Abstract
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 mutant pdm and the corresponding wild-type line ‘FT’. We performed transcriptome analysis on mRNA isolated from flower buds of pdm and ‘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 factors BIGPETAL (BPE) and MYB21 (v-myb avian myeloblastosis viral oncogene homolog); differential expression of these genes could potentially explain the difference in the flowers between pdm and ‘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.
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This work was supported by a grant from the National Natural Science Foundation of China (31272157) and the Postgraduate Innovation Cultivation Project of Shenyang Agricultural University.
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Communicated by S. Hohmann.
S. Huang and Z. Liu contributed equally to this work and share the first authorship
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438_2015_1041_MOESM6_ESM.xls
Table S4. Summary of SNPs detected in the EP and NEP libraries (XLS) The meaning of numbers in the columns labeled ‘EP’ and ‘NEP’ were as follows, ‘1’: SNP (genotype was consistent with the column labeled ‘ALT’), ‘0’: None (genotype was consistent with the column labeled ‘REF’), ‘.’: Uncertained (lack of data support) (XLS 4082 kb)
438_2015_1041_MOESM7_ESM.xls
Table S5. Summary of Indels detected in the EP and NEP libraries (XLS) The meaning of numbers in the columns labeled ‘EP’ and ‘NEP’ were as follows, ‘1’: Indel (genotype was consistent with the column labeled ‘ALT’), ‘0’: None (genotype was consistent with the column labeled ‘REF’), ‘.’: Uncertained (lack of data support) (XLS 358 kb)
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Huang, S., Liu, Z., Yao, R. et al. Comparative transcriptome analysis of the petal degeneration mutant pdm in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq. Mol Genet Genomics 290, 1833–1847 (2015). https://doi.org/10.1007/s00438-015-1041-7
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DOI: https://doi.org/10.1007/s00438-015-1041-7