Insight in single nucleotide polymorphisms focused on post transcriptional modifications in Arabidopsis thaliana

abstract

English

Current research in plant bioinformatics bears huge potential for plant breeding projects, given the abundance of high-quality genotype and phenotype data, as for example, for model organism Arabidopsis thaliana and crop plants. Genome-wide association studies (GWAS) and Quantitative Trait Loci (QTL) studies have already revealed many single nucleotide polymorphism (SNP) trait associations and identified causal genes, which was made possible also by applying advanced algorithms and computational approaches. We have established a study that searches for causal proteins and that assesses the relevance of post-transcriptional using published polymorphism data in A. thaliana studied under a wide range of environmental stress conditions, such as cold, salinity, starvation, etc. Candidate GWAS loci were analysed using the AraGWAS Catalog, which offers a publicly available, manually curated and standardized significance based on permutation threshold or Bonferroni threshold in GWAS for all publicly available phenotypes of A. thaliana, as available in the phenotype repository, AraPheno. Thus far, we identified 14 synonymous and 17 non-synonymous coding SNPs that are potentially connected to the post-transcriptional regulation of protein function. Also, we detected SNPs included 90 genic and 14 non genic candidate SNPs. After Bonferroni correction, only two SNPs were detected as significant. Specifically, these two SNPs are connected to SuperOxide Dismutases (SODs). SODs are usually expressed under stress conditions for the purpose of detoxification. In addition, recent studies indicate that CSD1 and CSD2 are transcribed at equal levels under normal or oxidative conditions. Thus, the candidate SNPs indicate that their mRNAs may either result in post-translationally changes or may have post-translational effects. In summary, we manually checked 104 possible SNPs that are suspected to modify the post-transcriptional/transcriptional modification of Arabidopsis proteins. Moreover, we identified four SNPs located in the 3’ UTR and nine analysed SNPs in 5’ UTR. In the future, we plan to also investigate promotors regions, as promoter SNPs can cause significant changesof gene expression regulation.

Arabidopsis thaliana, Single nucleotide polymorphism, Post-transcriptional regulations

SCHWARZEROVÁ, J.; WECKWERTH, W.; WALTHER, D.

24. 9. 2022

NGSymposium

Warsaw

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https://drive.google.com/file/d/1CjzmlmKxGlM0j91TYcB1mMCmnVEGeD59/view