Expression analysis of chinese cabbage (B.rapa ssp. pekinensis) : cold stress conditions
Ontology highlight
ABSTRACT:
ORGANISM(S): Brassica rapa subsp. pekinensis Brassica rapa
PROVIDER: GSE75145 | GEO | 2016/10/31
SECONDARY ACCESSION(S): PRJNA302637
REPOSITORIES: GEO
Similar Datasets
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
Project description:Identification of Chinese cabbage genes up-regulated by prolonged cold by using cDNA microarray.
2006-10-25 | E-MEXP-190 | biostudies-arrayexpress
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.
2016-03-01 | GSE75464 | GEO
Project description:The transition from vegetative growth to reproductive growth involves many pathways. Vernalization is crucial to the formation of floral organs, the regulation of flowering time and plant breeding. The purpose of this study was to identify the mRNA, microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) related to vernalization of Chinese cabbage, and to construct a competitive endogenous RNA (ceRNA) network, so as to provide valuable information for exploring the molecular mechanism of vernalization of Chinese cabbage. Results: The results of whole-transcriptome sequencing showed that 2702 mRNAs, 151 lncRNAs, 16 circRNA, and 233 miRNAs were differentially expressed in vernalized (‘Ver’) and non-vernalized (‘Nor’) seeds of Chinese cabbage. Some transcription factors and regulatory proteins that play important roles in vernalization pathway have been identified, such as the transcription factors of WRKY, MYB, NAC, bHLH, and MADS-box, zinc finger protein CONSTANS like gene and B3 domain protein. We constructed vernalization-related ceRNA-miRNA-target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA-DEmRNA, 67 DEmiRNA-DElncRNA, and 12 DEmiRNA-DEcircRNA interactions in Chinese cabbage. Meanwhile, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs were identified, which were involved in the regulation of flowering time, floral organ formation, bolting and flowering. Conclusions: The candidate differentially expressed mRNA, miRNA, lncRNA and circRNA for vernalization of Chinese cabbage were identified by the whole-transcriptome sequencing, and the ceRNA network was constructed. This study laid a foundation for further study on the molecular mechanism of vernalization in Chinese cabbage.
2021-11-17 | GSE171708 | GEO
Project description:The transition from vegetative growth to reproductive growth involves many pathways. Vernalization is crucial to the formation of floral organs, the regulation of flowering time and plant breeding. The purpose of this study was to identify the mRNA, microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) related to vernalization of Chinese cabbage, and to construct a competitive endogenous RNA (ceRNA) network, so as to provide valuable information for exploring the molecular mechanism of vernalization of Chinese cabbage. Results: The results of whole-transcriptome sequencing showed that 2702 mRNAs, 151 lncRNAs, 16 circRNA, and 233 miRNAs were differentially expressed in vernalized (‘Ver’) and non-vernalized (‘Nor’) seeds of Chinese cabbage. Some transcription factors and regulatory proteins that play important roles in vernalization pathway have been identified, such as the transcription factors of WRKY, MYB, NAC, bHLH, and MADS-box, zinc finger protein CONSTANS like gene and B3 domain protein. We constructed vernalization-related ceRNA-miRNA-target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA-DEmRNA, 67 DEmiRNA-DElncRNA, and 12 DEmiRNA-DEcircRNA interactions in Chinese cabbage. Meanwhile, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs were identified, which were involved in the regulation of flowering time, floral organ formation, bolting and flowering. Conclusions: The candidate differentially expressed mRNA, miRNA, lncRNA and circRNA for vernalization of Chinese cabbage were identified by the whole-transcriptome sequencing, and the ceRNA network was constructed. This study laid a foundation for further study on the molecular mechanism of vernalization in Chinese cabbage.
2021-11-17 | GSE171707 | GEO
Project description:The hybrid seed production was performed using the male sterility line, which is an important way of heterosis utilization in Chinese cabbage. A stably inherited male sterile mutant msm was obtained from a Chinese cabbage DH line ‘FT’ using the isolated microspore culture combined with 60Co γ-rays mutagenesis. Compared to the wild type ‘FT’, the msm exhibited completely degenerated stamens and no pollen phenotype, and other characters had no significant difference except for stamen. The genetic analysis indicated that the msm mutant phenotype was controlled by a single recessive nuclear gene. Cytological observation showed that the stamen abortion of msm began at the tetrad period, and tapetum cells were abnormally expanded and highly vacuolated, leading to microspore abortion. Comparative transcriptome analysis on the flower buds of ‘FT’ and msm using RNA-Seq technology revealed a total of 1,653 differentially expressed genes (DEGs). Among which, a large number of genes associated with male sterility were found, including 64 pollen development and pollen tube growth-related genes, 94 pollen wall development-related genes, 11 phytohormone-related genes and 16 transcription factor-related genes, and the overwhelming majority of these genes were down-regulated in the msm vs. ‘FT’ comparison. Furthermore, KEGG pathway analysis indicated that a variety of carbohydrate metabolic and lipid metabolic pathways were significantly enriched, which may be related to pollen abortion. The expression patterns of 24 male sterility-related genes were analyzed using qRT-PCR. In addition, a total of 24,476 single nucleotide polymorphisms and 413,073 insertion-deletion events were specifically detected in msm. These results facilitate to elucidate the regulatory mechanisms of male sterility in Chinese cabbage.
2019-01-23 | GSE125485 | GEO
Project description:To better examine the molecular mechanisms behind the virus infection, we conducted a correlation analysis of RNA-Seq and quantitative iTRAQ-LC-MS/MS in TuMV-infected and in healthy Chinese cabbage leaves.
2020-08-07 | GSE151932 | GEO
Project description:Leafy head is the main product of Chinese cabbage, and also is the primary character to determine its yield and quality. Cloning and characterizing key genes involved in leafy head formation is imperative for varietal improvement in Chinese cabbage. From an EMS mutagenesis population of a heading wild-type ‘FT’ of Chinese cabbage, we identified two allelic non-heading mutants, nhm3-1 and nhm3-2. Genetic analysis showed that the mutant character was controlled by a single recessive gene. MutMap and Kompetitive Allele Specific PCR genotyping results revealed that BraA05g012440.3C encoding an ent-kaurenoic acid oxidase 2 which functions in the GA biosynthetic pathway, was the causal gene for leafy-head formation, and we named it as BrKAO2. Two kinds of non-synonymous mutations in the second exon of BrKAO2 were responsible for the nhm3-1 and nhm3-2 mutant phenotype, respectively. BrKAO2 was expressed at all stages of leaf development, and there was no significant difference between the wild-type ‘FT’ and the mutants nhm3-1 and nhm3-2. The mutant phenotype was restored to the wild-type through the application of exogenous GA3. RNA-Seq was performed on the rosette leaves of wild-type ‘FT’, nhm3-1 and nhm3-1+GA3 plants, and a number of key genes involving in GA biosynthesis, signal transduction and leafy head development were identified. These findings indicated that BrKAO2 is responsible for leafy head formation of nhm3, and a new mechanism of the leafy head formation in Chinese cabbage was proposed.
2021-09-12 | GSE183651 | GEO
Project description:Anther development is a complex process, and the study of its molecular mechanism has an important impact on plant breeding. This study aims to identify microRNA (miRNA), mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) related to anther development of Chinese cabbage, so as to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge for the exploration of pollen development mechanism of Chinese cabbage. A total of 9055 mRNA, 585 miRNA, 1344 lncRNA, and 165 circRNA were identified as differentially expressed in the anther of Chinese cabbage compared with Mix (roots, stems and leaves) by whole-transcriptome sequencing. The anther-related ceRNA-miRNA-target gene regulatory network through miRNA targeting relationships was constructed and 450 pairs of ceRNA relationships, including 97 DEmiRNA-DEmRNA, 281 DEmiRNA-DElncRNA, and 23 DEmiRNA-DEcircRNA interactions were obtained in Chinese cabbage. The genes in the ceRNA network were enriched in the pathways including starch and sucrose metabolism, carbon metabolism, pyruvate metabolism and carbon fixation in photosynthetic organisms, plant hormone signal transduction, and RNA degradation. This study identified some important genes and their interaction lncRNAs, circRNAs, and miRNAs involved in microsporogenesis (BraA06g035480.3C), tapetum and callose layer development (BraA09g009280.3C, BraA04g028920.3C, and BraA10g022680.3C etc), pollen wall formation (BraA06g000980.3C, BraA02g023130.3C, and BraA10g029650.3C etc), and anther dehiscence (BraA10g027200.3C, BraA04g023740.3C, and BraA04g030860.3C etc). Additionally, we analyzed the promoter activity of six anther predominant expression genes, and the results showed that they were all expressed specifically in the anther of Chinese cabbage. This study lay the foundation for further research on the molecular mechanism of anther growth and development.
2022-02-23 | GSE171705 | GEO
Project description:Anther development is a complex process, and the study of its molecular mechanism has an important impact on plant breeding. This study aims to identify microRNA (miRNA), mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) related to anther development of Chinese cabbage, so as to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge for the exploration of pollen development mechanism of Chinese cabbage. A total of 9055 mRNA, 585 miRNA, 1344 lncRNA, and 165 circRNA were identified as differentially expressed in the anther of Chinese cabbage compared with Mix (roots, stems and leaves) by whole-transcriptome sequencing. The anther-related ceRNA-miRNA-target gene regulatory network through miRNA targeting relationships was constructed and 450 pairs of ceRNA relationships, including 97 DEmiRNA-DEmRNA, 281 DEmiRNA-DElncRNA, and 23 DEmiRNA-DEcircRNA interactions were obtained in Chinese cabbage. The genes in the ceRNA network were enriched in the pathways including starch and sucrose metabolism, carbon metabolism, pyruvate metabolism and carbon fixation in photosynthetic organisms, plant hormone signal transduction, and RNA degradation. This study identified some important genes and their interaction lncRNAs, circRNAs, and miRNAs involved in microsporogenesis (BraA06g035480.3C), tapetum and callose layer development (BraA09g009280.3C, BraA04g028920.3C, and BraA10g022680.3C etc), pollen wall formation (BraA06g000980.3C, BraA02g023130.3C, and BraA10g029650.3C etc), and anther dehiscence (BraA10g027200.3C, BraA04g023740.3C, and BraA04g030860.3C etc). Additionally, we analyzed the promoter activity of six anther predominant expression genes, and the results showed that they were all expressed specifically in the anther of Chinese cabbage. This study lay the foundation for further research on the molecular mechanism of anther growth and development.
2022-02-23 | GSE171706 | GEO