Comparative transcriptome analysis of the petal degeneration mutant pdm in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq
Comparative transcriptome analysis of the petal degeneration mutant pdm in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq
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DOI：
10.1007/s00438-015-1041-7
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发表时间：
2015-04
影响因子：
3.1
通讯作者：
Shengnan Huang;Zhiyong Liu;R. Yao;Danyang Li;H. Feng
中科院分区：
文献类型：
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作者：
Shengnan Huang;Zhiyong Liu;R. Yao;Danyang Li;H. Feng
开花是有花植物从营养生长向生殖生长转变的关键环节，在有花植物的生长发育中起着至关重要的作用。本研究的目的是检测大白菜突变体和相应的野生型品系“FT”的转录组之间的差异。我们使用Illumina RNA测序（RNA-Seq）数据对从pdand 'FT'的花蕾分离的mRNA进行转录组分析。共检测到117个差异表达基因。在DEG中，我们鉴定了许多参与花发育和开花的基因，包括F-box蛋白基因，EARLY FLOWARTH 4（ELF 4），以及转录因子BIGPETAL（BPE）和MYB 21（v-myb禽成髓细胞瘤病毒癌基因同源物）;这些基因的差异表达可能解释pdandFT之间花的差异。此外，对12个花发育和开花相关基因和8个随机选择的基因进行了qRT-PCR验证，结果与RNA-Seq结果高度一致。进行基因本体和京都基因百科全书和基因组途径富集分析以更好地理解这些DEG的功能。本研究还鉴定了大量的单核苷酸多态性和插入/缺失标记，为今后大白菜标记开发和育种研究提供了丰富的资源。此外，我们的分析揭示了许多新的转录本和选择性剪接事件。转录组分析为进一步了解大白菜开花过程的分子调控机制提供了有价值的信息，并为今后大白菜的遗传和功能基因组研究奠定了基础。
Flowering, which plays a crucial role in the growth and development of flowering plants, is a crucial point from vegetative growth to reproductive growth. The goal of this study was to examine the differences between the transcriptomes of the Chinese cabbage mutantpdmand the corresponding wild-type line ‘FT’. We performed transcriptome analysis on mRNA isolated from flower buds ofpdmand ‘FT’ using Illumina RNA sequencing (RNA-Seq) data. A total of 117 differentially expressed genes (DEGs) were detected. Among the DEGs, we identified a number of genes involved in floral development and flowering, including an F-box protein gene,EARLY FLOWERING 4(ELF4), and transcription factorsBIGPETAL(BPE) andMYB21(v-myb avian myeloblastosis viral oncogene homolog); differential expression of these genes could potentially explain the difference in the flowers betweenpdmand ‘FT’. In addition, the expression patterns of 20 DEGs, including 12 floral development and flowering-related genes and eight randomly selected genes, were validated by qRT-PCR, and the results were highly concordant with the RNA-Seq results. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to better understand the functions of these DEGs. We also identified a large number of single nucleotide polymorphism and insertion/deletion markers, which will be a rich resource for future marker development and breeding research in Chinese cabbage. Also, our analysis revealed numerous novel transcripts and alternative splicing events. The transcriptome analysis provides valuable information for furthering our understanding of the molecular mechanisms that regulate the flowering process, and establishes a solid foundation for future genetic and functional genomic studies in Chinese cabbage.