Global Analysis Of Gene Expression In Response To Whole-Chromosome Aneuploidy In Hexaploid Wheat

Gene duplication is a major source of new genes,and its occurrence leads to changes in dose,ranging from genome-wide replication to single-gene duplication.Therefore,polyploidy and aneuploidy may contribute to the emergence of new genes.Studies have shown that the newly synthesized allopolyploid often accompanied by a high frequency of aneuploidy,including variations in chromosomes number structure.Why is there an aneuploid? Aneuploidy is an ephemeral byproduct of whole genome duplication or represents an important contributing factor to polypoid genome evolution,there is still remaining largely unknown.Although aneuploidy has been described with the formation of allopolyploidization,variations in the level gene expression have rarely been reported.In this study,we collected a panel of diverse types of whole-chromosome aneuploidy,including variable doses of whole-chromosome gain,loss or concomitant gain and loss of homeologous chromosomes,primarily of the homeologous group 1 as representatives.By combining FISH/GISH with transcriptome sequencing to investigate how to respond to the occurrence of aneuploidy in allopolyploid.According to the partition of the different types in the RNA-sequencing results,we explored the effects of aneuploidy in polyploidy background and the final phenotypic consequences.Aneuploidy in allohexaploid wheat can induce a global effect at the transcriptional level,which is mainly regulated by cis-effects and trans-effects.In the meantime,allohexaploid wheat also has a certain proportion of dosage compensated genes to buffer the impacts of aneuploidy.Moreover,Gene Ontology(GO)analysis revealed that genes showing different types of effects were enriched for distinct terms.The dysregulated genes expression by aneuploidy were evenly distributed on each unvaried chromosome,and no aggregated distribution of the deviations of certain chromosome regions were found.However,we observed the preference of certain chromosomes as a whole.The most significant is that the chromosome 2B shows the most sensitive response in most aneuploids.In addition,subgenomes in hexaploid wheat are unequal in their responses to aneuploidy.The subgenome B is more sensitive to most types of the whole-chromosome aneuploidy than subgenomes A and D,while subgenomes A and D have similar degrees of response in all aneuploids.Strikingly,homeologous chromosomes were not more responsive than nonhomologous chromosomes regarding transcriptional responses to whole-chromosome aneuploidy in hexaploid wheat,suggesting that the three constituent subgenomes of hexaploid wheat are largely uncoupled at the transcriptional level of gene regulation.Expectedly,aneuploids in allohexaploid wheat caused aneuploidy phenotype syndrome,as well as observed chromosome-specific phenotypes.In summary,we first systemically investigated the impact of whole-chromosome aneuploidy on transcriptome level gene expression in hexaploid wheat.Compared with prior studies mainly concerning diploid or haploid genomes,we have unraveled novel features of chromosome-,subgenome-and genome-wide gene expression alterations associated with the diverse types of aneuploidy in an important allopolyploid genome that constitutes one of the most important agricultural crops human has ever domesticated.Our findings provide new insights towards deeper understanding of an allopolyploid genome in respect of its gene regulatory and functional interplay and their phenotypic manifestation,which bears significance in the contexts of polyploidy,a ubiquitous and cyclic event associated with the evolutionary history of all higher plants.Our results may also have implications in the translational aspect of functional genomics studies with respect to creating novel crops via hybridization and polyploidization.