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Identification of flowering time genes associated with vernalization in Chinese cabbage and their differential expression in radish

ABSTRACT: We conducted genome-wide transcriptome analysis using the inbred Chinese cabbage line, ‘4004’, which displayed early flowering in response to vernalization. A total of 1,677 differentially-expressed genes (DEGs) were identified with and without vernalization. Transcriptome analysis identified 223 homologs of Arabidopsis Ft genes in Chinese cabbage, and 50 of these genes responded to vernalization. RT-qPCR analysis of major Ft genes showed that the majority of flowering enhancers were up-regulated in response to vernalization, whereas most flowering repressors were down-regulated in response to vernalization. Among the major Ft genes, the expression of BrCOL1-2, BrFT1/2, BrSOC1/2/3, BrFLC1/2/3/5, and BrMAF was strongly affected by vernalization.

ORGANISM(S): Brassica rapa subsp. pekinensis

PROVIDER: GSE106444 | GEO | 2018/11/02

REPOSITORIES: GEO

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Project description:The leaf of Chinese cabbage is the major place of photosynthesis, the mutation of leaf may directly affect the rate of plant growth and development and the formation of leafy head, and ultimately influence the yield and quality of Chinese cabbage. We identified a developmentally retarded mutant (drm) exhibiting stable inheritance, which was derived from Chinese cabbage DH line ‘FT’ using a combination of isolated microspore culture and radiation treatment (60Co γ-rays). The drm exhibited slow growth and development at the seedling and heading stages, leading to the production of a tiny, leafy head, as well as chlorophyll-deficient leaves, especially in seedlings. Genetic analysis indicated that the phenotype of drm was controlled by a single recessive nuclear gene. Compared with wild-type line ‘FT’, the drm’s chlorophyll content was significantly reduced and its chloroplast structure was abnormal. Moreover, the photosynthetic efficiency and chlorophyll fluorescence parameters were significantly decreased. The changes in leaf color, combined with these altered physiological characters may influence the growth and development of plant, ultimately resulting in the developmentally retarded phenotype of drm. To further understand the molecular regulatory mechanisms of phenotypic differences between ‘FT’ and drm, comparative transcriptome analysis were performed using RNA-Seq, a total of 338 differentially expressed genes (DEGs) were detected between ‘FT’ and drm. According to GO and KEGG pathway analysis, a number of DEGs which involved in the chlorophyll degradation and photosynthesis were identified, such as chlorophyllase and ribulose-1,5-bisphosphate carboxylase/oxygenase. In addition, the expression patterns of 12 DEGs, including three chlorophyll degradation- and photosynthesis-related genes and nine randomly selected genes, were confirmed by qRT-PCR. Numerous single nucleotide polymorphisms were also identified, providing a valuable resource for research and molecular marker-assistant breeding in Chinese cabbage. These results contribute to our understanding of the molecular regulatory mechanisms underlying growth and development and lay the foundation for future genetic and functional genomics studies in Chinese cabbage.

Dataset Information

Identification of flowering time genes associated with vernalization in Chinese cabbage and their differential expression in radish

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