Transcriptome analysis of flowering variation under vernalization in two inbred lines of Chinese cabbage
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ABSTRACT:
ORGANISM(S): Brassica rapa subsp. pekinensis
PROVIDER: GSE139375 | GEO | 2019/10/25
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptome analysis of flowering variation under vernalization in two inbred lines of Chinese cabbage
| PRJNA579431 | ENA
Project description: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.
2018-11-02 | GSE106444 | GEO
Project description:Cabbage (Brassica oleracea var. capitata) requires a long-term low-temperature exposure for floral induction, causing a delay in the breeding cycle. The objective of this study is to develop a method to induce flowering in cabbage without low-temperature treatment, using a grafting method. We conducted grafting experiments using two flower-induced Chinese kale cultivars (B. oleracea var. alboglabra) and seven radish cultivars/accessions as rootstocks and investigated the flowering response of grafted cabbage scions without low-temperature treatment. "Watanabe-seiko No.1" cabbage, when grafted onto the two Chinese kale cultivars, did not formed flower buds. Flowering was successfully induced in "Watanabe-seiko No.1" by grafting onto three out of the seven tested radish cultivars, and in "Kinkei No.201" and "Red cabbage" by grafting onto one tested radish cultivar. In "Watanabe-seiko No.1," the earliest flower bud appearance was observed at 29 days after grafting. Seeds were also obtained from the three cabbage cultivars that flowered by grafting. Gene expression analysis of "Watanabe-seiko No.1" cabbage scions which formed flower buds by grafting, revealed high expression of the homolog of the floral integrator, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (BoSOC1), at the time of flower bud appearance. However, in the same leaf samples, we observed low expression of two homologs of florigen, FLOWERING LOCUS T (BoFT.C2 and BoFT.C6). In addition, two homologs of the floral repressor FLOWERING LOCUS C (BoFLC3 and BoFLC4), which are known to be down-regulated before flower bud differentiation in the vernalization pathway, were highly expressed, indicating that grafting onto radish induces cabbage flowering independently of the vernalization pathway. The expression level of the radish FT homolog (RsFT) in "Rat's tail-G2," which had highly induced flowering in the grafted cabbage scion, was higher than in the other radish cultivars. However, although "Rat's tail-CH" effectively induced flowering in the cabbage scion, the expression of RsFT was low in this cultivar. In this study, floral induction of non-vernalized cabbage cannot be explained by the expression levels of RsFT in rootstock plants, alone. The flowering of non-vernalized cabbage would be induced by transmissible agents from rootstocks and not by the expression of cabbage FT, BoFT, from the scion itself.
| S-EPMC6335391 | biostudies-literature
Project description:We analyze that the flowering integrators, FT and SOC, change to expression by GA treatment
2019-01-31 | GSE125875 | GEO
Project description:Ammonium transporters (AMTs), which include AMT1 and AMT2 subfamilies, have been identified and partially characterized in many plants. In this study, two AMT2-type genes from Brassica campestris, namely BcAMT2 and BcAMT2like, were identified and characterized. BcAMT2 and BcAMT2like are 2666 bp and 2952 bp, encode proteins of 490 and 489 amino acids, respectively, and contain five exons and four introns. Transient expression of these proteins labelled with green fluorescence protein in onion epidermal cells indicated that both are located on the plasma membrane. When expressing BcAMT2 or BcAMT2like, the mutant yeast strain 31019b could grow on medium containing 2 mM ammonium as the only nitrogen source when expressing BcAMT2 or BcAMT2like, indicating that both are functional AMT genes. Quantitative PCR results showed that BcAMT2 and BcAMT2like were expressed in all tissues, but they displayed different expression patterns in the reproductive stages. BcAMT2s transcript levels in leaves were positively correlated with ammonium concentration and external pH. Moreover, the expression BcAMT2s responded to diurnal change. Furthermore, the uncharged form of ammonium, i.e., ammonia, might also be transported by BcAMT2s. These results provide new insights into the molecular mechanisms underlying ammonium absorption and transportation by the AMT2 subfamily in B. campestris.
| S-EPMC6543737 | biostudies-literature
Project description:Late bolting after cold exposure is an economically important characteristic of radish (Raphanus sativus L.), an important Brassicaceae root vegetable crop. However, little information is available regarding the genes and pathways that govern flowering time in this species. We performed high-throughput RNA sequencing analysis to elucidate the molecular mechanisms that determine the differences in flowering times between two radish lines, NH-JS1 (late bolting) and NH-JS2 (early bolting). In total, 71,188 unigenes were identified by reference-guided assembly, of which 309, 788, and 980 genes were differentially expressed between the two inbred lines after 0, 15, and 35 days of vernalization, respectively. Among these genes, 218 homologs of Arabidopsis flowering-time (Ft) genes were identified in the radish, and 49 of these genes were differentially expressed between the two radish lines in the presence or absence of vernalization treatment. Most of the Ft genes up-regulated in NH-JS1 vs. NH-JS2 were repressors of flowering, such as RsFLC, consistent with the late-bolting phenotype of NH-JS1. Although, the functions of genes down-regulated in NH-JS1 were less consistent with late-bolting characteristics than the up-regulated Ft genes, several Ft enhancer genes, including RsSOC1, a key floral integrator, showed an appropriate expression to the late-bolting phenotype. In addition, the patterns of gene expression related to the vernalization pathway closely corresponded with the different bolting times of the two inbred lines. These results suggest that the vernalization pathway is conserved between radish and Arabidopsis.
| S-EPMC5145866 | biostudies-literature
Project description:PURPOSE:To clarify the mechanism of the wax deficiency, the wax-less flowering Chinese cabbage doubled-haploid (DH) line ‘CX001’ and Chinese cabbage DH line ‘FT’, obtained from isolated microspore culture, were used in the experiments. Transcriptome analysis indicated that BraA09g066480.3C was expressed in ‘FT’ but not in ‘CX001’.The work presented herein demonstrated that BraA09g066480.3C was the causal gene for wax-less flowering Chinese cabbage ‘CX001’
2022-12-29 | GSE221778 | GEO
Project description:In order to leverage novel sequencing techniques for cloning genes in eukaryotic organisms with complex genomes, the false positive rate of variant discovery must be controlled for by experimental design and informatics. We sequenced five lines from three pedigrees of ethyl methanesulfonate (EMS)-mutagenized Sorghum bicolor, including a pedigree segregating a recessive dwarf mutant. Comparing the sequences of the lines, we were able to identify and eliminate error-prone positions. One genomic region contained EMS mutant alleles in dwarfs that were homozygous reference sequences in wild-type siblings and heterozygous in segregating families. This region contained a single nonsynonymous change that cosegregated with dwarfism in a validation population and caused a premature stop codon in the Sorghum ortholog encoding the gibberellic acid (GA) biosynthetic enzyme ent-kaurene oxidase. Application of exogenous GA rescued the mutant phenotype. Our method for mapping did not require outcrossing and introduced no segregation variance. This enables work when line crossing is complicated by life history, permitting gene discovery outside of genetic models. This inverts the historical approach of first using recombination to define a locus and then sequencing genes. Our formally identical approach first sequences all the genes and then seeks cosegregation with the trait. Mutagenized lines lacking obvious phenotypic alterations are available for an extension of this approach: mapping with a known marker set in a line that is phenotypically identical to starting material for EMS mutant generation.
| S-EPMC5295590 | biostudies-literature
Project description:Plant growth and development are tightly regulated by phytohormones. However, little is known about the interaction between auxin and gibberellin acid (GA) during flower stalk elongation and how it is directly related to organ formation. Therefore, the effects of indole acetic acid (IAA) and GA3 treatments and their interaction on flower stalk elongation in flowering Chinese cabbage were investigated. The growth of flowering Chinese cabbage is regulated by IAA and GA3, and the opposite results were observed after treatments with uniconazole (GA synthesis inhibitor) and N-1-naphthylphthalamic acid (NPA) (auxin transport inhibitor). Anatomical analysis of the pith region in stalks revealed that IAA promoted expansion via signal transduction and transport pathways. GA3 regulated the elongation of flower stalks by controlling GA synthesis and partially controlling the IAA signaling pathway. GA3 also had a stronger effect on stalk elongation than IAA. The results of qRT-PCR and histological analysis revealed that GA3 and IAA induced the expansion of cell walls by activating the expression of genes encoding cell wall structural proteins such as Expansin (EXP). These findings provide new insights into the mechanism of stalk formation regulated by the combination of IAA and GA3.
| S-EPMC7889655 | biostudies-literature
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 âFTâ 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 âFTâ, the drmâs 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 âFTâ and drm, comparative transcriptome analysis were performed using RNA-Seq, a total of 338 differentially expressed genes (DEGs) were detected between âFTâ 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. The RNA from the third true leaves (day 15 to day 24 after the appearance of the third true leaves) of a developmentally retarded mutant (drm) and its wild type âFTâ in Chinese cabbage were sequenced by RNA-Seq, in triplicate.
2016-03-01 | E-GEOD-75464 | biostudies-arrayexpress