Gene Expressions And Interactions Of Ancestral Genomes In Natural Brassica Napus

Allopolyploidization is a common phenomenon of plant speciation,which is accompanied by the changes in genetics and epigenetics and gene expressions related to ancestral genomes.As the natural allopolyploids have a long history of evolution,their progenitor genotypes are difficult to find out.Through particular hybridization procedure,the restitution of ancestral species from one natural allopolyploid will provide unique materials and views to elucidate the behavior of the constitutional subgenomes and their interaction.Previously,by inducing the biased elimination of the C-subgenome chromosomes in natural Brasssica napus L.?A_nA_nC_nC_n,2n=38?,the ancestral B.rapa L.?A_nA_n,2n=20?was restituted,referred to as RBR;then the parental B.napus was backcrossed successively to RBR and a complete set of nine B.rapa-oleracea monosomic alien additional lines?MAALs,2n=21,A_nA_n+1Cn1-9?was established.In this study,combined with high-throughput sequencing technology,the gene expression changes between RBR and parental B.napus,and between RBR and the B.rapa-oleracea MAALs were compared,the results are as follows:1. Gene expression changes during the allo-/deallopolyploidization process of B.napusFrom the comparative leaves transcriptomic analyses between ZS11,RBR_ZS11,natural B.rapa and B.oleracea,a large number of differentially expressed genes?DEGs?between RBR_ZS11 and natural B.rapa were identified,suggesting potential effects of allopolyploidization/domestication of AA component of B.napus at the tetrapolyploid level.Meanwhile,it was revealed that up to 20%of gene expressions were immediately altered when compared with those in the A_n-subgenome.Interestingly,one fifth of these changes were in fact indicative of the recovery of ancestral gene expression alternations occurring since the origin of B.napus and showed association with homoeologous expression bias between A_n and C_n subgenome.Enrichment of Distinct Gene Ontology Categories of the above sets of genes further indicated potential cooperation of the A_n and C_n subgenomes of B.napus.Whole genome methylation analysis of ZS11 and RBR_ZS11revealed a small number of DEGs were identified in the differentially methylated regions,which only explained 6.4%of the down regulated expressed genes and 4.7%of the up-regulated expressed genes,respectively.2. Gene expressions of B.rapa-oleracea MAALs derived from natural B.napusThe transcriptomic analyses were carried out on the whole set of Brassica rapa-oleracea MAALs derived from the B.napus genotype Oro,to reveal the response of the A_nsubgenome to serial aneuploidy.Compared to diploid RBR_Oro,the genes of all MAALs showed various degrees of dysregulated expressions that resulted from cis-effects and more prevailing trans-effects.In addition,the trans-effect on gene expression in MAALs increased with higher levels of homology between the recipient A subgenome and additional C subgenome chromosomes,but less with gene numbers of extra chromosomes.A total of 10 trans-effect dysregulated genes from pairwise comparisons were mainly involved in the function of transporter activity.Furthermore,it was found that highly expressed genes were more inclined to downregulation and vice-versa,hinting a common trend for transcriptional responses to aneuploidy.Similar results were also detected in other studies related,suggesting a common trend of individual response to aneuploidy.