| In the present study, the petal degeneration mutant, pdm, and its wild type line’FT’in Chinese cabbage were the test materials, morphological description of petal in ’FT’ and pdm and the genetic characterization of petal degeneration trait were analyzed. A global analysis of mRNA isolated from flower buds of pdm and ’FT’ was performed using the RNA-Seq platform. The main results are as follows:1. Compared with wild type’FT’, the petals of pdm were degenerated, shriveled, and not expanded. The doubled-haploid lines of petal degeneration mutant pdm, and its wild type line ’FT’ in Chinese cabbage were selected as the parents. Genetic analysis was doing in the F1, F2 and BC1 generation. The results showed that the petal degeneration character was controlled by a pair of Nuclear allele.2. the two cDNA libraries separately constructed from flower buds of ’FT’ and pdm were sequenced using the Illumina HiSeq 2000 sequencing platform, and were named EP and NEP, respectively. We obtained a total of 95,588,252 raw reads from both libraries. After assessment and data filtering,45,781,982 reads were from EP and 46,990,196 were from NEP. A total of 89,245 and 89,630 AS events were identified in EP and NEP, respectively. Twelve different types of AS events were identified, the frequency of each AS event in EP was highly concordant with those in NEP. Of the 12 types of AS evemts, TSS and TTS were the most prevalent, occupy 80% of all AS events identified in the EP and NEP libraries, respectively. In addition, we map the reads against the reference genome, a total of 6,947 novel transcripts were identified in the EP and NEP libraries, respectively.3. We detected 185,445 SNPs from EP and 186,534 from NEP, respectively. In addition, 10,583 and 10,673 Indels were identified in EP and NEP, respectively. The molecular markers, SNPs and Indels, will provide a rich resource for the development valuable molecular markers and functional genomics studies in Chinese cabbage.4. A total of 117 differentially expressed genes were identified between EP and NEP based on RPKM, among them,40 genes were up-regulated,77 genes were down-regulated. In addition, two differentially-expressed novel genes (Novel 100483 and Novel 100708) were found. The biological functions of these two novel genes remain to be determined. It is notable that a number of stress genes that can respond to water, cold damage, mechanical injury, or plant diseases and insect pests were identified among the DEGs.5. Among the DEGs, a number of floral development and flowering-related genes were identified, including genes for an F-box protein (Bra014407), the EARLY FLOWERING 4 (ELF4) protein(Bra017035), the transcription factor BPE (Bra019935), and the transcription factor MYB21 (Bra025300 and Bra039067). Eight genes involved in floral reproductive system development (pollen and anther) were also found, such as pollen-specific leucine-rich repeat extensin-like protein (Bra001730, Bra017617 and Bra037543), beta-expansin protein 5 (Bra003421),protein SKU5-like 13 (Bra034679), ATOPT1 (Bra035596), and putative tapetum-specific A3 protein (Bra020920 and Bra038803). To analyse these gene expression patterns would offer some new informations to understand the flowering mechanism in Chinese cabbage.6. A total of 93 DEGs were assigned to 754 GO terms in three GO ontologies, which mainly included growth, development, metabolism, and immune defense. To identify the biological pathways in the NEP vs. EP comparison,117 DEGs were mapped to 41 KEGG pathways, the most terms were related to Metabolic pathways (ko01100), the next were biosynthesis of secondary metabolites (ko01110) and alpha-Linolenic acid metabolism (ko00592). |
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