Characterizing The Transcriptome Of Differetn Rapeseeds Under Different Breeding Process By RNA-SEQ

Brassica napus (AnAnCnCn) is an important oil crop not only in China even in worldwide, and is a typical allotetraploid species undergone interspecific hybridization in Brassica species. In breeding process of B. napus, interspecific hybridization and introgression of exogenous genome is a frequent approach to broaden the genetic background of B. napus and create new genetic resource. Our laboratory has created new B. napus through the large-scale interspecific hybridization, which An genome or AnCn genome was replaced by Ar of B. rapa and Cc of B. carinata. We found that a large number of chromosomal rearrangements events and new genomic variation accompanied by the reactivation of transposons would be happened in the genome of new type B. napus.In this study, the transcriptome sequence of eighteen cultivars of rapeseeds under different breeding process in seedling stage was analyzed by RNA-seq, which includes B. rapa, interspecific hybridization B. napus and no-interspecific hybridization B. napus. By use the genome-wide level analysis of express genes and transposons characteristics under different breeding process of B. napus, we try to detect the influence of different breeding process on B. napus genome, such as hybrid and introgression of exogenous genome. And analyzed the differently expressed transposons in different genome stress conditions, mainly analyzes and results are as follows:1. Using Brassica95k Unigene as reference, we analyzed gene expression of B. rapa and under different breeding process (interspecific hybridization and introgression of exogenous genome) of B. napus. The results showed that the number of gene expression of B. napus is more than B. rapa. The number of co-expressed genes in all rapeseed is43492(46%). And the number of only expressed genes in new type B. napus which import Ar of B. rapa and Cc of B. carinata is3814. This result indicated that the introgression of exogenous genome affects the original genome. 2. By analyzing differently expressed genes of different B. napus under different breeding process, we found that genes between different B. napus and B. rapa showed a gradual increase with the difference of breeding process and breeding time. It indicated that interspecific hybridization process changed rapeseed genes expression. Compared with B. rapa, the number of up-regulated genes was significantly more than the number of down-regulated genes, suggesting that most of the genes was excited. Analysis of expression between progeny and parents showed that the progeny has large difference with one of the parents, but the other parent and the average of the parental have smaller difference. The up-regulated genes and the down-regulated genes are almost the same. But if one of the parents is B. rapa, the number of up-regulated genes is more than the down-regulated between progeny and parents.3. We analyzed the differential type of expressed transposons of different B. napus using unigene by Trinity assembly. The results showed that about1%of transcriptome are repeats sequences. And the number of retro-elements is more than the number of DNA transposons, and the total number of DNA transposons (Class II) as well as the number of tourist/Harbinger of DNA transposons is significant different in different B. napus.4. We analyzed differently expressed transposons of different B. napus by the new Brassica transposons database. The results showed that about0.30%reads of B. napus by interspecific hybridization mapped new Brassica transposons database, which is three time of B.rapa. And0.23%reads of B. napus not by interspecific hybridization mapped new Brassica transposons database, which is twice of B. rapa.5. The transposons in different rapeseeds had different expression. The number of differently expressed transposons between B. napus and B. rapa is more than the number of which between B. napus under different breeding process. The EnSpm, HAT, MuDR, and Helitron and Copia and Gypsy have more differently expression transposons. The number of up-regulated transposons is more than down-regulated between B. napus and B. rapa. By the statistics of differential expressed transposons based on pedigree between progeny and parents, we found that most of the transposons are expressed, but the expression level is different. Most of differential expressed transposons had large difference with one of the parents, but the other parent and the average of the parental have smaller difference.