INSPIRATION · Investigation of the SNP-induced RNA structure variations between subgenomes in polyploid wheat
Horizon 2020 — Marie Skłodowska-Curie Actions
- Duration
- 2019-09-01 → 2022-10-24
- EU contribution
- €224,934
- Participants
- 1
- Scheme
- MSCA-IF
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Results in brief
Investigation of the SNP-induced RNA structure variations between subgenomes in polyploid wheat
This project was designed to investigate the RNA structural difference between subgenomes of polyploid wheat and its functional consequences. Polyploidization is very ubiquitous in the plant kingdom. Nearly all of the angiosperm plant species have been subjected to one or multiple rounds of polyploidization during their evolution. Polyploidization is one of the major driving forces of plant evolution and crop domestication and plays a key role in the success of plants adapting to a wide variety of environments on our planet. However, knowledge is still limited in understanding how the vast majority of sequence variations over the gene body drives homoeologs sub/neofunctionalization, evolution and environmental adaptation. Wheat is a wide-grown polyploid crop over the world. Thus, this project could address how RNA structure regulation is involved in subgenome functional diversification and environmental adaptation in polyploid plants. There are two overall objectives: 1) generate mRNA structure profiles for different subgenomes in wheat at a whole-genome scale; and 2) investigate the functional relevance of RNA structure difference between subgenomes.
Data: CORDIS, © European Union
Project objective
Polyploidization is one of the major driving forces of plant evolution and crop domestication and plays a key role in plant environmental adaptation. The function of multiple gene copies (homoeologous genes) from different subgenomes can vary from each other (sub/neofunctionalization), which is considered as the key to understanding polyploidy evolution and environmental adaptation. However, most sequence variations between homoeologous genes lie on the non-coding region or are synonymous mutations, which cannot lead to codon change. To data, very little is known about how the vast majority of sequence variations over the gene body regions drives subgenomes sub/neofunctionalization in polyploidy.Recently, Single Nucleotide Polymorphism (SNP) induced RNA structural alteration is demonstrated to play key roles in post-transcriptional regulations such as RNA decay and splicing. Further studies in human disease showed that SNP-induced RNA structural changes are associated with diverse human disease and phenotypes. And also, temperature can affect the RNA structures that more stably folded mRNAs tended to show lower decay rate. This brought attention to the existing function of synonymous mutations as well as non-coding SNPs. Thus, I hypothesize that SNP-induced RNA structural alteration might lead to the subgenomes sub/neofunctionalization and play an important role in temperature stress response.As tetraploid wheat is widely grown in the Europe and its yield is severely affected by heat stress, I will test my hypothesis in tetraploid wheat. Firstly, genome-wide RNA secondary structure profiling will be applied to compare SNP-induced RNA structure variations between subgenomes in tetraploid wheat. Secondly, I will investigate the roles of SNP-induced RNA structure variations in RNA stability and splicing pattern changes between subgenomes. Finally, I will assess the role of SNP-induced RNA structure variations in response to high temperature.
Original text from CORDIS.
Participants
- JOHN INNES CENTRE · NorwichCoordinatorUnited Kingdom
Links
Data: CORDIS, © European Union