Transcriptome Analysis And Genome-wide DNA Methylation Patterns Associated With Vernalization In Chinese Cabbage (Brassica Rapa L.ssp.pekinensis) Seeds

Flowering is the typical phenomenon in the process of transformation from vegetative growth to repro-ductive growth around the plants life cycle whie vernalization shows a crucial role in plants flowering time.Plants vernalization can mainly be divided in two types,one is green body-vernalization-type,the other is seed-vernalization-type while Chinese cabbage(Brassica rapa L.ssp.pekinensis)is the typical seed-vernalization-type plant.In this paper,we compared with two treatments of Chinese cabbage 'FT' seeds named as Normal(Nor)and Vernalization(Ver).Illumina high-throughput sequencing technology and bisulfite sequencing tech-nology were be used for transcriptome analysis and whole genome DNA methylation analysis,respectively.Through the correlation analysis between genes expression level and DNA methylation level to deeply comprehend the molecular mechanism in Chinese cabbage seeds associate with vernalization.Main con-clusions as follow:1.Acording to the transcriptome sequencing results,there were 3379 differently expressed genes(DEGs)with FDR<0.001 and |log2Ratio|>2 can be received,containing 1016 DEGs were up-regulated and 2363 DEGs were down-regulated from Nor vs Ver.DEGs were enriched in both GO and KEGG database,a to-tal of 2670 DEGs were enriched at last one GO terms of which 7 GO terms were related to vernalization and flowering.In KEGG Pathway approach,a total of 1875 DEGs enriched in 240 metaboic pathways of which 40 pathways were significantly enrichment,mainly include metaboic pathways,plant hormone signal transduction pathways.2.In the transcriptome database,there were 17 DEGs related to vernalization and flowering can be de-tected.Including 4 members of FLC family(Bra006051?Bra009055?Bra028599 and Bra022771)and 2 members of VIN3 family(Bra006824 and Bra010317).As a negative and positive factor in vernalization regulatory network,the expression level of FLC were down-regulated and the expression of VIN3 were up-regulated in vernalized seeds of Chinese cabbage in our study.3.Acording to the bisulfite sequencing,there were 1314 differently methylated genes(DMGs)can be detected which 734 genes presently high methylation level while 580 genes present low in Nor vs Ver.4.A conjoint analysis was accomplished between the combination with 3379 DEGs and 1314 DMGs.A total of 106 genes can be shared both in DEGs group and DMGs group.Furthermore,56 genes have nega-tive correlation between transcription level and methylation level,of which 46 genes expressed low but methyled high and 10 genes expressed high but methyled low during vernalization,mainly include 5 tran-scriptors and 1 heat shock protein.Still,8 genes with unknown function also be found.5.Relatively qPCR expression analysis was performed on 18 genes(10 vernalization related genes and 8 random genes from shared genes both in DEGs and DMGs),testing results revealed that the relative ex-pression analysis is consistent with genome sequencing,improving that our data is reliability and availabil-ity.