ~2-fold upregulation of this gene after leaf damage.
“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.
SuRE™ can be applied to any crop and trait and is being further optimized at Annogen 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. These results even exceed what we hoped for when we started this project 3 years ago” said Joris van Arensbergen, Annogen’s founder and CEO.
About Annogen
Annogen was founded in 2017 as a spin-out of the world-renowned Netherlands Cancer Institute and is focused on gene expression engineering in the fields of advanced therapies, biologics manufacturing and crop engineering. Annogen’s proprietary SuRE™ technology allows for the identification and optimization of regulatory DNA elements that enable tailored expression of therapeutic genes. In addition, SuRE™ is used to functionally annotate genome variants and identify gain-of-function variant for trait improvement. Annogen’s AIM™ technology allows for identification of favorable transgene insertion sites by analyzing the expression characteristics for >100,000 loci in parallel. Annogen is the trusted partner of leading biopharmaceutical, agricultural and academic research centers for bespoke gene expression engineering.
Contact: Martijn Kelder, Chief Strategy Officer, [email protected]
About KeyGene
KeyGene is the go-to research company for the development and application of technology innovation that boosts crop improvement. With its intellectual capital, solution-driven approach, and collaborative spirit, KeyGene passionately works for the future of global agriculture with partners in the breeding of vegetables and other crops, and with other organizations in the AgriFood sector.
Contact: Erik Toussaint, Senior PR & Communiation Officer, [email protected]
