Research On The Genomic Variations And Gene Expression Changes During Wheat Hexaploidization Events

Polyploidization has long been recognized as one of prominent driving force shaping the speciation and evolution of eukaryotes,and the newly formed allopolyploids will undergo extensive genomic variations and gene expression changes.Bread wheat(Triticum aestivum)is a typical allohexaploid and one of excellent models for the exploration of allopolyploidization.Comprehensive and systematic research on the genomic variation and gene expression changes can contribute to elucidating the formation of allohexaploid wheat and genomic evolution mechanisms,and is of great significance in exploring the molecular underpinnings of phenotypic variations accompanying the formation of allohexaploid wheat as well.To study the genomic variations and gene expression changes at the genome-wide level during wheat hexaploidization events,we performed high-throughput whole exome and transcriptome sequencing of three sets of independent synthetic allohexaploid wheat lines and their corresponding progenitors.The main results of this work are summarized as follows:1.A total of approximately 1.1 billion high-quality exon-captured reads were generated.In the three sets of materials,we observed that approximately 3.61%-5.04%of the parental sequences were eliminated during the formation of allohexaploid wheats,accounting for 1.70%～2.45%of the total length of the parental sequences.We found that the sequence elimination during the formation of hexaploid wheat follows somes rules:(1)more sequences were eliminated from the D genome compared with A and B genomes;(2)sequences were preferentially eliminated from exonic regions in D genome,with a high number of hotspots showing preferential sequence elimination in each of chromosome;a significant enrichment of sequence loss was observed in the repeat-rich intergenic regions on the A and B genomes,in contrast to gene density;(3)sequence elimination often occurred in the regions showing high similarity with their homeologous sequences,whereas homeologous sequences with unique variations were preferentially retained;(4)488 overlapped genes with sequence elimination were detected across all three sets of synthetic wheat in D genome,however,no gene with eliminated sequences was shared by the three sets of synthetic wheats in A and B genomes;(5)we compared gene ontology(GO)enrichments of genes in regions of sequence elimination from the three wheat subgenomes and found they were enriched in distinct functional pathways.2.The newly formed allohexaploid wheats were often accompanied by extensive gene express changes.We found that approximately 5.73～21.39%of the genes were differentially expressed in synthetized allohexaploid wheat lines compared to their parents.Besides,we identified about 2.33～44.80%non-additively expressed triplets,of which the proportion varied in different materials.We found that approximately 25.99～30.12%of triplets exhibiting homeolog-biased expression patterns.Among the homeolog-biased triplets,a higher proportion of triplets preferentially expressed the D-genome homeolog,compared with those that preferentially expressed toward to the A-genome and B-genome homeolog.Furthermore,approximately 41.84～64.52%of homeolog-biased triplets also exhibited unbalanced expression patterns among their parents,indicating that these biased expression profiles were vertically inherited from their respective progenitors.Finally,it was concluded that epigenetic modifications,rather than genomic variation,may cause most transcriptomic changes during wheat allohexaploidization.