Periodic Reporting for period 4 - BUNGEE (Directed crop breeding using jumping genes)
Berichtszeitraum: 2021-12-01 bis 2022-05-31
Climate change in becoming a major issue for plant breeding. Increased intensities and frequencies of drought and heat stresses and novel pathogens invading Europe represent a major challenge. Unfortunately, over the course of this project, the agricultural situation in Europe has rapidly worsened: We are now facing major droughts, temperature extremes and war which all affect food security not only in Europe. Unfortunately, it is now clear that crop breeding is advancing slower than climate change. To ensure food security in Europe and elsewhere, rapid advances in crop breeding must be made.
And yet, in this emergency context the EU keeps a blind eye on scientific evidence: Currently, novel methods that could greatly increase crop breeding speed, such as gene editing, are effectively prohibited. At the start of this project, we were convinced that our novel breeding method, which does not involve transgenesis at any step, would not produce plants that could be considered as GMOs.
In this context, the BUNGEE ERC Consolidator project had two major objectives: First, to study the impact climate change-related stresses on plant genomes, specifically focusing on transposable element (TE) activity. Here, we used a model plant to better understand how TEs may affect gene expression, development, and stress response. We have found that accelerated TE mobilization can change how plants respond to stresses thus lead to the acquisition of important traits, such as drought tolerance.
The second main objective was to directly implement our findings in crop breeding programs. For that, we have tested if controlled stress-induced TE mobilization can be used to breed climate-change ready crops. We focused our research on the two most important crops in the world: rice and wheat. In both crops, TE mobilization has led to phenotypic diversity and modified stress responses showing that it could be a useful tool for crop breeding. This strongly suggests that the methods tested in the frame of this project could be interesting for direct applications.
We then wanted to move on and test these novel traits actual in crop breeding programs, however in 2018 the EU and Switzerland have suddenly prohibited ALL novel crop breeding methods, including the one developed and used here. This meant that we could not perform field trials with wheat to see how our plants perform in a real-world scenario. This was a major unexpected drawback for this project. But we think that this is also an important and unexpected result: As it stands, all novel crop breeding methods invented after 2001 are effectively forbidden, no matter how they work.
The EU’s “precautionary principle” is being applied ad absurdum totally ignoring scientific evidence and advantages of novel technologies.
And yet, in this emergency context the EU keeps a blind eye on scientific evidence: Currently, novel methods that could greatly increase crop breeding speed, such as gene editing, are effectively prohibited. At the start of this project, we were convinced that our novel breeding method, which does not involve transgenesis at any step, would not produce plants that could be considered as GMOs.
In this context, the BUNGEE ERC Consolidator project had two major objectives: First, to study the impact climate change-related stresses on plant genomes, specifically focusing on transposable element (TE) activity. Here, we used a model plant to better understand how TEs may affect gene expression, development, and stress response. We have found that accelerated TE mobilization can change how plants respond to stresses thus lead to the acquisition of important traits, such as drought tolerance.
The second main objective was to directly implement our findings in crop breeding programs. For that, we have tested if controlled stress-induced TE mobilization can be used to breed climate-change ready crops. We focused our research on the two most important crops in the world: rice and wheat. In both crops, TE mobilization has led to phenotypic diversity and modified stress responses showing that it could be a useful tool for crop breeding. This strongly suggests that the methods tested in the frame of this project could be interesting for direct applications.
We then wanted to move on and test these novel traits actual in crop breeding programs, however in 2018 the EU and Switzerland have suddenly prohibited ALL novel crop breeding methods, including the one developed and used here. This meant that we could not perform field trials with wheat to see how our plants perform in a real-world scenario. This was a major unexpected drawback for this project. But we think that this is also an important and unexpected result: As it stands, all novel crop breeding methods invented after 2001 are effectively forbidden, no matter how they work.
The EU’s “precautionary principle” is being applied ad absurdum totally ignoring scientific evidence and advantages of novel technologies.
For the first aim we have been studying the genotypic variability induced by novel transposable element (TE) insertions in Arabidopsis and how these new insertions influence stress responses. We have mobilized TEs in Arabidopsis and generated plants with novel TE insertions. Using whole genome sequencing we detected the exact insertion sites of these novel TE copies in the genome. Notably, we discovered a strong preference of this TE to integrate into genes that are marked with specific histone modifications. We also identified several TE insertion hotspots in the Arabidopsis genome as several genes were hit by the same TE multiple times.
Interestingly, numerous lines with novel TE insertions showed a marked improvement in drought stress tolerance. By performing RNAseq on the selected lines containing novel TE insertions, we could precisely characterize how heat-stress response changes at genes targeted by this TE. This work has been published (Roquis et al., 2021).
Concerning the application of BUNGEE in crop breeding, we have made good progress: We have greatly improved the way we detect mobilized TEs after stress and drug treatments both at the molecular and at the bioinformatic levels (Zhang et al., 2021). To improve the sensitivity in the detection of novel TE insertions in our crops, we have generated reference genomes for the rice and soybean varieties used in this project using MinIon long read sequencing.
For rice, using these improved approaches we have identified at least three novel TEs that respond to the drugs and/or the applied stresses. Two of these respond specifically to heat stress and thus can now directly feed into a crop breeding program. We have produced large quantities of treated rice lines and tested them under control, heat, and drought stress in field trials at the Taiwan Agricultural Rice Institute (TARI) in 2020 and 2021. Due to Covid19 restrictions, we were not able to visit the field experiments. However, our collaborators at TARI performed phenotyping and sent us data. Using whole genome sequencing we could identify mutations in these plants that can explain the observed phenotypes.
The TE mobilization in soybean turned out to be more challenging. We have therefore decided to focus our efforts on wheat instead.
For wheat we rapidly managed to optimize stress and drug treatment conditions and have screened 24 varieties by mobilome sequencing. To be as fast as possible we are performing our experiments on spring wheat (2 months generation time). To also be able to directly implement this method for actual breeding programs in the future, we also included winter wheat (1 year generation time). Thanks to our systematic screening we identified a transposable element that could be mobilized in several wheat varieties. We were able to monitor phenotypic changes and modified stress responses under greenhouse condition.
We then wanted to carry out field trials with our treated lines, however and unexpectedly, there was a dispute on the legal status on our treated plant lines, leading to the assumption that these may be GMOs. Because of that it was then impossible to carry out the planned field trials in the frame of this project. Scientifically, this situation makes no sense at all, as numerous mutagenized crops are being grown on millions of hectares in Europe. This greatly limited the number of plants we could effectively screen (1000 instead of 100’000).
As planned in the frame of this project, an international conference on plant epigenetics and transposable elements has been organized. In 2018 the international plant epi/genetics conference took place in Angers, France, from October 29-31 and was attended by more than 130 international guests. Students and leaders in the fields of epigenetics and transposable elements presented their newest discoveries. Presentation and poster prizes were attributed to the best presentations and posters.
A second online conference was organized on the 25th of May 2022, at the end of this project, focusing novel crop breeding methods: “Novel Crop Breeding Techniques: Towards more sustainable agriculture”. This international conference was attended by 197 participants from all over the world.
Advances from this project were reported at 11 international conferences and at seminars in numerous universities in Switzerland and abroad.
Interestingly, numerous lines with novel TE insertions showed a marked improvement in drought stress tolerance. By performing RNAseq on the selected lines containing novel TE insertions, we could precisely characterize how heat-stress response changes at genes targeted by this TE. This work has been published (Roquis et al., 2021).
Concerning the application of BUNGEE in crop breeding, we have made good progress: We have greatly improved the way we detect mobilized TEs after stress and drug treatments both at the molecular and at the bioinformatic levels (Zhang et al., 2021). To improve the sensitivity in the detection of novel TE insertions in our crops, we have generated reference genomes for the rice and soybean varieties used in this project using MinIon long read sequencing.
For rice, using these improved approaches we have identified at least three novel TEs that respond to the drugs and/or the applied stresses. Two of these respond specifically to heat stress and thus can now directly feed into a crop breeding program. We have produced large quantities of treated rice lines and tested them under control, heat, and drought stress in field trials at the Taiwan Agricultural Rice Institute (TARI) in 2020 and 2021. Due to Covid19 restrictions, we were not able to visit the field experiments. However, our collaborators at TARI performed phenotyping and sent us data. Using whole genome sequencing we could identify mutations in these plants that can explain the observed phenotypes.
The TE mobilization in soybean turned out to be more challenging. We have therefore decided to focus our efforts on wheat instead.
For wheat we rapidly managed to optimize stress and drug treatment conditions and have screened 24 varieties by mobilome sequencing. To be as fast as possible we are performing our experiments on spring wheat (2 months generation time). To also be able to directly implement this method for actual breeding programs in the future, we also included winter wheat (1 year generation time). Thanks to our systematic screening we identified a transposable element that could be mobilized in several wheat varieties. We were able to monitor phenotypic changes and modified stress responses under greenhouse condition.
We then wanted to carry out field trials with our treated lines, however and unexpectedly, there was a dispute on the legal status on our treated plant lines, leading to the assumption that these may be GMOs. Because of that it was then impossible to carry out the planned field trials in the frame of this project. Scientifically, this situation makes no sense at all, as numerous mutagenized crops are being grown on millions of hectares in Europe. This greatly limited the number of plants we could effectively screen (1000 instead of 100’000).
As planned in the frame of this project, an international conference on plant epigenetics and transposable elements has been organized. In 2018 the international plant epi/genetics conference took place in Angers, France, from October 29-31 and was attended by more than 130 international guests. Students and leaders in the fields of epigenetics and transposable elements presented their newest discoveries. Presentation and poster prizes were attributed to the best presentations and posters.
A second online conference was organized on the 25th of May 2022, at the end of this project, focusing novel crop breeding methods: “Novel Crop Breeding Techniques: Towards more sustainable agriculture”. This international conference was attended by 197 participants from all over the world.
Advances from this project were reported at 11 international conferences and at seminars in numerous universities in Switzerland and abroad.
Surprisingly, we managed to mobilize a TE family that has never been observed being active in real time before. This may represent a major breakthrough in TE biology.