The Molecular Basis for Evolution and Adaptation in Brassica Polyploid Plants
|Keywords||Brassica allohexaploid Raphanobrassica transcriptome geneexpression differentially expressed genes stress response|
Polyploidization has played a very important role in plant evolution and speciation. The researches of polyploidy plant had developed from morphological and physiological level to the genomic and transcriptomic level. However, there were relative little researches about distant hybridization polyploid and hexaploid. We chose an intrageneric allopolyploid and an intergeneric allopolyploid, and studied their gene expression under both regular growth and abiotic stress environment.We explored the transcriptomic changes of synthetic Brassica allohexaploid by comparing to its parents using a high-throughput RNA-Seq method. A total of35644409sequence reads were generated, and32642genes were aligned from the data. There were29260,29060and29697genes identified in B. rapa, B. carinata, and Brassica allohexaploid, respectively. We screened differentially expressed genes (DEGs) by a standard of two-fold or greater change in expression and false discovery rate (FDR) no more than0.001. As a result,7397DEGs were detected between Brassica hexaploid and its parents. A large proportion of the3184DEGs between Brassica hexaploid and its paternal B. rapa was involved in biosynthesis of secondary metabolites, plant-pathogen interaction, photosynthesis, and circadian rhythm. Between Brassica hexaploid and its maternal B. carinata,2233DEGs were screened. A lot of them had functions of plant-pathogen interaction, plant hormone signal transduction, ribosome, limonene and pinene degradation, photosynthesis, and also biosynthesis of secondary metabolites. Based on the analysis of the DEGs between Brassica hexaploid and its parents, we discovered there were bigger differences on the level of gene expression between the allohexaploid and its paternal parent than that between the allohexaploid and its maternal parent. This variation may partly be affected by the cytoplasmic and maternal effects. In addition, we found many transcription factor genes, methyltransferase and methylation genes that showed differential expression between Brassica hexaploid and its parents. Accounting to7.797%of the total detected genes was nonadditively expressed in Brassica hexaploid. Compared with the additive genes in Brassica hexaploid, the nonadditive genes were significantly enriched in biological processes related to stimulus response, immune system, cellular metabolic, rhythmic process, developmental process, pigmentation, seed germination, and tropism, and in the molecular functions associated with catalytic activity, antioxidant activity, and transcription regulator activity. Our results demonstrated that Brassica allohexaploid can generate extensive transcriptomic diversity compared to its parents. These changes may contribute to the normal growth and reproduction of allohexaploid.By comparing the sequences of some homoeologous genes from different parents, we found that there was high homology between sequences from Brassica carinata and Brassica rapa. The sequences from Raphanus sativus and Brassica alboglabra were also highly homologous, while the homology was lower than that between B. carinata and B. rapa. Under regular growth, most of genes we studied were non-additive expressed in Raphanobrassica and Brassica allohexaploid. The genes in Raphanobrassica showed maternal-biased expression. Several genes in Brassica allohexaploid had an expression level higher than the union of two parents, which showed an effect of gene dosage. But the gene-dosage effect were not seen in other genes.In the low temperature stress experiment, the expression level of most genes was down-regulated after six hour treatment. The reason of this result may be the longer time of stress. We noticed that the expression level of PAL was significantly up-regulated after six hour stress, which indicated that the time needed by metabolic pathway to respond to low temperature stress was a little longer than antioxidant enzyme system. The tendency to increase first and then decrease was observed in the gene expression of Raphanobrassica, Brassica allohexaploid and their parents under salt and drought conditions. The rate of gene expression change in Raphanobrassica was lower than its parents, with no significant differences between the ranges of expression change. A lot of genes in Brassica allohexaploid showed a quick and significant up-regulation under salt and drought stress. These results showed that the ability of bearing abiotic stress in Raphanobrassica were much higher, while the adaptive capacity to abiotic stress in Brassica allohexaploid were much higher. In short, there were different molecular mechanisms for stress-resistant in different polyploid.By the study of Brassica allohexaploid and Raphanobrassica, we explored the influences of distant hybridization on polyploidization process; searched the molecular mechanisms of stress-resistant in polyploid; and also provided a fundamental research for the investigation of evolution and adaptation mechanisms in polyploid plant.