Gene Expression Perturbation By Intra-and Interspecific Aneuploidy In Brassica Napus L.

Aneuploids for one species refer to the individuals or cells with one or more extra or missing chromosomes in the normal number(2n),including intra-/ interspecific types.Plants are more tolerable to aneuploidy than animals,and particularly the allopolyploids can tolerate the loss of individual chromosomes from their complements.One nullisomics(2n = 36)of B.napus was previously obtained and showed the much shorter plant height and smaller size than the donor,but the identity of the chromosome lost remained unknown.In this study,the cytology and global gene expressions of the nullisomics and the monosomics derived are investigated in comparison with original euploid B.napus,to reveal the dosage effects of different copies of one particular chromosome on the transcriptomic disturbances,and the gene expressions associated with the phenotypic devaition.Together,global gene expressions of two disomic additions(2n=40,AACC+1II RR1-9)between B.napus and Raphanus sativus L.(2n=18,RR)are studied in comparison with two parents,to determine the effects of individual alien chromosome on the Brassica transcriptome perturbation and their interplay.The main results are described as follows:1.Transcriptomic analysis of monosomics and nullisomics in B.napusFluorescence in situ hybridization(FISH)analysis with the C-genome specific BAC probe demonstrated that the missing chromosomes in nullisomics and monosomics were from C-genome.The gene expressions specific for each chromosome further confirmed that the chromosome pair C2 in B.napus was missing in the nullisomics.By the comparative analyses on the global transcript profiles with the euploid donor,genome-wide alterations in gene expressions were revealed in two aneuploids,and their majority of differentially expressed genes(DEGs)resulted from the trans-acting effects of the zero and one copy of C2 chromosome,as only 3.89% of DEGS in monosomics and8.22% in nullisomics were directly contributed by the missing chromosome C2.The higher number of up-regulated genes than down-regulated genes on other chromosomessuggested that the genome responded to the C2 loss via enhancing the expression of certain genes.Particularly,more DEGs were detected in the monosomics than nullisomics,contrasting with their phenotypes.The gene expressions of the other chromosomes were differently affected,and several dysregulated domains in which up-or downregulated genes obviously clustered were identifiable.But the mean gene expression for homoeologous chromosome A2 reduced with the C2 loss.Despite immense difference of DEGs number in two aneuploids,the proportions of Go terms for DEGs were quite similar for both pair comparisons,which,together with a comparatively high proportion of common DEGs,further highlighted the speculation that a similar mechanism emerged to respond to the C2 missing.In accordance with the phenotypic alterations of the nullisomics,the expressions of the genes related with auxin and those controlling flowering also showed consequent changes,which gave partial explanations for the phenotype associated with the C2 loss,despite the temporality and spatiality of gene expression.2.Transcriptomic analysis of B.napus-R.sativus disomic additionsFrom pairwise comparisons on genome-specific genes across addition lines and their parents,there were significantly less genes showing differential expression(DEGs)between BNR1 and BN than those between BNR2 and BN.Whereas the reverse was true when the addition lines were compared with radish parent,for more DEGs were observed in BNR1 BNR2.The distributions of fold change were distinct between the additions and two parents,and also between two additions.In comparison with B.napus,the up-/down regulated genes distributed evenly,with most genes unexpressed.But compared with radish,down-regulated genes were dominant.These results showed that the addition of different radish chromosomes might have different effect on the gene expression.Significant differences in the distributions of DEGs on A and C genomes and their chromosomes existed between additions and B.napus.In the comparison between BNR1 and B.napus,the number of up-and down-regulated genes was very close for A genome and its every chromosome,while C genome had three times more the down-than up-regulated genes,and its each chromosome also showed more downs than ups,particularly on C1、C3、C6.In the comparison between BNR2 and B.napus,A genome and its every chromosome kept the similar number of up-and down-regulated genes,and C genome gave no obvious bias,only C2、C3 chromosomes had more downs,and its each chromosome also showed more downs than ups,particularly on C1、C3、C6.The overall distribution of most DEGs along the chromosomes seemed to be random,especially in A genome.However,large regions of up-or down-regulated genes were observed some C genome chromosomes(C1,2,3,5,6).The analysis of the co-differentially expressed genes between both addition lines and B.napus illustrated that about one half of the differentially expressed genes(1103 in 2349)between BNR1 and BN were also shared in the other comparison(BNR2 vs BN),suggesting that they were sensitive to aneuploidy.269 genes were up-regulated in both additions,and some were associated with the responses to stimuli and stress.The co-down-regulated 693 genes were mainly related with cellular,metabolic and synthetic processes.By comparing the expression levels of homoeologous gene pairs between A and C subgenomes in both addition lines and B.napus,3867 gene pairs showed homoeolog expression bias(1846 A-bias and 2021 A-bias)in B.napus.However,both additions showed more biases overall than B.napus,suggesting that addition of radish chromosome might increase the expression bias between B.napus A and C genome.The expression bias in B.napus was largely maintained in additions,and the common biases in the additions should result from the alien chromosomes.