Preliminary Study Of RNA/DNA Difference(RDD) Landscape And Its Regulatory Function In Wild Emmer Wheat(Triticum Dicoccoides Koern.)

RDD(RNA/DNA difference),also known as RNA editing,refers to the conversion,insertion or deletion of the bases in the process of genetic information from DNA transcription to RNA.It is a conserved post-transcriptional regulation mechanism commonly found in organisms.At present,a large number of studies has been carried out in human,mouse,yeast and other organisms.In plants,RNA editing related research mainly focuses on organelle genomes and has been shown to be involved in regulating plant growth and development and stress response.However,there are few studies on RNA editing in plant nucleus.Wild emmer wheat is a close ancestor of common wheat.As the donor of A and B subgenome,it has always been an important germplasm and gene pool for wheat genetic improvement.In order to excavate and utilize the excellent gene resources of wild emmer wheat and enrich the understanding of its growth,development and stress response regulation mechanism,this study used the excellent germplasm A5 of wild emmer wheat as the material,based on its genome resequencing data and 138 RNAseq datas under different tissues,parts and stress treatments,the RNA editing sites related to its growth and development and stress response were identified by REDItools software,and the RNA editing map of the nuclear genome of wild emmer wheat was preliminarily constructed.On this basis,the effects of RNA editing on RNA secondary structure,protein coding and mi RNA binding were predicted,and the regulatory role of RNA editing was preliminarily clarified,which laid a foundation for further analysis of the biological function of RNA editing.The main results are as follows :1.Construction of RNA editing map of wild emmer wheat.Based on resequencing data,138 RNA-seq datasets were used to identify the RDD sites in the nuclear genome of wild emmer wheat.A total of 3,420 RDDs were identified,distributed in 832 genes,of which 1,513 RDDs were located in CDS region,305 in UTR region,and 1,062 in intergenic region.They were distributed on 14 chromosomes of wild emmer wheat,among which 6A was the most with 199,followed by 2B with 180,and 4A chromosome contained the least with 27.Compared with SNP sites in the genome,the differences of RDDs in genomic distribution regions and base variants indicated the accuracy of our prediction results,and the RNA editing map of wild emmer wheat was preliminatively constructed.2.Identification and regulation of growth and development related RDD in wild emmer wheat.A total of 2,479 growth-development-related RDDs were identified,distributed in 643 genes.The 10 nt base sequences of the upstream and downstream sites of RDD were extracted and analyzed.It was found that RDDs had a certain preference for the bases adjacent to the mutation site.The occurrence of RDD changed the minimum free energy of 544 genes,and then changed the secondary structure of RNA.In addition,RDD altered the binding of 76 mi RNAs to target genes and altered the conserved domains of 7proteins.Functional enrichment of the genes where RDDs are located revealed that these genes were enriched in several items related to plant organ development,signal transduction,substance synthesis and transportation.These results suggest that RDDs can regulate gene expression by affecting RNA secondary structure,mi RNA targeting,protein conserved domain,and protein tertiary structure,and play an important role in plant growth and development.3.Identification and regulation of RDD related to stress response in wild emmer wheat.By analysis,362,347,551 and 410 RDDs related to salt stress,drought stress,heat stress and cold stress response were identified,which caused changes in the minimum free energy of 78,81,64 and 95 RNAs,respectively.The binding of 22,28,12 and 30 mi RNAs to target genes was changed.There were 1,1,1 and 4 RDDs related to salt stress,drought stress,heat stress and cold stress,respectively,which caused changes in their protein conserved domain.In addition,differential expression analysis of RDD genes indicated that they play an important role in plant resistance to stress.In this study,we systematically identified and analyzed the RDD sites in the nuclear genome of wild emmer wheat,constructed its RNA editing map,and preliminarily revealed the regulatory function of RDD.This study laid a foundation for further analysis of the biological functions of RNA editing in regulating growth and development and stress response of wild emmer wheat.The established analytical methods and procedures can provide tools and references for RNA editing analysis in other plant nuclear genomes.